One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file Myogenin_Rep3_motifs50/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o Myogenin_Rep3_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m20_shift0 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m20_shift0 (dyads_m20dyads_m20)
; dyads_m20 (dyads_m20dyads_m20); m=0 (reference); ncol1=23; shift=0; ncol=27; TCCTAmAGTGTGyaTTTCTCATT---- ; Alignment reference a 8 3 0 0 60 18 46 6 2 2 7 5 7 40 6 1 5 5 0 1 59 3 5 0 0 0 0 c 0 44 60 0 0 35 5 6 9 3 1 3 23 2 4 3 3 47 0 59 0 7 4 0 0 0 0 g 4 3 0 0 0 3 4 44 2 49 4 46 2 11 2 5 3 4 1 0 1 5 4 0 0 0 0 t 48 10 0 60 0 4 5 4 47 6 48 6 28 7 48 51 49 4 59 0 0 45 47 0 0 0 0

dyads_m20_shift0 (dyads_m20dyads_m20)
; dyads_m20 versus dyads_m20 (dyads_m20dyads_m20); m=1/10; ncol2=23; w=23; offset=0; strand=D; shift=0; score= 1; TCCTAmAGTGTGyaTTTCTCATT---- ; cor=; Ncor= a 8 3 0 0 60 18 46 6 2 2 7 5 7 40 6 1 5 5 0 1 59 3 5 0 0 0 0 c 0 44 60 0 0 35 5 6 9 3 1 3 23 2 4 3 3 47 0 59 0 7 4 0 0 0 0 g 4 3 0 0 0 3 4 44 2 49 4 46 2 11 2 5 3 4 1 0 1 5 4 0 0 0 0 t 48 10 0 60 0 4 5 4 47 6 48 6 28 7 48 51 49 4 59 0 0 45 47 0 0 0 0

dyads_m40_rc_shift0 (dyads_m40dyads_m40_rc)
; dyads_m20 versus dyads_m40_rc (dyads_m40dyads_m40_rc); m=2/10; ncol2=25; w=23; offset=0; strand=R; shift=0; score=0.902772; TCCTAmAgTGTGyATTTCTCATTTT-- ; cor=; Ncor= a 3 2 0 0 64 18 51 8 3 1 2 6 1 44 6 1 0 4 3 7 64 0 0 3 4 0 0 c 2 45 63 0 0 35 4 4 5 7 6 1 28 5 1 2 4 47 7 51 0 0 0 3 6 0 0 g 5 3 0 0 0 4 7 42 1 50 3 50 4 11 9 10 7 5 5 3 0 0 1 2 2 0 0 t 54 14 1 64 0 7 2 10 55 6 53 7 31 4 48 51 53 8 49 3 0 64 63 56 52 0 0

dyads_m9_rc_shift1 (dyads_m9dyads_m9_rc)
; dyads_m20 versus dyads_m9_rc (dyads_m9dyads_m9_rc); m=3/10; ncol2=26; w=22; offset=1; strand=R; shift=1; score=0.737463; -yCTACAgTGtgcaTTTytyawTTTyC ; cor=; Ncor= a 0 10 13 0 86 0 67 14 6 6 6 14 7 47 4 3 4 7 17 15 53 33 0 0 0 8 4 c 0 47 64 0 1 82 8 7 5 8 7 6 41 5 7 10 7 51 11 35 19 0 1 0 0 30 64 g 0 6 7 0 0 0 5 58 4 68 17 52 20 15 8 7 5 4 8 15 5 7 1 0 0 7 3 t 0 24 3 87 0 5 7 8 72 5 57 15 19 20 68 67 71 25 51 22 10 47 85 87 87 42 16

dyads_m6_rc_shift0 (dyads_m6dyads_m6_rc)
; dyads_m20 versus dyads_m6_rc (dyads_m6dyads_m6_rc); m=4/10; ncol2=14; w=14; offset=0; strand=R; shift=0; score=0.596039; TyCTAcAGTGTGya------------- ; cor=; Ncor= a 8 1 0 0 91 19 76 7 8 0 0 1 3 51 0 0 0 0 0 0 0 0 0 0 0 0 0 c 1 59 92 0 1 62 5 8 3 0 0 0 36 10 0 0 0 0 0 0 0 0 0 0 0 0 0 g 5 7 0 0 0 6 7 72 1 92 0 91 19 15 0 0 0 0 0 0 0 0 0 0 0 0 0 t 78 25 0 92 0 5 4 5 80 0 92 0 34 16 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m11_rc_shift6 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc)
; dyads_m20 versus oligos_8nt_mkv2_m11_rc (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc); m=5/10; ncol2=13; w=13; offset=6; strand=R; shift=6; score=0.547874; ------AGTGTGYATTTCT-------- ; cor=; Ncor= a 0 0 0 0 0 0 66 10 0 0 2 1 2 69 1 0 0 3 10 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 3 9 0 0 1 0 50 1 0 0 0 63 3 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 52 0 72 1 71 2 2 0 0 1 2 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 1 72 0 68 0 18 0 71 72 71 4 59 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m26_shift2 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26)
; dyads_m20 versus oligos_8nt_mkv2_m26 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26); m=6/10; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.494047; --CTACAGTGTGya------------- ; cor=; Ncor= a 0 0 6 14 87 12 82 1 0 1 0 8 5 56 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 63 7 0 69 1 0 0 0 0 0 24 3 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 10 1 0 1 0 85 0 86 0 79 18 9 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 8 65 0 5 4 1 87 0 87 0 40 19 0 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m29_rc_shift11 (dyads_m29dyads_m29_rc)
; dyads_m20 versus dyads_m29_rc (dyads_m29dyads_m29_rc); m=7/10; ncol2=12; w=12; offset=11; strand=R; shift=11; score=0.483333; -----------ryrTTTyTCAkT---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 65 5 46 0 1 0 0 0 1 154 3 6 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 5 48 0 0 0 0 108 0 160 0 19 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 87 6 103 0 0 0 0 0 0 9 43 4 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 6 104 14 163 162 163 55 163 2 0 98 139 0 0 0 0

dyads_m23_rc_shift1 (dyads_m23dyads_m23_rc)
; dyads_m20 versus dyads_m23_rc (dyads_m23dyads_m23_rc); m=8/10; ncol2=12; w=12; offset=1; strand=R; shift=1; score=0.478283; -yCTACAgTGTKc-------------- ; cor=; Ncor= a 0 1 16 0 95 0 84 21 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 44 67 0 0 95 4 14 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 3 2 0 0 0 1 55 0 95 0 67 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 47 10 95 0 0 6 5 95 0 95 26 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m33_rc_shift1 (dyads_m33dyads_m33_rc)
; dyads_m20 versus dyads_m33_rc (dyads_m33dyads_m33_rc); m=9/10; ncol2=10; w=10; offset=1; strand=R; shift=1; score=0.414113; -yCTACAGTGT---------------- ; cor=; Ncor= a 0 1 2 0 76 0 75 0 0 1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 48 66 0 0 76 1 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 6 3 0 0 0 0 76 0 68 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 21 5 76 0 0 0 0 76 1 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_6nt_mkv2_m8_rc_shift12 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc)
; dyads_m20 versus oligos_6nt_mkv2_m8_rc (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc); m=10/10; ncol2=10; w=10; offset=12; strand=R; shift=12; score=0.407724; ------------tdTTTCTCay----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 5 54 0 0 0 0 0 0 98 6 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 34 5 0 0 0 154 0 154 11 44 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 30 52 0 0 0 0 0 0 32 3 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 85 43 154 154 154 0 154 0 13 101 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4dyads_m4)
; dyads_m4 (dyads_m4dyads_m4); m=0 (reference); ncol1=21; shift=0; ncol=29; gCkRRAAAACTGAAAATCAyR-------- ; Alignment reference a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 0 0 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 0 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 0 0 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0 0 0 0 0 0

dyads_m4_shift0 (dyads_m4dyads_m4)
; dyads_m4 versus dyads_m4 (dyads_m4dyads_m4); m=1/8; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 1; gCkRRAAAACTGAAAATCAyR-------- ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 0 0 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 0 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 0 0 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0 0 0 0 0 0

dyads_m24_shift1 (dyads_m24dyads_m24)
; dyads_m4 versus dyads_m24 (dyads_m24dyads_m24); m=2/8; ncol2=18; w=18; offset=1; strand=D; shift=1; score=0.700623; -ygRRAAAmsTGAAAAwyr---------- ; cor=; Ncor= a 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 0 0 0 0 0 0 0 0 0 c 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 g 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 0 0 0 0 0 0 0 0 0 t 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; dyads_m4 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=3/8; ncol2=13; w=13; offset=5; strand=D; shift=5; score=0.563196; -----WAmACTGAAAAwC----------- ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m16_shift9 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; dyads_m4 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=4/8; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.542879; ---------YkGAAAATsAyr-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0 0 0 0 0 0 0

oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; dyads_m4 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=5/8; ncol2=11; w=11; offset=6; strand=D; shift=6; score=0.489718; ------AmACTGAAAAw------------ ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; dyads_m4 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=6/8; ncol2=12; w=12; offset=8; strand=R; shift=8; score=0.445154; --------MsTGAAAAACrt--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0 0 0 0 0 0

dyads_m7_shift6 (dyads_m7dyads_m7)
; dyads_m4 versus dyads_m7 (dyads_m7dyads_m7); m=7/8; ncol2=23; w=15; offset=6; strand=D; shift=6; score=0.432109; ------mmACTkrAAAwcdTGrAAAATgA ; cor=; Ncor= a 0 0 0 0 0 0 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 107 107 0 7 81 c 0 0 0 0 0 0 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 0 0 0 15 2 g 0 0 0 0 0 0 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 0 0 0 71 6 t 0 0 0 0 0 0 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4 0 0 107 14 18

dyads_m29_shift8 (dyads_m29dyads_m29)
; dyads_m4 versus dyads_m29 (dyads_m29dyads_m29); m=8/8; ncol2=12; w=12; offset=8; strand=D; shift=8; score=0.409592; --------AmTGArAAAyry--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift3 ; 30 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift3 (dyads_m3dyads_m3)
; dyads_m3 (dyads_m3dyads_m3); m=0 (reference); ncol1=15; shift=3; ncol=18; ---rmArCAGCTGTCwyy ; Alignment reference a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

dyads_m3_shift3 (dyads_m3dyads_m3)
; dyads_m3 versus dyads_m3 (dyads_m3dyads_m3); m=1/29; ncol2=15; w=15; offset=0; strand=D; shift=3; score= 1; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; dyads_m3 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=2/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.936315; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; dyads_m3 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=3/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.914462; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; dyads_m3 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=4/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.91171; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; dyads_m3 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=5/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.911546; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; dyads_m3 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=6/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.911042; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; dyads_m3 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=7/29; ncol2=16; w=15; offset=-1; strand=R; shift=2; score=0.878388; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; dyads_m3 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=8/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.87481; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; dyads_m3 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=9/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.872422; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

dyads_m8_shift3 (dyads_m8dyads_m8)
; dyads_m3 versus dyads_m8 (dyads_m8dyads_m8); m=10/29; ncol2=15; w=15; offset=0; strand=D; shift=3; score=0.868842; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; dyads_m3 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=11/29; ncol2=14; w=14; offset=0; strand=R; shift=3; score=0.867342; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; dyads_m3 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=12/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.85086; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; dyads_m3 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=13/29; ncol2=17; w=15; offset=-2; strand=R; shift=1; score=0.836515; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; dyads_m3 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=14/29; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.829785; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; dyads_m3 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=15/29; ncol2=14; w=14; offset=1; strand=R; shift=4; score=0.828376; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; dyads_m3 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=16/29; ncol2=14; w=14; offset=1; strand=R; shift=4; score=0.828216; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; dyads_m3 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=17/29; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.82507; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; dyads_m3 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=18/29; ncol2=18; w=15; offset=-3; strand=R; shift=0; score=0.771503; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; dyads_m3 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=19/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.764256; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; dyads_m3 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=20/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.727804; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; dyads_m3 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=21/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.726765; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m1_shift2 (dyads_m1dyads_m1)
; dyads_m3 versus dyads_m1 (dyads_m1dyads_m1); m=22/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.726765; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; dyads_m3 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=23/29; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.723834; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; dyads_m3 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=24/29; ncol2=16; w=14; offset=-2; strand=R; shift=1; score=0.716962; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; dyads_m3 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=25/29; ncol2=17; w=15; offset=-2; strand=R; shift=1; score=0.71002; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

dyads_m21_shift3 (dyads_m21dyads_m21)
; dyads_m3 versus dyads_m21 (dyads_m21dyads_m21); m=26/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.69303; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; dyads_m3 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=27/29; ncol2=17; w=14; offset=-3; strand=R; shift=0; score=0.662588; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

oligos_8nt_mkv2_m25_shift3 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; dyads_m3 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=28/29; ncol2=12; w=12; offset=0; strand=D; shift=3; score=0.574341; ---gvAACAGTTGcr--- ; cor=; Ncor= a 0 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 c 0 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 g 0 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 t 0 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0

oligos_7nt_mkv2_m12_shift4 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; dyads_m3 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=29/29; ncol2=11; w=11; offset=1; strand=D; shift=4; score=0.532562; ----smACAGTTGym--- ; cor=; Ncor= a 0 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 c 0 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 g 0 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 t 0 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m23_shift14 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m23_shift14 (dyads_m23dyads_m23)
; dyads_m23 (dyads_m23dyads_m23); m=0 (reference); ncol1=12; shift=14; ncol=26; --------------gMACAcTGTAGr ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1

dyads_m23_shift14 (dyads_m23dyads_m23)
; dyads_m23 versus dyads_m23 (dyads_m23dyads_m23); m=1/8; ncol2=12; w=12; offset=0; strand=D; shift=14; score= 1; --------------gMACAcTGTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1

dyads_m6_shift13 (dyads_m6dyads_m6)
; dyads_m23 versus dyads_m6 (dyads_m6dyads_m6); m=2/8; ncol2=14; w=12; offset=-1; strand=D; shift=13; score=0.811881; -------------trCACACTgTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 c 0 0 0 0 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 g 0 0 0 0 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 t 0 0 0 0 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1

oligos_8nt_mkv2_m26_rc_shift13 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)
; dyads_m23 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=3/8; ncol2=12; w=11; offset=-1; strand=R; shift=13; score=0.799973; -------------trCACACTGTAG- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 19 40 0 87 0 87 1 4 5 0 65 8 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 79 0 86 0 85 0 1 0 1 10 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 3 24 0 0 0 0 0 1 69 0 7 63 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 56 5 8 0 1 0 1 82 12 87 14 6 0

dyads_m33_shift16 (dyads_m33dyads_m33)
; dyads_m23 versus dyads_m33 (dyads_m33dyads_m33); m=4/8; ncol2=10; w=10; offset=2; strand=D; shift=16; score=0.794922; ----------------ACACTGTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 1 76 0 0 0 0 76 5 21 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 68 0 76 0 0 0 0 3 6 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1 76 0 0 66 48 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 75 0 76 0 2 1

dyads_m20_rc_shift4 (dyads_m20dyads_m20_rc)
; dyads_m23 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=5/8; ncol2=23; w=12; offset=-10; strand=R; shift=4; score=0.478283; ----AATGAGAAAtrCACACTkTAGG ; cor=; Ncor= a 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 4 0 60 0 10 c 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 3 0 0 0 3 g 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 35 0 0 60 44 t 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46 18 60 0 0 3

dyads_m32_shift14 (dyads_m32dyads_m32)
; dyads_m23 versus dyads_m32 (dyads_m32dyads_m32); m=6/8; ncol2=25; w=12; offset=0; strand=D; shift=14; score=0.45898; --------------rCACAcTGTAGG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 7 83 1 84 8 4 5 10 72 8 19 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 64 0 82 0 56 5 3 3 4 9 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 4 1 1 0 14 5 58 6 5 63 60 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 9 0 0 0 6 70 18 65 3 4 2

dyads_m9_shift0 (dyads_m9dyads_m9)
; dyads_m23 versus dyads_m9 (dyads_m9dyads_m9); m=7/8; ncol2=26; w=12; offset=-14; strand=D; shift=0; score=0.447898; GrAAAwtrarAAAtgcaCAcTGTAGr ; cor=; Ncor= a 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 24 c 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 6 g 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 47 t 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13 10

dyads_m40_shift2 (dyads_m40dyads_m40)
; dyads_m23 versus dyads_m40 (dyads_m40dyads_m40); m=8/8; ncol2=25; w=12; offset=-12; strand=D; shift=2; score=0.44426; --AAAATGAGAAATrCACAcTkTAGG ; cor=; Ncor= a 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 14 c 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 3 g 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 45 t 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0 2

One-to-n matrix alignment; reference matrix: dyads_m26_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m26_shift2 (dyads_m26dyads_m26)
; dyads_m26 (dyads_m26dyads_m26); m=0 (reference); ncol1=12; shift=2; ncol=14; --csCCGcsGCGss ; Alignment reference a 0 0 1 0 1 0 1 4 3 0 1 0 3 2 c 0 0 19 15 25 27 1 15 13 2 24 3 10 8 g 0 0 6 10 2 1 26 6 11 24 2 25 12 16 t 0 0 2 3 0 0 0 3 1 2 1 0 3 2

dyads_m26_shift2 (dyads_m26dyads_m26)
; dyads_m26 versus dyads_m26 (dyads_m26dyads_m26); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=2; score= 1; --csCCGcsGCGss ; cor=; Ncor= a 0 0 1 0 1 0 1 4 3 0 1 0 3 2 c 0 0 19 15 25 27 1 15 13 2 24 3 10 8 g 0 0 6 10 2 1 26 6 11 24 2 25 12 16 t 0 0 2 3 0 0 0 3 1 2 1 0 3 2

oligos_8nt_mkv2_m15_shift2 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)
; dyads_m26 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=2/7; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.931423; --vcCCGCCGcGss ; cor=; Ncor= a 0 0 4 0 0 1 0 1 0 0 2 0 1 1 c 0 0 6 9 14 13 0 12 12 1 9 0 5 4 g 0 0 4 3 0 0 14 1 2 13 2 14 8 7 t 0 0 0 2 0 0 0 0 0 0 1 0 0 2

oligos_6nt_mkv2_m6_shift2 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)
; dyads_m26 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=3/7; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.742676; --ssCCGCCGGGs- ; cor=; Ncor= a 0 0 3 2 1 0 0 0 0 0 2 2 4 0 c 0 0 11 13 21 25 1 23 22 3 3 4 10 0 g 0 0 10 9 3 1 25 3 4 23 20 18 11 0 t 0 0 2 2 1 0 0 0 0 0 1 2 1 0

oligos_7nt_mkv2_m7_rc_shift3 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc)
; dyads_m26 versus oligos_7nt_mkv2_m7_rc (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc); m=4/7; ncol2=11; w=11; offset=1; strand=R; shift=3; score=0.71108; ---ssCGCCGGGss ; cor=; Ncor= a 0 0 0 2 4 3 0 0 0 0 3 0 6 4 c 0 0 0 16 17 33 1 28 32 4 3 1 14 11 g 0 0 0 14 11 0 33 5 4 32 29 34 11 17 t 0 0 0 4 4 0 2 3 0 0 1 1 5 4

oligos_7nt_mkv2_m15_shift1 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; dyads_m26 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=5/7; ncol2=11; w=10; offset=-1; strand=D; shift=1; score=0.678867; -ssCCCGCCGsg-- ; cor=; Ncor= a 0 4 4 0 1 0 0 3 0 0 3 3 0 0 c 0 7 11 23 24 26 0 19 23 2 10 5 0 0 g 0 11 8 3 2 1 27 5 4 25 11 18 0 0 t 0 5 4 1 0 0 0 0 0 0 3 1 0 0

dyads_m12_rc_shift2 (dyads_m12dyads_m12_rc)
; dyads_m26 versus dyads_m12_rc (dyads_m12dyads_m12_rc); m=6/7; ncol2=14; w=12; offset=0; strand=R; shift=2; score=0.62499; --ssCCSGCGSGGs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 4 7 8 10 3 1 11 0 3 2 1 4 g 0 0 6 3 2 1 8 10 0 11 8 9 9 6 t 0 0 1 1 1 0 0 0 0 0 0 0 1 1

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; dyads_m26 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=7/7; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=0.521724; ssCCCCGCsg---- ; cor=; Ncor= a 0 3 0 0 0 0 0 0 2 1 0 0 0 0 c 10 7 23 21 23 24 0 25 8 6 0 0 0 0 g 11 9 2 4 2 1 25 0 9 15 0 0 0 0 t 4 6 0 0 0 0 0 0 6 3 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m36_shift1 ; 31 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m36_shift1 (dyads_m36dyads_m36)
; dyads_m36 (dyads_m36dyads_m36); m=0 (reference); ncol1=15; shift=1; ncol=18; -rvkGACAGCTGctks-- ; Alignment reference a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

dyads_m36_shift1 (dyads_m36dyads_m36)
; dyads_m36 versus dyads_m36 (dyads_m36dyads_m36); m=1/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score= 1; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; dyads_m36 versus dyads_m19 (dyads_m19dyads_m19); m=2/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score= 0.9759; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; dyads_m36 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=3/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.970708; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; dyads_m36 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=4/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.969149; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0

oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; dyads_m36 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=5/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.934337; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; dyads_m36 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=6/30; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.912193; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; dyads_m36 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=7/30; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.911042; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; dyads_m36 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=8/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.908563; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; dyads_m36 versus dyads_m5 (dyads_m5dyads_m5); m=9/30; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.906945; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; dyads_m36 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=10/30; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.905622; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; dyads_m36 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=11/30; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.886652; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; dyads_m36 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=12/30; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.872768; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; dyads_m36 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=13/30; ncol2=16; w=15; offset=0; strand=R; shift=1; score=0.840281; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; dyads_m36 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=14/30; ncol2=17; w=15; offset=0; strand=R; shift=1; score=0.830296; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; dyads_m36 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=15/30; ncol2=17; w=15; offset=0; strand=D; shift=1; score=0.827072; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; dyads_m36 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=16/30; ncol2=17; w=15; offset=0; strand=R; shift=1; score=0.818534; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; dyads_m36 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=17/30; ncol2=16; w=15; offset=0; strand=R; shift=1; score=0.802625; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0

oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; dyads_m36 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=18/30; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.795203; --cwGaCAGCTGtCwg-- ; cor=; Ncor= a 0 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 c 0 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 t 0 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0

dyads_m1_shift1 (dyads_m1dyads_m1)
; dyads_m36 versus dyads_m1 (dyads_m1dyads_m1); m=19/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.774901; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; dyads_m36 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=20/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.774901; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; dyads_m36 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=21/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.763326; -gmyGaCAGCTGtCrkc- ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0

dyads_m2_shift1 (dyads_m2dyads_m2)
; dyads_m36 versus dyads_m2 (dyads_m2dyads_m2); m=22/30; ncol2=18; w=15; offset=0; strand=D; shift=1; score=0.742126; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; dyads_m36 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=23/30; ncol2=17; w=15; offset=0; strand=R; shift=1; score=0.735751; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; dyads_m36 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=24/30; ncol2=17; w=15; offset=0; strand=D; shift=1; score=0.729473; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; dyads_m36 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=25/30; ncol2=16; w=14; offset=1; strand=D; shift=2; score=0.713013; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

dyads_m21_shift2 (dyads_m21dyads_m21)
; dyads_m36 versus dyads_m21 (dyads_m21dyads_m21); m=26/30; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.706576; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0

dyads_m25_shift2 (dyads_m25dyads_m25)
; dyads_m36 versus dyads_m25 (dyads_m25dyads_m25); m=27/30; ncol2=17; w=14; offset=1; strand=D; shift=2; score=0.652863; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8

oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; dyads_m36 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=28/30; ncol2=12; w=12; offset=1; strand=D; shift=2; score=0.596803; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; dyads_m36 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=29/30; ncol2=18; w=15; offset=-1; strand=D; shift=0; score=0.583601; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; dyads_m36 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=30/30; ncol2=11; w=11; offset=2; strand=D; shift=3; score=0.525172; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m9_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m9_shift1 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9)
; oligos_7nt_mkv2_m9 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9); m=0 (reference); ncol1=11; shift=1; ncol=12; -wtTAAATAAag ; Alignment reference a 0 4 3 0 12 12 13 1 13 12 6 3 c 0 3 3 0 0 0 0 0 0 1 3 1 g 0 1 3 0 1 0 0 0 0 0 2 6 t 0 5 4 13 0 1 0 12 0 0 2 3

oligos_7nt_mkv2_m9_shift1 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9)
; oligos_7nt_mkv2_m9 versus oligos_7nt_mkv2_m9 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9); m=1/4; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 1; -wtTAAATAAag ; cor=; Ncor= a 0 4 3 0 12 12 13 1 13 12 6 3 c 0 3 3 0 0 0 0 0 0 1 3 1 g 0 1 3 0 1 0 0 0 0 0 2 6 t 0 5 4 13 0 1 0 12 0 0 2 3

dyads_m38_shift0 (dyads_m38dyads_m38)
; oligos_7nt_mkv2_m9 versus dyads_m38 (dyads_m38dyads_m38); m=2/4; ncol2=12; w=11; offset=-1; strand=D; shift=0; score=0.860166; twTTAAATAAww ; cor=; Ncor= a 6 9 3 0 27 27 22 3 26 27 12 8 c 7 5 1 0 0 1 1 0 0 0 3 6 g 5 3 2 1 0 1 2 0 1 1 5 6 t 11 12 23 28 2 0 4 26 2 1 9 9

oligos_8nt_mkv2_m24_shift1 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24)
; oligos_7nt_mkv2_m9 versus oligos_8nt_mkv2_m24 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24); m=3/4; ncol2=12; w=11; offset=0; strand=D; shift=1; score=0.851868; -wwTAAATAAAa ; cor=; Ncor= a 0 11 13 1 31 31 23 1 29 29 28 16 c 0 4 1 1 0 0 1 0 0 2 0 4 g 0 3 6 2 0 0 1 1 2 1 2 5 t 0 14 12 28 1 1 7 30 1 0 2 7

dyads_m16_shift0 (dyads_m16dyads_m16)
; oligos_7nt_mkv2_m9 versus dyads_m16 (dyads_m16dyads_m16); m=4/4; ncol2=12; w=11; offset=-1; strand=D; shift=0; score= 0.7004; ttTTAATTAAaa ; cor=; Ncor= a 6 6 0 1 24 23 3 1 27 26 14 12 c 4 4 0 0 3 1 1 0 0 2 4 6 g 6 4 2 0 0 1 1 3 0 0 4 4 t 12 14 26 27 1 3 23 24 1 0 6 6

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m8_shift2 ; 28 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=0 (reference); ncol1=16; shift=2; ncol=18; --rgmACAGCTGCTGcws ; Alignment reference a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=1/27; ncol2=16; w=16; offset=0; strand=D; shift=2; score= 1; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=2/27; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.89486; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=3/27; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.88696; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=4/27; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.883572; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=5/27; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.869366; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=6/27; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.866139; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6

dyads_m25_shift2 (dyads_m25dyads_m25)
; oligos_8nt_mkv2_m8 versus dyads_m25 (dyads_m25dyads_m25); m=7/27; ncol2=17; w=16; offset=0; strand=D; shift=2; score=0.828996; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=8/27; ncol2=16; w=15; offset=-1; strand=D; shift=1; score=0.814765; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m8 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=9/27; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.802692; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

dyads_m2_shift1 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m8 versus dyads_m2 (dyads_m2dyads_m2); m=10/27; ncol2=18; w=16; offset=-1; strand=D; shift=1; score=0.800214; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=11/27; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.760891; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m8 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=12/27; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.725047; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=13/27; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.722913; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0

dyads_m21_shift2 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m8 versus dyads_m21 (dyads_m21dyads_m21); m=14/27; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.719563; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; oligos_8nt_mkv2_m8 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=15/27; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.716962; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=16/27; ncol2=18; w=16; offset=-2; strand=D; shift=0; score=0.716124; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

dyads_m36_shift1 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m8 versus dyads_m36 (dyads_m36dyads_m36); m=17/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.713013; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; oligos_8nt_mkv2_m8 versus dyads_m19 (dyads_m19dyads_m19); m=18/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.662736; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=19/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.646746; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=20/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.645441; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; oligos_8nt_mkv2_m8 versus dyads_m5 (dyads_m5dyads_m5); m=21/27; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.620177; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=22/27; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.618683; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0

oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=23/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.594322; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; oligos_8nt_mkv2_m8 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=24/27; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.587616; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0

oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=25/27; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.547171; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0

oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)
; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=26/27; ncol2=12; w=12; offset=2; strand=R; shift=4; score=0.541527; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0

oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=27/27; ncol2=11; w=11; offset=1; strand=D; shift=3; score=0.491725; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift1 ; 28 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=0 (reference); ncol1=17; shift=1; ncol=18; -vbdmAGCAGCTGTCmym ; Alignment reference a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=1/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score= 1; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=2/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.969442; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=3/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.969232; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=4/27; ncol2=16; w=16; offset=1; strand=R; shift=2; score=0.899735; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=5/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.882741; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_8nt_mkv2_m1 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=6/27; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=0.88046; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=7/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.871323; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=8/27; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.869366; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=9/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.846661; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=10/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.840343; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

dyads_m3_shift3 (dyads_m3dyads_m3)
; oligos_8nt_mkv2_m1 versus dyads_m3 (dyads_m3dyads_m3); m=11/27; ncol2=15; w=15; offset=2; strand=D; shift=3; score=0.829785; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; oligos_8nt_mkv2_m1 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=12/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.818534; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; oligos_8nt_mkv2_m1 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=13/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.798678; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=14/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.792927; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=15/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.791251; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=16/27; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.783988; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_8nt_mkv2_m1 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=17/27; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.759677; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=18/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.753963; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=19/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.742298; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=20/27; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.732546; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; oligos_8nt_mkv2_m1 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=21/27; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.732454; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

dyads_m8_shift3 (dyads_m8dyads_m8)
; oligos_8nt_mkv2_m1 versus dyads_m8 (dyads_m8dyads_m8); m=22/27; ncol2=15; w=15; offset=2; strand=D; shift=3; score=0.695913; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=23/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.682354; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=24/27; ncol2=18; w=17; offset=0; strand=D; shift=1; score=0.675737; -sygCAGCAGCTGCTGcr ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4

dyads_m21_shift3 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m1 versus dyads_m21 (dyads_m21dyads_m21); m=25/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.622768; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=26/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.600967; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=27/27; ncol2=12; w=12; offset=2; strand=D; shift=3; score=0.511066; ---rmAGCAGGTGst--- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m24_shift4 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m24_shift4 (dyads_m24dyads_m24)
; dyads_m24 (dyads_m24dyads_m24); m=0 (reference); ncol1=18; shift=4; ncol=23; ----ygRRAAAmsTGAAAAwyr- ; Alignment reference a 0 0 0 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 c 0 0 0 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 g 0 0 0 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 t 0 0 0 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0

dyads_m24_shift4 (dyads_m24dyads_m24)
; dyads_m24 versus dyads_m24 (dyads_m24dyads_m24); m=1/9; ncol2=18; w=18; offset=0; strand=D; shift=4; score= 1; ----ygRRAAAmsTGAAAAwyr- ; cor=; Ncor= a 0 0 0 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 c 0 0 0 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 g 0 0 0 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 t 0 0 0 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0

dyads_m27_shift4 (dyads_m27dyads_m27)
; dyads_m24 versus dyads_m27 (dyads_m27dyads_m27); m=2/9; ncol2=18; w=18; offset=0; strand=D; shift=4; score=0.701163; ----yGGAAAATkAdAAAAwsh- ; cor=; Ncor= a 0 0 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 c 0 0 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 g 0 0 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 t 0 0 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0

dyads_m4_shift3 (dyads_m4dyads_m4)
; dyads_m24 versus dyads_m4 (dyads_m4dyads_m4); m=3/9; ncol2=21; w=18; offset=-1; strand=D; shift=3; score=0.700623; ---gCkRRAAAACTGAAAATCAy ; cor=; Ncor= a 0 0 0 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 c 0 0 0 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 g 0 0 0 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 t 0 0 0 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4

dyads_m7_shift0 (dyads_m7dyads_m7)
; dyads_m24 versus dyads_m7 (dyads_m7dyads_m7); m=4/9; ncol2=23; w=18; offset=-4; strand=D; shift=0; score=0.638194; mmACTkrAAAwcdTGrAAAATgA ; cor=; Ncor= a 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 107 107 0 7 81 c 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 0 0 0 15 2 g 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 0 0 0 71 6 t 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4 0 0 107 14 18

oligos_8nt_mkv2_m4_shift8 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; dyads_m24 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=5/9; ncol2=13; w=13; offset=4; strand=D; shift=8; score=0.594764; --------WAmACTGAAAAwC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 c 0 0 0 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 g 0 0 0 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 t 0 0 0 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0

oligos_7nt_mkv2_m6_shift11 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; dyads_m24 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=6/9; ncol2=11; w=11; offset=7; strand=D; shift=11; score=0.583076; -----------msTGAAAAAyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 0 c 0 0 0 0 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 0 g 0 0 0 0 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 0 t 0 0 0 0 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4 0

oligos_7nt_mkv2_m5_shift9 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; dyads_m24 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=7/9; ncol2=11; w=11; offset=5; strand=D; shift=9; score=0.533199; ---------AmACTGAAAAw--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 c 0 0 0 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 g 0 0 0 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 t 0 0 0 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0

oligos_8nt_mkv2_m9_rc_shift11 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; dyads_m24 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=8/9; ncol2=12; w=11; offset=7; strand=R; shift=11; score=0.531012; -----------MsTGAAAAACrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 c 0 0 0 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 g 0 0 0 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 t 0 0 0 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51

dyads_m29_shift11 (dyads_m29dyads_m29)
; dyads_m24 versus dyads_m29 (dyads_m29dyads_m29); m=9/9; ncol2=12; w=11; offset=7; strand=D; shift=11; score=0.449941; -----------AmTGArAAAyry ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 c 0 0 0 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 g 0 0 0 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 t 0 0 0 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65

One-to-n matrix alignment; reference matrix: dyads_m15_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m15_shift0 (dyads_m15dyads_m15)
; dyads_m15 (dyads_m15dyads_m15); m=0 (reference); ncol1=15; shift=0; ncol=16; scCCGTssycGCggs- ; Alignment reference a 0 2 0 0 0 0 1 1 1 1 0 0 0 2 0 0 c 5 3 8 9 0 1 4 4 3 6 0 9 1 2 3 0 g 3 2 0 0 9 1 4 3 2 1 9 0 6 3 4 0 t 1 2 1 0 0 7 0 1 3 1 0 0 2 2 2 0

dyads_m15_shift0 (dyads_m15dyads_m15)
; dyads_m15 versus dyads_m15 (dyads_m15dyads_m15); m=1/2; ncol2=15; w=15; offset=0; strand=D; shift=0; score= 1; scCCGTssycGCggs- ; cor=; Ncor= a 0 2 0 0 0 0 1 1 1 1 0 0 0 2 0 0 c 5 3 8 9 0 1 4 4 3 6 0 9 1 2 3 0 g 3 2 0 0 9 1 4 3 2 1 9 0 6 3 4 0 t 1 2 1 0 0 7 0 1 3 1 0 0 2 2 2 0

dyads_m34_rc_shift1 (dyads_m34dyads_m34_rc)
; dyads_m15 versus dyads_m34_rc (dyads_m34dyads_m34_rc); m=2/2; ncol2=15; w=14; offset=1; strand=R; shift=1; score=0.636357; -sbCGGsssygCGTss ; cor=; Ncor= a 0 3 2 0 0 0 3 1 3 2 2 0 0 1 3 4 c 0 8 7 21 2 3 9 11 9 7 5 20 0 2 7 10 g 0 8 6 0 19 15 7 7 7 4 11 1 21 3 7 6 t 0 2 6 0 0 3 2 2 2 8 3 0 0 15 4 1

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m2_shift1 ; 26 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=0 (reference); ncol1=17; shift=1; ncol=18; -swsAACAGCTGCTGchm ; Alignment reference a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=1/25; ncol2=17; w=17; offset=0; strand=D; shift=1; score= 1; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=2/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.969646; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=3/25; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.88696; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=4/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.86851; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=5/25; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.848932; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=6/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.846661; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=7/25; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.828917; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=8/25; ncol2=18; w=17; offset=-1; strand=D; shift=0; score=0.827759; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

dyads_m25_shift2 (dyads_m25dyads_m25)
; oligos_8nt_mkv2_m2 versus dyads_m25 (dyads_m25dyads_m25); m=9/25; ncol2=17; w=16; offset=1; strand=D; shift=2; score=0.805868; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8

dyads_m2_shift1 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m2 versus dyads_m2 (dyads_m2dyads_m2); m=10/25; ncol2=18; w=17; offset=0; strand=D; shift=1; score=0.804693; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=11/25; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.751148; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0

dyads_m21_shift2 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m2 versus dyads_m21 (dyads_m21dyads_m21); m=12/25; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.745037; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=13/25; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.733631; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

dyads_m36_shift1 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m2 versus dyads_m36 (dyads_m36dyads_m36); m=14/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.729473; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; oligos_8nt_mkv2_m2 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=15/25; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.71002; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=16/25; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.703385; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; oligos_8nt_mkv2_m2 versus dyads_m19 (dyads_m19dyads_m19); m=17/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.653747; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=18/25; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.652231; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=19/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.629598; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=20/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.627706; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; oligos_8nt_mkv2_m2 versus dyads_m5 (dyads_m5dyads_m5); m=21/25; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.624237; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=22/25; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.621102; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0

oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=23/25; ncol2=12; w=12; offset=1; strand=D; shift=2; score=0.553124; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0

oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=24/25; ncol2=12; w=12; offset=3; strand=R; shift=4; score=0.535045; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0

oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=25/25; ncol2=11; w=11; offset=2; strand=D; shift=3; score=0.468748; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 22 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=0 (reference); ncol1=14; shift=2; ncol=17; --cwGaCAGCTGtCwg- ; Alignment reference a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=1/21; ncol2=14; w=14; offset=0; strand=D; shift=2; score= 1; --cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=2/21; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.894525; --hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=3/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.868996; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m1_shift1 (dyads_m1dyads_m1)
; oligos_6nt_mkv2_m1 versus dyads_m1 (dyads_m1dyads_m1); m=4/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.868996; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m19_rc_shift2 (dyads_m19dyads_m19_rc)
; oligos_6nt_mkv2_m1 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=5/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.824628; --smrbCAGCTGTChby ; cor=; Ncor= a 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=6/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.822782; -gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_8nt_mkv2_m22_rc_shift2 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=7/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.816836; --cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

oligos_8nt_mkv2_m17_rc_shift2 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=8/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.814029; --cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_8nt_mkv2_m3_rc_shift2 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=9/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.808925; --cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; oligos_6nt_mkv2_m1 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=10/21; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.79691; -mvrGACAGCTGwGsv- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0

dyads_m36_rc_shift2 (dyads_m36dyads_m36_rc)
; oligos_6nt_mkv2_m1 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=11/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.795203; --smagCAGCTGTCmby ; cor=; Ncor= a 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=12/21; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.785906; --kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=13/21; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.771906; -rswGACAGCTGmsg-- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; oligos_6nt_mkv2_m1 versus dyads_m5 (dyads_m5dyads_m5); m=14/21; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.771828; -rvdGACAGCTGmsg-- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0

dyads_m3_shift2 (dyads_m3dyads_m3)
; oligos_6nt_mkv2_m1 versus dyads_m3 (dyads_m3dyads_m3); m=15/21; ncol2=15; w=14; offset=0; strand=D; shift=2; score=0.764256; --rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=16/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.716528; -srsAACAGCTGTswmm ; cor=; Ncor= a 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

oligos_7nt_mkv2_m13_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=17/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.70475; -grmArCAGCTGTCwyc ; cor=; Ncor= a 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=18/21; ncol2=16; w=14; offset=-1; strand=R; shift=1; score=0.680013; -akmAGCAGCTGTCysc ; cor=; Ncor= a 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_8nt_mkv2_m10_rc_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=19/21; ncol2=17; w=14; offset=-2; strand=R; shift=0; score=0.609995; rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=20/21; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=0.600967; vbdmAGCAGCTGTCmym ; cor=; Ncor= a 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_8nt_mkv2_m27_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=21/21; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=0.587165; vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m9_shift9 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m9_shift9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9)
; oligos_8nt_mkv2_m9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9); m=0 (reference); ncol1=12; shift=9; ncol=23; ---------ayGTTTTTCAsK-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 51 4 20 1 2 1 0 3 0 95 8 1 0 0 c 0 0 0 0 0 0 0 0 0 7 52 1 0 0 1 2 0 94 1 29 3 0 0 g 0 0 0 0 0 0 0 0 0 19 5 77 0 1 0 0 0 0 0 47 27 0 0 t 0 0 0 0 0 0 0 0 0 23 39 2 99 97 98 98 97 6 4 16 69 0 0

oligos_8nt_mkv2_m9_shift9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9)
; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9); m=1/12; ncol2=12; w=12; offset=0; strand=D; shift=9; score= 1; ---------ayGTTTTTCAsK-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 51 4 20 1 2 1 0 3 0 95 8 1 0 0 c 0 0 0 0 0 0 0 0 0 7 52 1 0 0 1 2 0 94 1 29 3 0 0 g 0 0 0 0 0 0 0 0 0 19 5 77 0 1 0 0 0 0 0 47 27 0 0 t 0 0 0 0 0 0 0 0 0 23 39 2 99 97 98 98 97 6 4 16 69 0 0

oligos_7nt_mkv2_m6_rc_shift10 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6_rc)
; oligos_8nt_mkv2_m9 versus oligos_7nt_mkv2_m6_rc (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6_rc); m=2/12; ncol2=11; w=11; offset=1; strand=R; shift=10; score=0.894083; ----------yrTTTTTCAsk-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 4 58 0 15 1 0 0 0 139 16 2 0 0 c 0 0 0 0 0 0 0 0 0 0 93 16 0 0 0 1 1 138 0 41 1 0 0 g 0 0 0 0 0 0 0 0 0 0 4 59 0 0 0 0 0 0 0 59 58 0 0 t 0 0 0 0 0 0 0 0 0 0 38 6 139 124 138 138 138 1 0 23 78 0 0

dyads_m29_rc_shift9 (dyads_m29dyads_m29_rc)
; oligos_8nt_mkv2_m9 versus dyads_m29_rc (dyads_m29dyads_m29_rc); m=3/12; ncol2=12; w=12; offset=0; strand=R; shift=9; score=0.872856; ---------ryrTTTyTCAkT-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 65 5 46 0 1 0 0 0 1 154 3 6 0 0 c 0 0 0 0 0 0 0 0 0 5 48 0 0 0 0 108 0 160 0 19 14 0 0 g 0 0 0 0 0 0 0 0 0 87 6 103 0 0 0 0 0 0 9 43 4 0 0 t 0 0 0 0 0 0 0 0 0 6 104 14 163 162 163 55 163 2 0 98 139 0 0

oligos_8nt_mkv2_m4_rc_shift11 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4_rc)
; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m4_rc (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4_rc); m=4/12; ncol2=13; w=10; offset=2; strand=R; shift=11; score=0.623539; -----------GwTTTTCAGTkT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 4 44 1 1 0 0 2 118 0 0 3 24 c 0 0 0 0 0 0 0 0 0 0 0 30 1 1 2 0 1 126 11 2 0 0 11 g 0 0 0 0 0 0 0 0 0 0 0 92 3 3 1 1 0 0 0 115 0 77 1 t 0 0 0 0 0 0 0 0 0 0 0 5 83 126 127 130 130 3 2 14 131 51 95

dyads_m39_rc_shift10 (dyads_m39dyads_m39_rc)
; oligos_8nt_mkv2_m9 versus dyads_m39_rc (dyads_m39dyads_m39_rc); m=5/12; ncol2=10; w=10; offset=1; strand=R; shift=10; score=0.608481; ----------yrTATTTCwC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 6 26 0 56 0 0 0 0 27 4 0 0 0 c 0 0 0 0 0 0 0 0 0 0 23 5 0 0 0 0 0 56 3 40 0 0 0 g 0 0 0 0 0 0 0 0 0 0 6 20 0 0 0 0 0 0 1 7 0 0 0 t 0 0 0 0 0 0 0 0 0 0 21 5 56 0 56 56 56 0 25 5 0 0 0

oligos_8nt_mkv2_m16_rc_shift8 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16_rc)
; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m16_rc (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16_rc); m=6/12; ncol2=12; w=11; offset=-1; strand=R; shift=8; score=0.604377; --------yrTsATTTTCmR--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 5 36 0 0 73 0 1 0 0 0 39 19 0 0 0 c 0 0 0 0 0 0 0 0 36 15 0 26 0 0 0 0 0 72 25 0 0 0 0 g 0 0 0 0 0 0 0 0 1 19 1 46 0 0 1 0 0 0 2 52 0 0 0 t 0 0 0 0 0 0 0 0 31 3 72 1 0 73 71 73 73 1 7 2 0 0 0

oligos_6nt_mkv2_m8_rc_shift10 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc)
; oligos_8nt_mkv2_m9 versus oligos_6nt_mkv2_m8_rc (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc); m=7/12; ncol2=10; w=10; offset=1; strand=R; shift=10; score=0.603326; ----------tdTTTCTCay--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 5 54 0 0 0 0 0 0 98 6 0 0 0 c 0 0 0 0 0 0 0 0 0 0 34 5 0 0 0 154 0 154 11 44 0 0 0 g 0 0 0 0 0 0 0 0 0 0 30 52 0 0 0 0 0 0 32 3 0 0 0 t 0 0 0 0 0 0 0 0 0 0 85 43 154 154 154 0 154 0 13 101 0 0 0

oligos_7nt_mkv2_m5_rc_shift12 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5_rc)
; oligos_8nt_mkv2_m9 versus oligos_7nt_mkv2_m5_rc (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5_rc); m=8/12; ncol2=11; w=9; offset=3; strand=R; shift=12; score=0.596075; ------------wTTTTCAGTkT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 36 2 0 0 0 0 98 0 0 3 8 c 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 98 0 0 0 0 10 g 0 0 0 0 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 98 0 40 0 t 0 0 0 0 0 0 0 0 0 0 0 0 60 90 98 98 98 0 0 0 98 55 80

dyads_m24_rc_shift10 (dyads_m24dyads_m24_rc)
; oligos_8nt_mkv2_m9 versus dyads_m24_rc (dyads_m24dyads_m24_rc); m=9/12; ncol2=18; w=11; offset=1; strand=R; shift=10; score=0.531012; ----------yrwTTTTCAskTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1 17 14 0 0 0 0 0 31 2 0 0 0 c 0 0 0 0 0 0 0 0 0 0 21 6 0 0 0 1 1 34 0 15 1 0 0 g 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 14 20 1 0 t 0 0 0 0 0 0 0 0 0 0 12 1 20 34 34 33 33 0 3 3 13 33 34

dyads_m7_rc_shift0 (dyads_m7dyads_m7_rc)
; oligos_8nt_mkv2_m9 versus dyads_m7_rc (dyads_m7dyads_m7_rc); m=10/12; ncol2=23; w=12; offset=-9; strand=R; shift=0; score= 0.4461; TcATTTTyCAhgwTTTymAGTkk ; cor=; Ncor= a 18 14 107 0 0 4 4 3 2 75 31 7 35 6 10 4 4 28 106 0 0 7 16 c 6 71 0 0 0 3 15 51 83 16 31 15 3 16 3 2 29 65 1 0 0 13 6 g 2 15 0 0 0 5 1 16 2 13 5 68 2 3 14 5 4 4 0 107 0 38 27 t 81 7 0 107 107 95 87 37 20 3 40 17 67 82 80 96 70 10 0 0 107 49 58

dyads_m4_rc_shift8 (dyads_m4dyads_m4_rc)
; oligos_8nt_mkv2_m9 versus dyads_m4_rc (dyads_m4dyads_m4_rc); m=11/12; ncol2=21; w=12; offset=-1; strand=R; shift=8; score=0.445154; --------YrTGATTTTCAGTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4 0 0 15 0 0 0 0 0 13 0 0 0 0 c 0 0 0 0 0 0 0 0 12 3 2 3 0 0 0 0 0 16 0 1 0 0 0 g 0 0 0 0 0 0 0 0 0 9 0 13 0 0 0 0 0 0 0 15 0 2 0 t 0 0 0 0 0 0 0 0 4 0 14 0 1 16 16 16 16 0 3 0 16 14 16

oligos_8nt_mkv2_m6_rc_shift10 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6_rc)
; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m6_rc (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6_rc); m=12/12; ncol2=18; w=11; offset=1; strand=R; shift=10; score=0.422138; ----------ywTTTCTCATTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1 52 2 0 0 15 4 1 99 1 1 0 0 c 0 0 0 0 0 0 0 0 0 0 32 0 0 0 1 85 2 99 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 1 23 0 1 1 1 0 0 1 1 0 0 0 t 0 0 0 0 0 0 0 0 0 0 68 27 100 101 100 1 96 2 2 100 101 102 102

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m20_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m20_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)
; oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=0 (reference); ncol1=13; shift=0; ncol=13; swGAGGCAGGGrG ; Alignment reference a 2 11 1 25 0 0 1 25 0 6 0 8 2 c 13 2 2 0 0 0 25 0 0 0 0 1 3 g 11 6 23 0 26 25 0 0 26 20 26 14 19 t 0 7 0 1 0 1 0 1 0 0 0 3 2

oligos_8nt_mkv2_m20_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)
; oligos_8nt_mkv2_m20 versus oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=1/7; ncol2=13; w=13; offset=0; strand=D; shift=0; score= 1; swGAGGCAGGGrG ; cor=; Ncor= a 2 11 1 25 0 0 1 25 0 6 0 8 2 c 13 2 2 0 0 0 25 0 0 0 0 1 3 g 11 6 23 0 26 25 0 0 26 20 26 14 19 t 0 7 0 1 0 1 0 1 0 0 0 3 2

dyads_m11_rc_shift1 (dyads_m11dyads_m11_rc)
; oligos_8nt_mkv2_m20 versus dyads_m11_rc (dyads_m11dyads_m11_rc); m=2/7; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 0.8834; -agwGGCAGGGgg ; cor=; Ncor= a 0 13 3 18 0 0 0 29 0 0 0 4 1 c 0 3 5 0 0 0 29 0 0 0 1 3 7 g 0 6 16 2 29 28 0 0 29 29 28 15 19 t 0 7 5 9 0 1 0 0 0 0 0 7 2

oligos_7nt_mkv2_m11_rc_shift0 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc)
; oligos_8nt_mkv2_m20 versus oligos_7nt_mkv2_m11_rc (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc); m=3/7; ncol2=11; w=11; offset=0; strand=R; shift=0; score=0.830223; sdGAGGCAGrG-- ; cor=; Ncor= a 3 12 0 35 0 0 0 34 0 15 4 0 0 c 17 2 0 0 0 0 35 1 1 2 1 0 0 g 15 11 35 0 35 35 0 0 34 18 27 0 0 t 0 10 0 0 0 0 0 0 0 0 3 0 0

oligos_7nt_mkv2_m8_rc_shift2 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc)
; oligos_8nt_mkv2_m20 versus oligos_7nt_mkv2_m8_rc (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc); m=4/7; ncol2=11; w=11; offset=2; strand=R; shift=2; score=0.790515; --gwGGCAGGGks ; cor=; Ncor= a 0 0 6 16 0 0 0 31 0 0 0 4 1 c 0 0 6 5 0 0 32 0 0 1 0 5 9 g 0 0 16 4 34 34 0 3 34 33 34 15 20 t 0 0 6 9 0 0 2 0 0 0 0 10 4

oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4)
; oligos_8nt_mkv2_m20 versus oligos_6nt_mkv2_m4 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4); m=5/7; ncol2=10; w=10; offset=1; strand=D; shift=1; score=0.724907; -dsAGGCAGrg-- ; cor=; Ncor= a 0 17 7 59 0 0 0 59 0 18 13 0 0 c 0 10 15 0 0 0 59 0 0 12 6 0 0 g 0 16 33 0 59 59 0 0 59 23 32 0 0 t 0 16 4 0 0 0 0 0 0 6 8 0 0

oligos_8nt_mkv2_m23_rc_shift0 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc)
; oligos_8nt_mkv2_m20 versus oligos_8nt_mkv2_m23_rc (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc); m=6/7; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.663767; vrGAGGAAGGmd- ; cor=; Ncor= a 3 4 0 8 0 0 8 7 0 0 4 3 0 c 2 1 0 0 0 0 0 1 0 0 2 0 0 g 3 3 8 0 8 8 0 0 8 8 1 2 0 t 0 0 0 0 0 0 0 0 0 0 1 3 0

dyads_m30_rc_shift2 (dyads_m30dyads_m30_rc)
; oligos_8nt_mkv2_m20 versus dyads_m30_rc (dyads_m30dyads_m30_rc); m=7/7; ncol2=11; w=11; offset=2; strand=R; shift=2; score=0.596506; --yrGGCKGGGkr ; cor=; Ncor= a 0 0 2 3 0 0 0 0 0 0 0 2 4 c 0 0 4 2 0 0 11 0 0 0 0 2 2 g 0 0 2 4 11 11 0 3 11 11 11 3 3 t 0 0 3 2 0 0 0 8 0 0 0 4 2

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m7_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m7_shift4 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7)
; oligos_6nt_mkv2_m7 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7); m=0 (reference); ncol1=10; shift=4; ncol=14; ----hgCCTCCCwa ; Alignment reference a 0 0 0 0 10 6 0 0 0 0 0 0 17 16 c 0 0 0 0 10 7 40 40 0 40 40 40 6 9 g 0 0 0 0 5 19 0 0 0 0 0 0 5 8 t 0 0 0 0 15 8 0 0 40 0 0 0 12 7

oligos_6nt_mkv2_m7_shift4 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7)
; oligos_6nt_mkv2_m7 versus oligos_6nt_mkv2_m7 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7); m=1/4; ncol2=10; w=10; offset=0; strand=D; shift=4; score= 1; ----hgCCTCCCwa ; cor=; Ncor= a 0 0 0 0 10 6 0 0 0 0 0 0 17 16 c 0 0 0 0 10 7 40 40 0 40 40 40 6 9 g 0 0 0 0 5 19 0 0 0 0 0 0 5 8 t 0 0 0 0 15 8 0 0 40 0 0 0 12 7

oligos_7nt_mkv2_m11_shift1 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11)
; oligos_6nt_mkv2_m7 versus oligos_7nt_mkv2_m11 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11); m=2/4; ncol2=11; w=8; offset=-3; strand=D; shift=1; score=0.47595; -CyCTGCCTChs-- ; cor=; Ncor= a 0 3 0 0 0 0 0 0 0 0 10 0 0 0 c 0 27 18 34 0 0 35 35 0 35 11 15 0 0 g 0 1 2 1 1 35 0 0 0 0 2 17 0 0 t 0 4 15 0 34 0 0 0 35 0 12 3 0 0

oligos_8nt_mkv2_m23_shift0 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23)
; oligos_6nt_mkv2_m7 versus oligos_8nt_mkv2_m23 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23); m=3/4; ncol2=12; w=8; offset=-4; strand=D; shift=0; score=0.412254; hkCCTTCCTCyb-- ; cor=; Ncor= a 3 1 0 0 0 0 0 0 0 0 0 0 0 0 c 2 1 8 8 0 0 8 8 0 8 3 3 0 0 g 0 2 0 0 1 0 0 0 0 0 1 2 0 0 t 3 4 0 0 7 8 0 0 8 0 4 3 0 0

oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m7 versus oligos_6nt_mkv2_m4_rc (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc); m=4/4; ncol2=10; w=7; offset=-3; strand=R; shift=1; score=0.406966; -cyCTGCCTsh--- ; cor=; Ncor= a 0 8 6 0 0 0 0 0 0 4 16 0 0 0 c 0 32 23 59 0 0 59 59 0 33 16 0 0 0 g 0 6 12 0 0 59 0 0 0 15 10 0 0 0 t 0 13 18 0 59 0 0 0 59 7 17 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m7_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m7_shift2 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)
; oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=0 (reference); ncol1=11; shift=2; ncol=14; --ssCCCGGCGss- ; Alignment reference a 0 0 4 5 1 1 0 0 3 2 0 4 4 0 c 0 0 17 11 34 29 32 4 5 33 0 11 14 0 g 0 0 11 14 1 3 4 32 28 1 33 17 16 0 t 0 0 4 6 0 3 0 0 0 0 3 4 2 0

oligos_7nt_mkv2_m7_shift2 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)
; oligos_7nt_mkv2_m7 versus oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=1/7; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 1; --ssCCCGGCGss- ; cor=; Ncor= a 0 0 4 5 1 1 0 0 3 2 0 4 4 0 c 0 0 17 11 34 29 32 4 5 33 0 11 14 0 g 0 0 11 14 1 3 4 32 28 1 33 17 16 0 t 0 0 4 6 0 3 0 0 0 0 3 4 2 0

oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; oligos_7nt_mkv2_m7 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=2/7; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.885944; --ssCCCGCCGsg- ; cor=; Ncor= a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0

oligos_6nt_mkv2_m6_rc_shift3 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6_rc)
; oligos_7nt_mkv2_m7 versus oligos_6nt_mkv2_m6_rc (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6_rc); m=3/7; ncol2=11; w=10; offset=1; strand=R; shift=3; score=0.801271; ---sCCCGGCGGss ; cor=; Ncor= a 0 0 0 1 2 1 0 0 0 0 0 1 2 2 c 0 0 0 11 18 20 23 4 3 25 1 3 9 10 g 0 0 0 10 4 3 3 22 23 1 25 21 13 11 t 0 0 0 4 2 2 0 0 0 0 0 1 2 3

oligos_8nt_mkv2_m15_rc_shift2 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15_rc)
; oligos_7nt_mkv2_m7 versus oligos_8nt_mkv2_m15_rc (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15_rc); m=4/7; ncol2=12; w=11; offset=0; strand=R; shift=2; score=0.787447; --ssCgCGGCGGgb ; cor=; Ncor= a 0 0 2 0 0 1 0 0 0 0 0 0 2 0 c 0 0 7 8 14 2 13 2 1 14 0 0 3 4 g 0 0 4 5 0 9 1 12 12 0 13 14 9 6 t 0 0 1 1 0 2 0 0 1 0 1 0 0 4

dyads_m26_rc_shift2 (dyads_m26dyads_m26_rc)
; oligos_7nt_mkv2_m7 versus dyads_m26_rc (dyads_m26dyads_m26_rc); m=5/7; ncol2=12; w=11; offset=0; strand=R; shift=2; score=0.71108; --ssCGCsgCGGsg ; cor=; Ncor= a 0 0 2 3 0 1 2 1 3 0 0 0 3 2 c 0 0 16 12 25 2 24 11 6 26 1 2 10 6 g 0 0 8 10 3 24 2 13 15 1 27 25 15 19 t 0 0 2 3 0 1 0 3 4 1 0 1 0 1

oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m7 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=6/7; ncol2=10; w=10; offset=0; strand=D; shift=2; score=0.681037; --ssCCCCGCsg-- ; cor=; Ncor= a 0 0 0 3 0 0 0 0 0 0 2 1 0 0 c 0 0 10 7 23 21 23 24 0 25 8 6 0 0 g 0 0 11 9 2 4 2 1 25 0 9 15 0 0 t 0 0 4 6 0 0 0 0 0 0 6 3 0 0

dyads_m12_shift0 (dyads_m12dyads_m12)
; oligos_7nt_mkv2_m7 versus dyads_m12 (dyads_m12dyads_m12); m=7/7; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=0.626799; vssCCSCGCSGGss ; cor=; Ncor= a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m39_shift3 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m39_shift3 (dyads_m39dyads_m39)
; dyads_m39 (dyads_m39dyads_m39); m=0 (reference); ncol1=10; shift=3; ncol=14; ---GwGAAATAyr- ; Alignment reference a 0 0 0 5 25 0 56 56 56 0 56 5 21 0 c 0 0 0 7 1 0 0 0 0 0 0 20 6 0 g 0 0 0 40 3 56 0 0 0 0 0 5 23 0 t 0 0 0 4 27 0 0 0 0 56 0 26 6 0

dyads_m39_shift3 (dyads_m39dyads_m39)
; dyads_m39 versus dyads_m39 (dyads_m39dyads_m39); m=1/6; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 1; ---GwGAAATAyr- ; cor=; Ncor= a 0 0 0 5 25 0 56 56 56 0 56 5 21 0 c 0 0 0 7 1 0 0 0 0 0 0 20 6 0 g 0 0 0 40 3 56 0 0 0 0 0 5 23 0 t 0 0 0 4 27 0 0 0 0 56 0 26 6 0

oligos_7nt_mkv2_m6_shift2 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; dyads_m39 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=2/6; ncol2=11; w=10; offset=-1; strand=D; shift=2; score=0.700857; --msTGAAAAAyr- ; cor=; Ncor= a 0 0 78 23 0 1 138 138 138 124 139 6 38 0 c 0 0 58 59 0 0 0 0 0 0 0 59 4 0 g 0 0 1 41 0 138 1 1 0 0 0 16 93 0 t 0 0 2 16 139 0 0 0 1 15 0 58 4 0

oligos_8nt_mkv2_m9_rc_shift2 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; dyads_m39 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=3/6; ncol2=12; w=10; offset=-1; strand=R; shift=2; score=0.608481; --MsTGAAAAACrt ; cor=; Ncor= a 0 0 69 16 4 6 97 98 98 97 99 2 39 23 c 0 0 27 47 0 0 0 0 0 1 0 77 5 19 g 0 0 3 29 1 94 0 2 1 0 0 1 52 7 t 0 0 1 8 95 0 3 0 1 2 1 20 4 51

oligos_6nt_mkv2_m8_shift1 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)
; dyads_m39 versus oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=4/6; ncol2=10; w=8; offset=-2; strand=D; shift=1; score=0.559766; -rtGAGAAAha--- ; cor=; Ncor= a 0 101 13 0 154 0 154 154 154 43 85 0 0 0 c 0 3 32 0 0 0 0 0 0 52 30 0 0 0 g 0 44 11 154 0 154 0 0 0 5 34 0 0 0 t 0 6 98 0 0 0 0 0 0 54 5 0 0 0

dyads_m29_shift0 (dyads_m29dyads_m29)
; dyads_m39 versus dyads_m29 (dyads_m29dyads_m29); m=5/6; ncol2=12; w=9; offset=-3; strand=D; shift=0; score=0.547389; AmTGArAAAyry-- ; cor=; Ncor= a 139 98 0 2 163 55 163 162 163 14 104 6 0 0 c 4 43 9 0 0 0 0 0 0 103 6 87 0 0 g 14 19 0 160 0 108 0 0 0 0 48 5 0 0 t 6 3 154 1 0 0 0 1 0 46 5 65 0 0

oligos_8nt_mkv2_m11_shift4 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11)
; dyads_m39 versus oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=6/6; ncol2=13; w=9; offset=1; strand=D; shift=4; score=0.49244; ----AGAAATRCAC ; cor=; Ncor= a 0 0 0 0 59 4 71 72 71 0 18 0 68 0 c 0 0 0 0 0 2 1 0 0 2 2 71 1 72 g 0 0 0 0 3 63 0 0 0 1 50 0 1 0 t 0 0 0 0 10 3 0 0 1 69 2 1 2 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m4_shift5 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=0 (reference); ncol1=13; shift=5; ncol=24; -----WAmACTGAAAAwC------ ; Alignment reference a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0

oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=1/9; ncol2=13; w=13; offset=0; strand=D; shift=5; score= 1; -----WAmACTGAAAAwC------ ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0

oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; oligos_8nt_mkv2_m4 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=2/9; ncol2=11; w=11; offset=1; strand=D; shift=6; score=0.838355; ------AmACTGAAAAw------- ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0 0

oligos_7nt_mkv2_m6_shift8 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; oligos_8nt_mkv2_m4 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=3/9; ncol2=11; w=10; offset=3; strand=D; shift=8; score=0.639996; --------msTGAAAAAyr----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 0 0 0 0 0 c 0 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4 0 0 0 0 0

oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=4/9; ncol2=12; w=10; offset=3; strand=R; shift=8; score=0.623539; --------MsTGAAAAACrt---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0

dyads_m24_shift1 (dyads_m24dyads_m24)
; oligos_8nt_mkv2_m4 versus dyads_m24 (dyads_m24dyads_m24); m=5/9; ncol2=18; w=13; offset=-4; strand=D; shift=1; score=0.594764; -ygRRAAAmsTGAAAAwyr----- ; cor=; Ncor= a 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 0 0 0 0 c 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 0 0 0 0 g 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 0 0 0 0 t 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0 0 0 0 0

dyads_m4_shift0 (dyads_m4dyads_m4)
; oligos_8nt_mkv2_m4 versus dyads_m4 (dyads_m4dyads_m4); m=6/9; ncol2=21; w=13; offset=-5; strand=D; shift=0; score=0.563196; gCkRRAAAACTGAAAATCAyR--- ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0

dyads_m29_shift8 (dyads_m29dyads_m29)
; oligos_8nt_mkv2_m4 versus dyads_m29 (dyads_m29dyads_m29); m=7/9; ncol2=12; w=10; offset=3; strand=D; shift=8; score=0.555704; --------AmTGArAAAyry---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 c 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 g 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 t 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0

oligos_8nt_mkv2_m16_shift9 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=8/9; ncol2=12; w=9; offset=4; strand=D; shift=9; score=0.498435; ---------YkGAAAATsAyr--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 0 c 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 0 g 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 0 t 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0 0

dyads_m7_shift6 (dyads_m7dyads_m7)
; oligos_8nt_mkv2_m4 versus dyads_m7 (dyads_m7dyads_m7); m=9/9; ncol2=23; w=12; offset=1; strand=D; shift=6; score=0.472281; ------mmACTkrAAAwcdTGrAA ; cor=; Ncor= a 0 0 0 0 0 0 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 c 0 0 0 0 0 0 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 g 0 0 0 0 0 0 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 t 0 0 0 0 0 0 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 20 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=0 (reference); ncol1=16; shift=1; ncol=17; -vmwGaCAGCTGtCwkb ; Alignment reference a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=1/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m1_shift1 (dyads_m1dyads_m1)
; oligos_7nt_mkv2_m1 versus dyads_m1 (dyads_m1dyads_m1); m=2/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=3/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.928003; -gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=4/19; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.868996; --cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; oligos_7nt_mkv2_m1 versus dyads_m19 (dyads_m19dyads_m19); m=5/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.812212; -rvdGACAGCTGvyks- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=6/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.808909; -rvtGACAGCTGmhkg- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=7/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.805464; -rstGACAGCTGmhkg- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0

oligos_8nt_mkv2_m3_rc_shift2 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=8/19; ncol2=15; w=15; offset=1; strand=R; shift=2; score=0.801669; --cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

dyads_m36_shift1 (dyads_m36dyads_m36)
; oligos_7nt_mkv2_m1 versus dyads_m36 (dyads_m36dyads_m36); m=9/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.774901; -rvkGACAGCTGctks- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=10/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.764901; -srsAACAGCTGTswmm ; cor=; Ncor= a 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

dyads_m8_shift2 (dyads_m8dyads_m8)
; oligos_7nt_mkv2_m1 versus dyads_m8 (dyads_m8dyads_m8); m=11/19; ncol2=15; w=15; offset=1; strand=D; shift=2; score=0.763334; --bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

dyads_m5_rc_shift3 (dyads_m5dyads_m5_rc)
; oligos_7nt_mkv2_m1 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=12/19; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.760426; ---cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=13/19; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.759761; ---cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/19; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.756774; -grwGACAGCTGyTkyc ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=15/19; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.748158; --hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=16/19; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.737151; -akmAGCAGCTGTCysc ; cor=; Ncor= a 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; oligos_7nt_mkv2_m1 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=17/19; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.726765; -rrwGACAGCTGyTky- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0

oligos_8nt_mkv2_m10_rc_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=18/19; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.662618; rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=19/19; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.655261; --kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m26_shift14 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m26_shift14 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26)
; oligos_8nt_mkv2_m26 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26); m=0 (reference); ncol1=12; shift=14; ncol=26; --------------CTACAGTGTGya ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 14 87 12 82 1 0 1 0 8 5 56 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 7 0 69 1 0 0 0 0 0 24 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 0 1 0 85 0 86 0 79 18 9 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 65 0 5 4 1 87 0 87 0 40 19

oligos_8nt_mkv2_m26_shift14 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26)
; oligos_8nt_mkv2_m26 versus oligos_8nt_mkv2_m26 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26); m=1/9; ncol2=12; w=12; offset=0; strand=D; shift=14; score= 1; --------------CTACAGTGTGya ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 14 87 12 82 1 0 1 0 8 5 56 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 7 0 69 1 0 0 0 0 0 24 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 0 1 0 85 0 86 0 79 18 9 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 65 0 5 4 1 87 0 87 0 40 19

dyads_m6_rc_shift12 (dyads_m6dyads_m6_rc)
; oligos_8nt_mkv2_m26 versus dyads_m6_rc (dyads_m6dyads_m6_rc); m=2/9; ncol2=14; w=12; offset=-2; strand=R; shift=12; score=0.831536; ------------TyCTAcAGTGTGya ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 8 1 0 0 91 19 76 7 8 0 0 1 3 51 c 0 0 0 0 0 0 0 0 0 0 0 0 1 59 92 0 1 62 5 8 3 0 0 0 36 10 g 0 0 0 0 0 0 0 0 0 0 0 0 5 7 0 0 0 6 7 72 1 92 0 91 19 15 t 0 0 0 0 0 0 0 0 0 0 0 0 78 25 0 92 0 5 4 5 80 0 92 0 34 16

dyads_m23_rc_shift13 (dyads_m23dyads_m23_rc)
; oligos_8nt_mkv2_m26 versus dyads_m23_rc (dyads_m23dyads_m23_rc); m=3/9; ncol2=12; w=11; offset=-1; strand=R; shift=13; score=0.799973; -------------yCTACAgTGTKc- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 1 16 0 95 0 84 21 0 0 0 2 3 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 44 67 0 0 95 4 14 0 0 0 0 50 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 1 55 0 95 0 67 21 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 47 10 95 0 0 6 5 95 0 95 26 21 0

dyads_m33_rc_shift13 (dyads_m33dyads_m33_rc)
; oligos_8nt_mkv2_m26 versus dyads_m33_rc (dyads_m33dyads_m33_rc); m=4/9; ncol2=10; w=9; offset=-1; strand=R; shift=13; score=0.671399; -------------yCTACAGTGT--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 76 0 75 0 0 1 5 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 48 66 0 0 76 1 0 0 6 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 76 0 68 17 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 21 5 76 0 0 0 0 76 1 54 0 0 0

dyads_m20_shift12 (dyads_m20dyads_m20)
; oligos_8nt_mkv2_m26 versus dyads_m20 (dyads_m20dyads_m20); m=5/9; ncol2=23; w=12; offset=-2; strand=D; shift=12; score=0.494047; ------------TCCTAmAGTGTGya ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 8 3 0 0 60 18 46 6 2 2 7 5 7 40 c 0 0 0 0 0 0 0 0 0 0 0 0 0 44 60 0 0 35 5 6 9 3 1 3 23 2 g 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 0 0 3 4 44 2 49 4 46 2 11 t 0 0 0 0 0 0 0 0 0 0 0 0 48 10 0 60 0 4 5 4 47 6 48 6 28 7

dyads_m40_rc_shift12 (dyads_m40dyads_m40_rc)
; oligos_8nt_mkv2_m26 versus dyads_m40_rc (dyads_m40dyads_m40_rc); m=6/9; ncol2=25; w=12; offset=-2; strand=R; shift=12; score=0.452904; ------------TCCTAmAgTGTGyA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 64 18 51 8 3 1 2 6 1 44 c 0 0 0 0 0 0 0 0 0 0 0 0 2 45 63 0 0 35 4 4 5 7 6 1 28 5 g 0 0 0 0 0 0 0 0 0 0 0 0 5 3 0 0 0 4 7 42 1 50 3 50 4 11 t 0 0 0 0 0 0 0 0 0 0 0 0 54 14 1 64 0 7 2 10 55 6 53 7 31 4

oligos_8nt_mkv2_m11_rc_shift18 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc)
; oligos_8nt_mkv2_m26 versus oligos_8nt_mkv2_m11_rc (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc); m=7/9; ncol2=13; w=8; offset=4; strand=R; shift=18; score=0.44416; ------------------AGTGTGYA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 10 0 0 2 1 2 69 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 9 0 0 1 0 50 1 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 0 72 1 71 2 2 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 72 0 68 0 18 0

dyads_m9_rc_shift13 (dyads_m9dyads_m9_rc)
; oligos_8nt_mkv2_m26 versus dyads_m9_rc (dyads_m9dyads_m9_rc); m=8/9; ncol2=26; w=12; offset=-1; strand=R; shift=13; score=0.431592; -------------yCTACAgTGtgca ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 10 13 0 86 0 67 14 6 6 6 14 7 47 c 0 0 0 0 0 0 0 0 0 0 0 0 0 47 64 0 1 82 8 7 5 8 7 6 41 5 g 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 0 0 0 5 58 4 68 17 52 20 15 t 0 0 0 0 0 0 0 0 0 0 0 0 0 24 3 87 0 5 7 8 72 5 57 15 19 20

dyads_m32_rc_shift0 (dyads_m32dyads_m32_rc)
; oligos_8nt_mkv2_m26 versus dyads_m32_rc (dyads_m32dyads_m32_rc); m=9/9; ncol2=25; w=11; offset=-14; strand=R; shift=0; score=0.41068; cCATATTyCAgGTCCTACAgTGTGy- ; cor=; Ncor= a 14 8 84 0 84 6 10 7 9 66 17 11 9 2 4 3 65 18 70 6 0 0 0 9 6 0 c 50 68 0 0 0 11 3 49 58 3 17 4 5 60 63 5 6 58 5 14 0 1 1 4 42 0 g 6 4 0 0 0 7 3 6 3 10 37 65 4 3 9 4 3 3 5 56 0 82 0 64 6 0 t 14 4 0 84 0 60 68 22 14 5 13 4 66 19 8 72 10 5 4 8 84 1 83 7 30 0

One-to-n matrix alignment; reference matrix: dyads_m28_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m28_shift0 (dyads_m28dyads_m28)
; dyads_m28 (dyads_m28dyads_m28); m=0 (reference); ncol1=24; shift=0; ncol=26; ssGCGssssssssssssssCGCss-- ; Alignment reference a 4 5 1 1 1 6 3 5 5 4 4 3 8 4 3 3 3 4 6 0 1 1 1 3 0 0 c 17 16 3 31 1 12 18 11 21 17 16 11 18 15 16 10 21 14 15 37 5 34 17 14 0 0 g 14 16 34 6 37 15 14 20 10 16 15 17 11 16 16 21 10 18 12 1 32 3 16 18 0 0 t 4 2 1 1 0 6 4 3 3 2 4 8 2 4 4 5 5 3 6 1 1 1 5 4 0 0

dyads_m28_shift0 (dyads_m28dyads_m28)
; dyads_m28 versus dyads_m28 (dyads_m28dyads_m28); m=1/2; ncol2=24; w=24; offset=0; strand=D; shift=0; score= 1; ssGCGssssssssssssssCGCss-- ; cor=; Ncor= a 4 5 1 1 1 6 3 5 5 4 4 3 8 4 3 3 3 4 6 0 1 1 1 3 0 0 c 17 16 3 31 1 12 18 11 21 17 16 11 18 15 16 10 21 14 15 37 5 34 17 14 0 0 g 14 16 34 6 37 15 14 20 10 16 15 17 11 16 16 21 10 18 12 1 32 3 16 18 0 0 t 4 2 1 1 0 6 4 3 3 2 4 8 2 4 4 5 5 3 6 1 1 1 5 4 0 0

dyads_m31_rc_shift0 (dyads_m31dyads_m31_rc)
; dyads_m28 versus dyads_m31_rc (dyads_m31dyads_m31_rc); m=2/2; ncol2=26; w=24; offset=0; strand=R; shift=0; score=0.727254; ysGCGssgbsscsscgsssssCCGsb ; cor=; Ncor= a 7 7 2 0 0 3 4 6 6 4 4 6 7 3 5 5 6 4 6 2 5 2 0 1 7 5 c 14 10 1 33 4 11 10 8 10 17 12 17 14 12 18 6 13 13 11 16 17 30 32 4 12 11 g 6 12 31 2 31 17 17 19 10 9 16 7 11 19 8 20 12 15 14 13 10 3 3 30 11 10 t 9 7 2 1 1 5 5 3 10 6 4 6 4 2 5 5 5 4 5 5 4 1 1 1 6 10

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4); m=0 (reference); ncol1=10; shift=3; ncol=13; ---dsAGGCAGrg ; Alignment reference a 0 0 0 17 7 59 0 0 0 59 0 18 13 c 0 0 0 10 15 0 0 0 59 0 0 12 6 g 0 0 0 16 33 0 59 59 0 0 59 23 32 t 0 0 0 16 4 0 0 0 0 0 0 6 8

oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4); m=1/7; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 1; ---dsAGGCAGrg ; cor=; Ncor= a 0 0 0 17 7 59 0 0 0 59 0 18 13 c 0 0 0 10 15 0 0 0 59 0 0 12 6 g 0 0 0 16 33 0 59 59 0 0 59 23 32 t 0 0 0 16 4 0 0 0 0 0 0 6 8

oligos_7nt_mkv2_m11_rc_shift2 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m11_rc (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc); m=2/7; ncol2=11; w=10; offset=-1; strand=R; shift=2; score=0.875357; --sdGAGGCAGrG ; cor=; Ncor= a 0 0 3 12 0 35 0 0 0 34 0 15 4 c 0 0 17 2 0 0 0 0 35 1 1 2 1 g 0 0 15 11 35 0 35 35 0 0 34 18 27 t 0 0 0 10 0 0 0 0 0 0 0 0 3

dyads_m11_rc_shift3 (dyads_m11dyads_m11_rc)
; oligos_6nt_mkv2_m4 versus dyads_m11_rc (dyads_m11dyads_m11_rc); m=3/7; ncol2=12; w=10; offset=0; strand=R; shift=3; score=0.749262; ---agwGGCAGGG ; cor=; Ncor= a 0 0 0 13 3 18 0 0 0 29 0 0 0 c 0 0 0 3 5 0 0 0 29 0 0 0 1 g 0 0 0 6 16 2 29 28 0 0 29 29 28 t 0 0 0 7 5 9 0 1 0 0 0 0 0

oligos_8nt_mkv2_m20_shift2 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)
; oligos_6nt_mkv2_m4 versus oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=4/7; ncol2=13; w=10; offset=-1; strand=D; shift=2; score=0.724907; --swGAGGCAGGG ; cor=; Ncor= a 0 0 2 11 1 25 0 0 1 25 0 6 0 c 0 0 13 2 2 0 0 0 25 0 0 0 0 g 0 0 11 6 23 0 26 25 0 0 26 20 26 t 0 0 0 7 0 1 0 1 0 1 0 0 0

oligos_7nt_mkv2_m8_rc_shift4 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m8_rc (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc); m=5/7; ncol2=11; w=9; offset=1; strand=R; shift=4; score=0.659469; ----gwGGCAGGG ; cor=; Ncor= a 0 0 0 0 6 16 0 0 0 31 0 0 0 c 0 0 0 0 6 5 0 0 32 0 0 1 0 g 0 0 0 0 16 4 34 34 0 3 34 33 34 t 0 0 0 0 6 9 0 0 2 0 0 0 0

oligos_8nt_mkv2_m23_rc_shift2 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc)
; oligos_6nt_mkv2_m4 versus oligos_8nt_mkv2_m23_rc (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc); m=6/7; ncol2=12; w=10; offset=-1; strand=R; shift=2; score=0.588894; --vrGAGGAAGGm ; cor=; Ncor= a 0 0 3 4 0 8 0 0 8 7 0 0 4 c 0 0 2 1 0 0 0 0 0 1 0 0 2 g 0 0 3 3 8 0 8 8 0 0 8 8 1 t 0 0 0 0 0 0 0 0 0 0 0 0 1

oligos_6nt_mkv2_m7_rc_shift0 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7_rc)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m7_rc (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7_rc); m=7/7; ncol2=10; w=7; offset=-3; strand=R; shift=0; score=0.406966; twGGGAGGcd--- ; cor=; Ncor= a 7 12 0 0 0 40 0 0 8 15 0 0 0 c 8 5 0 0 0 0 0 0 19 5 0 0 0 g 9 6 40 40 40 0 40 40 7 10 0 0 0 t 16 17 0 0 0 0 0 0 6 10 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m21_shift3 ; 18 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m21_shift3 (dyads_m21dyads_m21)
; dyads_m21 (dyads_m21dyads_m21); m=0 (reference); ncol1=14; shift=3; ncol=18; ---ssAGCAGCTGCTss- ; Alignment reference a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

dyads_m21_shift3 (dyads_m21dyads_m21)
; dyads_m21 versus dyads_m21 (dyads_m21dyads_m21); m=1/17; ncol2=14; w=14; offset=0; strand=D; shift=3; score= 1; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; dyads_m21 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=2/17; ncol2=14; w=14; offset=0; strand=R; shift=3; score=0.81204; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; dyads_m21 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=3/17; ncol2=18; w=14; offset=-2; strand=D; shift=1; score=0.762862; -sygCAGCAGCTGCTGcr ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; dyads_m21 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=4/17; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.745137; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; dyads_m21 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=5/17; ncol2=17; w=14; offset=-2; strand=R; shift=1; score=0.745037; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

oligos_8nt_mkv2_m8_shift3 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; dyads_m21 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=6/17; ncol2=16; w=14; offset=0; strand=D; shift=3; score=0.719563; ---rgmACAGCTGCTGcw ; cor=; Ncor= a 0 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 c 0 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 g 0 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 t 0 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; dyads_m21 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=7/17; ncol2=17; w=14; offset=-2; strand=D; shift=1; score=0.71772; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

dyads_m25_shift3 (dyads_m25dyads_m25)
; dyads_m21 versus dyads_m25 (dyads_m25dyads_m25); m=8/17; ncol2=17; w=14; offset=0; strand=D; shift=3; score=0.714677; ---dkAACAGCTGCTGyC ; cor=; Ncor= a 0 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 c 0 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 g 0 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 t 0 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2

dyads_m36_shift2 (dyads_m36dyads_m36)
; dyads_m21 versus dyads_m36 (dyads_m36dyads_m36); m=9/17; ncol2=15; w=14; offset=-1; strand=D; shift=2; score=0.706576; --rvkGACAGCTGctks- ; cor=; Ncor= a 0 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 c 0 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 g 0 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 t 0 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; dyads_m21 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=10/17; ncol2=16; w=14; offset=-1; strand=R; shift=2; score=0.704539; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

dyads_m3_rc_shift2 (dyads_m3dyads_m3_rc)
; dyads_m21 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=11/17; ncol2=15; w=14; offset=-1; strand=R; shift=2; score=0.69303; --rrwGACAGCTGyTky- ; cor=; Ncor= a 0 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 c 0 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 g 0 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 t 0 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0

oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; dyads_m21 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=12/17; ncol2=12; w=12; offset=0; strand=D; shift=3; score=0.684465; ---rmAGCAGGTGst--- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0

oligos_8nt_mkv2_m27_rc_shift2 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; dyads_m21 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=13/17; ncol2=17; w=14; offset=-1; strand=R; shift=2; score=0.651207; --drrGACAGCTGCTGhb ; cor=; Ncor= a 0 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 c 0 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 g 0 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 t 0 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5

oligos_7nt_mkv2_m13_rc_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; dyads_m21 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/17; ncol2=16; w=14; offset=-1; strand=R; shift=2; score=0.645862; --grwGACAGCTGyTkyc ; cor=; Ncor= a 0 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 c 0 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 g 0 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 t 0 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; dyads_m21 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=15/17; ncol2=17; w=14; offset=-2; strand=R; shift=1; score=0.627824; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; dyads_m21 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=16/17; ncol2=18; w=14; offset=-3; strand=R; shift=0; score=0.624225; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_8nt_mkv2_m1_rc_shift2 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; dyads_m21 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=17/17; ncol2=17; w=14; offset=-1; strand=R; shift=2; score=0.622768; --krkGACAGCTGCTkhv ; cor=; Ncor= a 0 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 c 0 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 g 0 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 t 0 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift2 ; 32 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=0 (reference); ncol1=14; shift=2; ncol=18; --grgACAGCTGCtkm-- ; Alignment reference a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=1/31; ncol2=14; w=14; offset=0; strand=D; shift=2; score= 1; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=2/31; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.930869; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0

dyads_m36_shift1 (dyads_m36dyads_m36)
; oligos_6nt_mkv2_m2 versus dyads_m36 (dyads_m36dyads_m36); m=3/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.912193; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=4/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.872015; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; oligos_6nt_mkv2_m2 versus dyads_m19 (dyads_m19dyads_m19); m=5/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.870723; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; oligos_6nt_mkv2_m2 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=6/31; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.867342; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=7/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.862061; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=8/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.861474; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0

dyads_m21_shift2 (dyads_m21dyads_m21)
; oligos_6nt_mkv2_m2 versus dyads_m21 (dyads_m21dyads_m21); m=9/31; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.81204; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0

oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=10/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.80933; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=11/31; ncol2=16; w=14; offset=-1; strand=R; shift=1; score=0.803906; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=12/31; ncol2=17; w=14; offset=-1; strand=R; shift=1; score=0.803149; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=13/31; ncol2=16; w=14; offset=0; strand=D; shift=2; score=0.802692; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=14/31; ncol2=17; w=14; offset=-1; strand=D; shift=1; score=0.799103; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6

dyads_m5_shift1 (dyads_m5dyads_m5)
; oligos_6nt_mkv2_m2 versus dyads_m5 (dyads_m5dyads_m5); m=15/31; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.79754; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=16/31; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.796612; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; oligos_6nt_mkv2_m2 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=17/31; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.788588; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0

oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=18/31; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.785906; --cwGaCAGCTGtCwg-- ; cor=; Ncor= a 0 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 c 0 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 t 0 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=19/31; ncol2=17; w=14; offset=-1; strand=R; shift=1; score=0.783988; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=20/31; ncol2=16; w=14; offset=-1; strand=R; shift=1; score=0.764672; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=21/31; ncol2=17; w=14; offset=-1; strand=R; shift=1; score=0.737374; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=22/31; ncol2=17; w=14; offset=-1; strand=D; shift=1; score=0.733631; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

dyads_m25_shift2 (dyads_m25dyads_m25)
; oligos_6nt_mkv2_m2 versus dyads_m25 (dyads_m25dyads_m25); m=23/31; ncol2=17; w=14; offset=0; strand=D; shift=2; score=0.72895; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8

dyads_m2_shift1 (dyads_m2dyads_m2)
; oligos_6nt_mkv2_m2 versus dyads_m2 (dyads_m2dyads_m2); m=24/31; ncol2=18; w=14; offset=-1; strand=D; shift=1; score=0.720512; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=25/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.657097; -gmyGaCAGCTGtCrkc- ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0

dyads_m1_shift1 (dyads_m1dyads_m1)
; oligos_6nt_mkv2_m2 versus dyads_m1 (dyads_m1dyads_m1); m=26/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.655261; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=27/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.655261; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=28/31; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.651707; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0

oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=29/31; ncol2=12; w=12; offset=2; strand=R; shift=4; score=0.60547; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=30/31; ncol2=18; w=14; offset=-2; strand=D; shift=0; score=0.593376; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=31/31; ncol2=11; w=11; offset=1; strand=D; shift=3; score=0.561346; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m30_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m30_shift1 (dyads_m30dyads_m30)
; dyads_m30 (dyads_m30dyads_m30); m=0 (reference); ncol1=11; shift=1; ncol=14; -ymCCCMGCCyr-- ; Alignment reference a 0 2 4 0 0 0 8 0 0 0 2 3 0 0 c 0 3 3 11 11 11 3 0 11 11 4 2 0 0 g 0 2 2 0 0 0 0 11 0 0 2 4 0 0 t 0 4 2 0 0 0 0 0 0 0 3 2 0 0

dyads_m30_shift1 (dyads_m30dyads_m30)
; dyads_m30 versus dyads_m30 (dyads_m30dyads_m30); m=1/8; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 1; -ymCCCMGCCyr-- ; cor=; Ncor= a 0 2 4 0 0 0 8 0 0 0 2 3 0 0 c 0 3 3 11 11 11 3 0 11 11 4 2 0 0 g 0 2 2 0 0 0 0 11 0 0 2 4 0 0 t 0 4 2 0 0 0 0 0 0 0 3 2 0 0

oligos_7nt_mkv2_m8_shift1 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8)
; dyads_m30 versus oligos_7nt_mkv2_m8 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8); m=2/8; ncol2=11; w=11; offset=0; strand=D; shift=1; score=0.815323; -smCCCTGCCwc-- ; cor=; Ncor= a 0 4 10 0 0 0 0 2 0 0 9 6 0 0 c 0 20 15 34 33 34 3 0 34 34 4 16 0 0 g 0 9 5 0 1 0 0 32 0 0 5 6 0 0 t 0 1 4 0 0 0 31 0 0 0 16 6 0 0

dyads_m11_shift1 (dyads_m11dyads_m11)
; dyads_m30 versus dyads_m11 (dyads_m11dyads_m11); m=3/8; ncol2=12; w=11; offset=0; strand=D; shift=1; score=0.714061; -ccCCCTGCCwct- ; cor=; Ncor= a 0 2 7 0 0 0 0 0 1 0 9 5 7 0 c 0 19 15 28 29 29 0 0 28 29 2 16 6 0 g 0 7 3 1 0 0 0 29 0 0 0 5 3 0 t 0 1 4 0 0 0 29 0 0 0 18 3 13 0

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; dyads_m30 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=4/8; ncol2=10; w=10; offset=0; strand=D; shift=1; score=0.690755; -ssCCCCGCsg--- ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 2 1 0 0 0 c 0 10 7 23 21 23 24 0 25 8 6 0 0 0 g 0 11 9 2 4 2 1 25 0 9 15 0 0 0 t 0 4 6 0 0 0 0 0 0 6 3 0 0 0

oligos_8nt_mkv2_m20_rc_shift1 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc)
; dyads_m30 versus oligos_8nt_mkv2_m20_rc (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc); m=5/8; ncol2=13; w=11; offset=0; strand=R; shift=1; score=0.596506; -CyCCCTGCCTCws ; cor=; Ncor= a 0 2 3 0 0 0 1 0 1 0 1 0 7 0 c 0 19 14 26 20 26 0 0 25 26 0 23 6 11 g 0 3 1 0 0 0 0 25 0 0 0 2 2 13 t 0 2 8 0 6 0 25 1 0 0 25 1 11 2

oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; dyads_m30 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=6/8; ncol2=11; w=10; offset=1; strand=D; shift=2; score=0.59112; --ssCCCGCCGsg- ; cor=; Ncor= a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0

dyads_m12_shift0 (dyads_m12dyads_m12)
; dyads_m30 versus dyads_m12 (dyads_m12dyads_m12); m=7/8; ncol2=14; w=11; offset=-1; strand=D; shift=0; score=0.566606; vssCCSCGCSGGss ; cor=; Ncor= a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m15_shift3 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)
; dyads_m30 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=8/8; ncol2=12; w=9; offset=2; strand=D; shift=3; score=0.457706; ---vcCCGCCGcGs ; cor=; Ncor= a 0 0 0 4 0 0 1 0 1 0 0 2 0 1 c 0 0 0 6 9 14 13 0 12 12 1 9 0 5 g 0 0 0 4 3 0 0 14 1 2 13 2 14 8 t 0 0 0 0 2 0 0 0 0 0 0 1 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m5_shift1 ; 15 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=0 (reference); ncol1=18; shift=1; ncol=19; -sygCAGCAGCTGCTGcrs ; Alignment reference a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=1/14; ncol2=18; w=18; offset=0; strand=D; shift=1; score= 1; -sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=2/14; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.827759; -kdgCAGCAGCTGTTsws- ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 0 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 0 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 0 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1 0

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=3/14; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.78672; -wdgCAGCAGCTGTTCwv- ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 0 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 0 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 0 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0 0

dyads_m21_shift3 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m5 versus dyads_m21 (dyads_m21dyads_m21); m=4/14; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.762862; ---ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=5/14; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.716124; -swgCAGCAGCTGTkcy-- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0 0

oligos_8nt_mkv2_m27_rc_shift2 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=6/14; ncol2=17; w=17; offset=1; strand=R; shift=2; score=0.701806; --drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=7/14; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.675737; -vbdmAGCAGCTGTCmym- ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 0 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 0 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 0 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2 0

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=8/14; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.670588; -rrrcAGCAGCTGTCtyy- ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 0 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 0 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 0 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5 0

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=9/14; ncol2=16; w=16; offset=1; strand=R; shift=2; score=0.66825; --akmAGCAGCTGTCysc- ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 0 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 0 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 0 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8 0

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_8nt_mkv2_m5 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=10/14; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.666952; arGrCAGCAGCTGTTmh-- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0 0

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_8nt_mkv2_m5 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=11/14; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=0.663081; tagaCAGCAGCTGTyyym- ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 0 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 0 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 0 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3 0

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m5 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=12/14; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.593376; ---grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; oligos_8nt_mkv2_m5 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=13/14; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.583601; ---smagCAGCTGTCmby- ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 0 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 0 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 0 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22 0

oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=14/14; ncol2=12; w=12; offset=2; strand=D; shift=3; score=0.532923; ---rmAGCAGGTGst---- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m9_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m9_shift3 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9)
; oligos_6nt_mkv2_m9 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9); m=0 (reference); ncol1=10; shift=3; ncol=13; ---rrAGGTGGaa ; Alignment reference a 0 0 0 24 16 41 0 0 0 0 0 17 25 c 0 0 0 4 10 0 0 0 0 0 0 10 5 g 0 0 0 12 11 0 41 41 0 41 41 7 5 t 0 0 0 1 4 0 0 0 41 0 0 7 6

oligos_6nt_mkv2_m9_shift3 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9)
; oligos_6nt_mkv2_m9 versus oligos_6nt_mkv2_m9 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9); m=1/3; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 1; ---rrAGGTGGaa ; cor=; Ncor= a 0 0 0 24 16 41 0 0 0 0 0 17 25 c 0 0 0 4 10 0 0 0 0 0 0 10 5 g 0 0 0 12 11 0 41 41 0 41 41 7 5 t 0 0 0 1 4 0 0 0 41 0 0 7 6

dyads_m17_rc_shift4 (dyads_m17dyads_m17_rc)
; oligos_6nt_mkv2_m9 versus dyads_m17_rc (dyads_m17dyads_m17_rc); m=2/3; ncol2=10; w=9; offset=1; strand=R; shift=4; score=0.679742; ----kwGGTGGCh ; cor=; Ncor= a 0 0 0 0 4 11 0 0 0 0 0 0 9 c 0 0 0 0 5 1 0 0 1 0 0 27 9 g 0 0 0 0 11 5 27 27 0 27 27 0 1 t 0 0 0 0 7 10 0 0 26 0 0 0 8

oligos_8nt_mkv2_m7_shift0 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; oligos_6nt_mkv2_m9 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=3/3; ncol2=12; w=9; offset=-3; strand=D; shift=0; score=0.507586; rmAGCAGGTGst- ; cor=; Ncor= a 8 5 16 0 0 15 0 0 0 0 2 2 0 c 3 8 1 0 16 1 0 0 1 1 7 4 0 g 5 3 0 17 0 1 17 17 0 16 5 1 0 t 1 1 0 0 1 0 0 0 16 0 3 10 0

One-to-n matrix alignment; reference matrix: dyads_m14_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m14_shift0 (dyads_m14dyads_m14)
; dyads_m14 (dyads_m14dyads_m14); m=0 (reference); ncol1=21; shift=0; ncol=25; cCATAtwCcakGTcCTACAgT---- ; Alignment reference a 19 7 90 0 89 3 28 6 21 58 18 14 15 7 11 8 90 0 90 16 16 0 0 0 0 c 52 64 0 0 1 16 3 67 51 16 9 5 3 58 64 14 0 89 0 7 4 0 0 0 0 g 1 14 0 0 0 11 2 9 5 10 36 67 3 5 9 2 0 0 0 54 2 0 0 0 0 t 18 5 0 90 0 60 57 8 13 6 27 4 69 20 6 66 0 1 0 13 68 0 0 0 0

dyads_m14_shift0 (dyads_m14dyads_m14)
; dyads_m14 versus dyads_m14 (dyads_m14dyads_m14); m=1/5; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 1; cCATAtwCcakGTcCTACAgT---- ; cor=; Ncor= a 19 7 90 0 89 3 28 6 21 58 18 14 15 7 11 8 90 0 90 16 16 0 0 0 0 c 52 64 0 0 1 16 3 67 51 16 9 5 3 58 64 14 0 89 0 7 4 0 0 0 0 g 1 14 0 0 0 11 2 9 5 10 36 67 3 5 9 2 0 0 0 54 2 0 0 0 0 t 18 5 0 90 0 60 57 8 13 6 27 4 69 20 6 66 0 1 0 13 68 0 0 0 0

dyads_m18_shift0 (dyads_m18dyads_m18)
; dyads_m14 versus dyads_m18 (dyads_m18dyads_m18); m=2/5; ncol2=19; w=19; offset=0; strand=D; shift=0; score=0.872917; CCATATTCCAkGTCCTACA------ ; cor=; Ncor= a 9 3 95 1 94 3 16 6 22 74 16 3 2 3 0 1 94 19 80 0 0 0 0 0 0 c 65 72 0 0 0 10 3 65 65 16 18 4 6 69 95 0 0 67 6 0 0 0 0 0 0 g 1 17 0 0 0 6 4 4 3 1 37 78 8 8 0 1 0 3 3 0 0 0 0 0 0 t 20 3 0 94 1 76 72 20 5 4 24 10 79 15 0 93 1 6 6 0 0 0 0 0 0

dyads_m32_rc_shift0 (dyads_m32dyads_m32_rc)
; dyads_m14 versus dyads_m32_rc (dyads_m32dyads_m32_rc); m=3/5; ncol2=25; w=21; offset=0; strand=R; shift=0; score=0.805402; cCATATTyCAgGTCCTACAgTGTGy ; cor=; Ncor= a 14 8 84 0 84 6 10 7 9 66 17 11 9 2 4 3 65 18 70 6 0 0 0 9 6 c 50 68 0 0 0 11 3 49 58 3 17 4 5 60 63 5 6 58 5 14 0 1 1 4 42 g 6 4 0 0 0 7 3 6 3 10 37 65 4 3 9 4 3 3 5 56 0 82 0 64 6 t 14 4 0 84 0 60 68 22 14 5 13 4 66 19 8 72 10 5 4 8 84 1 83 7 30

oligos_8nt_mkv2_m21_rc_shift8 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21_rc)
; dyads_m14 versus oligos_8nt_mkv2_m21_rc (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21_rc); m=4/5; ncol2=12; w=12; offset=8; strand=R; shift=8; score=0.455219; --------wmTGTTCTACAr----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 16 20 0 2 0 0 0 0 32 0 31 11 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 10 0 0 0 0 31 0 0 32 1 4 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 0 0 30 0 0 1 0 0 0 0 16 0 0 0 0 0 t 0 0 0 0 0 0 0 0 14 2 32 0 32 32 0 32 0 0 0 1 0 0 0 0 0

oligos_8nt_mkv2_m14_rc_shift2 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc)
; dyads_m14 versus oligos_8nt_mkv2_m14_rc (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc); m=5/5; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.403477; --ATTTTCCATGwT----------- ; cor=; Ncor= a 0 0 79 2 10 0 1 0 0 72 0 3 34 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 1 0 0 0 1 83 80 0 9 0 0 14 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 3 0 0 0 0 2 11 0 79 3 1 0 0 0 0 0 0 0 0 0 0 0 t 0 0 3 78 73 83 81 0 1 0 74 1 46 68 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m6_shift5 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m6_shift5 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)
; oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=0 (reference); ncol1=11; shift=5; ncol=16; -----ssCCGCCGGGs ; Alignment reference a 0 0 0 0 0 3 2 1 0 0 0 0 0 2 2 4 c 0 0 0 0 0 11 13 21 25 1 23 22 3 3 4 10 g 0 0 0 0 0 10 9 3 1 25 3 4 23 20 18 11 t 0 0 0 0 0 2 2 1 0 0 0 0 0 1 2 1

oligos_6nt_mkv2_m6_shift5 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)
; oligos_6nt_mkv2_m6 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=1/8; ncol2=11; w=11; offset=0; strand=D; shift=5; score= 1; -----ssCCGCCGGGs ; cor=; Ncor= a 0 0 0 0 0 3 2 1 0 0 0 0 0 2 2 4 c 0 0 0 0 0 11 13 21 25 1 23 22 3 3 4 10 g 0 0 0 0 0 10 9 3 1 25 3 4 23 20 18 11 t 0 0 0 0 0 2 2 1 0 0 0 0 0 1 2 1

oligos_8nt_mkv2_m15_shift5 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)
; oligos_6nt_mkv2_m6 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=2/8; ncol2=12; w=11; offset=0; strand=D; shift=5; score=0.823855; -----vcCCGCCGcGs ; cor=; Ncor= a 0 0 0 0 0 4 0 0 1 0 1 0 0 2 0 1 c 0 0 0 0 0 6 9 14 13 0 12 12 1 9 0 5 g 0 0 0 0 0 4 3 0 0 14 1 2 13 2 14 8 t 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 0

oligos_7nt_mkv2_m7_rc_shift6 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc)
; oligos_6nt_mkv2_m6 versus oligos_7nt_mkv2_m7_rc (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc); m=3/8; ncol2=11; w=10; offset=1; strand=R; shift=6; score=0.801271; ------ssCGCCGGGs ; cor=; Ncor= a 0 0 0 0 0 0 2 4 3 0 0 0 0 3 0 6 c 0 0 0 0 0 0 16 17 33 1 28 32 4 3 1 14 g 0 0 0 0 0 0 14 11 0 33 5 4 32 29 34 11 t 0 0 0 0 0 0 4 4 0 2 3 0 0 1 1 5

oligos_7nt_mkv2_m15_shift4 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; oligos_6nt_mkv2_m6 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=4/8; ncol2=11; w=10; offset=-1; strand=D; shift=4; score=0.78658; ----ssCCCGCCGsg- ; cor=; Ncor= a 0 0 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 0 0 5 4 1 0 0 0 0 0 0 3 1 0

dyads_m12_shift2 (dyads_m12dyads_m12)
; oligos_6nt_mkv2_m6 versus dyads_m12 (dyads_m12dyads_m12); m=5/8; ncol2=14; w=11; offset=-3; strand=D; shift=2; score=0.743492; --vssCCSCGCSGGss ; cor=; Ncor= a 0 0 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 0 0 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 0 0 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m26_shift5 (dyads_m26dyads_m26)
; oligos_6nt_mkv2_m6 versus dyads_m26 (dyads_m26dyads_m26); m=6/8; ncol2=12; w=11; offset=0; strand=D; shift=5; score=0.742676; -----csCCGcsGCGs ; cor=; Ncor= a 0 0 0 0 0 1 0 1 0 1 4 3 0 1 0 3 c 0 0 0 0 0 19 15 25 27 1 15 13 2 24 3 10 g 0 0 0 0 0 6 10 2 1 26 6 11 24 2 25 12 t 0 0 0 0 0 2 3 0 0 0 3 1 2 1 0 3

oligos_6nt_mkv2_m5_rc_shift7 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m6 versus oligos_6nt_mkv2_m5_rc (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5_rc); m=7/8; ncol2=10; w=9; offset=2; strand=R; shift=7; score=0.565184; -------csGCGGGGs ; cor=; Ncor= a 0 0 0 0 0 0 0 3 6 0 0 0 0 0 0 6 c 0 0 0 0 0 0 0 15 9 0 25 1 2 4 2 9 g 0 0 0 0 0 0 0 6 8 25 0 24 23 21 23 7 t 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 3

dyads_m34_shift0 (dyads_m34dyads_m34)
; oligos_6nt_mkv2_m6 versus dyads_m34 (dyads_m34dyads_m34); m=8/8; ncol2=15; w=10; offset=-5; strand=D; shift=0; score=0.442045; ssACGcrsssCCGvs- ; cor=; Ncor= a 1 4 15 0 0 3 8 2 2 2 3 0 0 6 2 0 c 6 7 3 21 1 11 4 7 7 7 15 19 0 6 8 0 g 10 7 2 0 20 5 7 9 11 9 3 2 21 7 8 0 t 4 3 1 0 0 2 2 3 1 3 0 0 0 2 3 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m15_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=0 (reference); ncol1=11; shift=2; ncol=14; --ssCCCGCCGsg- ; Alignment reference a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0

oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; oligos_7nt_mkv2_m15 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=1/8; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 1; --ssCCCGCCGsg- ; cor=; Ncor= a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0

oligos_7nt_mkv2_m7_shift2 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)
; oligos_7nt_mkv2_m15 versus oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=2/8; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.885944; --ssCCCGGCGss- ; cor=; Ncor= a 0 0 4 5 1 1 0 0 3 2 0 4 4 0 c 0 0 17 11 34 29 32 4 5 33 0 11 14 0 g 0 0 11 14 1 3 4 32 28 1 33 17 16 0 t 0 0 4 6 0 3 0 0 0 0 3 4 2 0

oligos_6nt_mkv2_m6_shift3 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)
; oligos_7nt_mkv2_m15 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=3/8; ncol2=11; w=10; offset=1; strand=D; shift=3; score=0.78658; ---ssCCGCCGGGs ; cor=; Ncor= a 0 0 0 3 2 1 0 0 0 0 0 2 2 4 c 0 0 0 11 13 21 25 1 23 22 3 3 4 10 g 0 0 0 10 9 3 1 25 3 4 23 20 18 11 t 0 0 0 2 2 1 0 0 0 0 0 1 2 1

oligos_8nt_mkv2_m15_shift3 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)
; oligos_7nt_mkv2_m15 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=4/8; ncol2=12; w=10; offset=1; strand=D; shift=3; score=0.732153; ---vcCCGCCGcGs ; cor=; Ncor= a 0 0 0 4 0 0 1 0 1 0 0 2 0 1 c 0 0 0 6 9 14 13 0 12 12 1 9 0 5 g 0 0 0 4 3 0 0 14 1 2 13 2 14 8 t 0 0 0 0 2 0 0 0 0 0 0 1 0 0

dyads_m12_shift0 (dyads_m12dyads_m12)
; oligos_7nt_mkv2_m15 versus dyads_m12 (dyads_m12dyads_m12); m=5/8; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=0.729556; vssCCSCGCSGGss ; cor=; Ncor= a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m26_shift3 (dyads_m26dyads_m26)
; oligos_7nt_mkv2_m15 versus dyads_m26 (dyads_m26dyads_m26); m=6/8; ncol2=12; w=10; offset=1; strand=D; shift=3; score=0.678867; ---csCCGcsGCGs ; cor=; Ncor= a 0 0 0 1 0 1 0 1 4 3 0 1 0 3 c 0 0 0 19 15 25 27 1 15 13 2 24 3 10 g 0 0 0 6 10 2 1 26 6 11 24 2 25 12 t 0 0 0 2 3 0 0 0 3 1 2 1 0 3

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; oligos_7nt_mkv2_m15 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=7/8; ncol2=10; w=9; offset=-1; strand=D; shift=1; score=0.653332; -ssCCCCGCsg--- ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 2 1 0 0 0 c 0 10 7 23 21 23 24 0 25 8 6 0 0 0 g 0 11 9 2 4 2 1 25 0 9 15 0 0 0 t 0 4 6 0 0 0 0 0 0 6 3 0 0 0

dyads_m30_shift1 (dyads_m30dyads_m30)
; oligos_7nt_mkv2_m15 versus dyads_m30 (dyads_m30dyads_m30); m=8/8; ncol2=11; w=10; offset=-1; strand=D; shift=1; score=0.59112; -ymCCCMGCCyr-- ; cor=; Ncor= a 0 2 4 0 0 0 8 0 0 0 2 3 0 0 c 0 3 3 11 11 11 3 0 11 11 4 2 0 0 g 0 2 2 0 0 0 0 11 0 0 2 4 0 0 t 0 4 2 0 0 0 0 0 0 0 3 2 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m28_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m28_shift0 (oligos_8nt_mkv2_m28oligos_8nt_mkv2_m28)
; oligos_8nt_mkv2_m28 (oligos_8nt_mkv2_m28oligos_8nt_mkv2_m28); m=0 (reference); ncol1=12; shift=0; ncol=12; hsTCAAGTARvw ; Alignment reference a 2 0 0 0 7 7 0 0 7 5 3 2 c 3 4 0 6 0 0 0 0 0 0 2 1 g 0 3 0 0 0 0 7 0 0 2 2 1 t 2 0 7 1 0 0 0 7 0 0 0 3

oligos_8nt_mkv2_m28_shift0 (oligos_8nt_mkv2_m28oligos_8nt_mkv2_m28)
; oligos_8nt_mkv2_m28 versus oligos_8nt_mkv2_m28 (oligos_8nt_mkv2_m28oligos_8nt_mkv2_m28); m=1/1; ncol2=12; w=12; offset=0; strand=D; shift=0; score= 1; hsTCAAGTARvw ; cor=; Ncor= a 2 0 0 0 7 7 0 0 7 5 3 2 c 3 4 0 6 0 0 0 0 0 0 2 1 g 0 3 0 0 0 0 7 0 0 2 2 1 t 2 0 7 1 0 0 0 7 0 0 0 3

One-to-n matrix alignment; reference matrix: dyads_m25_shift2 ; 25 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m25_shift2 (dyads_m25dyads_m25)
; dyads_m25 (dyads_m25dyads_m25); m=0 (reference); ncol1=17; shift=2; ncol=19; --dkAACAGCTGCTGyCyt ; Alignment reference a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

dyads_m25_shift2 (dyads_m25dyads_m25)
; dyads_m25 versus dyads_m25 (dyads_m25dyads_m25); m=1/24; ncol2=17; w=17; offset=0; strand=D; shift=2; score= 1; --dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

dyads_m2_shift1 (dyads_m2dyads_m2)
; dyads_m25 versus dyads_m2 (dyads_m2dyads_m2); m=2/24; ncol2=18; w=17; offset=-1; strand=D; shift=1; score=0.88108; -krrrACAGCTGCTGtcta ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; dyads_m25 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=3/24; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.829159; -bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; dyads_m25 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=4/24; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.828996; --rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; dyads_m25 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=5/24; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.805868; -swsAACAGCTGCTGchm- ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; dyads_m25 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=6/24; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.788345; -drrGACAGCTGCTGhbb- ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; dyads_m25 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=7/24; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.759677; -krkGACAGCTGCTkhvb- ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; dyads_m25 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=8/24; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.758892; -rraGACAGCTGCTgyyy- ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; dyads_m25 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=9/24; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.72895; --grgACAGCTGCtkm--- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

dyads_m21_shift2 (dyads_m21dyads_m21)
; dyads_m25 versus dyads_m21 (dyads_m21dyads_m21); m=10/24; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.714677; --ssAGCAGCTGCTss--- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0 0

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; dyads_m25 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=11/24; ncol2=16; w=15; offset=-1; strand=D; shift=1; score=0.714485; -gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; dyads_m25 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=12/24; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.697775; -grwGACAGCTGyTkyc-- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; dyads_m25 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=13/24; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.670975; --vwGACAGCTGytkd--- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; dyads_m25 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=14/24; ncol2=18; w=16; offset=-2; strand=D; shift=0; score=0.666952; sygCAGCAGCTGCTGcrs- ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 0 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 0 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 0 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2 0

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; dyads_m25 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=15/24; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.662588; -rrwGACAGCTGyTky--- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

dyads_m36_shift1 (dyads_m36dyads_m36)
; dyads_m25 versus dyads_m36 (dyads_m36dyads_m36); m=16/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.652863; -rvkGACAGCTGctks--- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; dyads_m25 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=17/24; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.652721; -kkwsACAGCTGTTsys-- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; dyads_m25 versus dyads_m19 (dyads_m19dyads_m19); m=18/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.595154; -rvdGACAGCTGvyks--- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; dyads_m25 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=19/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.584481; -rstGACAGCTGmhkg--- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; dyads_m25 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=20/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.582771; -rvtGACAGCTGmhkg--- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; dyads_m25 versus dyads_m5 (dyads_m5dyads_m5); m=21/24; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.561534; -rvdGACAGCTGmsg---- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; dyads_m25 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=22/24; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.560227; -rswGACAGCTGmsg---- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)
; dyads_m25 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=23/24; ncol2=12; w=12; offset=2; strand=R; shift=4; score=0.549659; ----asCACCTGCTky--- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0 0

oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; dyads_m25 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=24/24; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.547102; --gvAACAGTTGcr----- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift1 ; 31 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=0 (reference); ncol1=16; shift=1; ncol=18; -gsrGACAGCTGCTkmt- ; Alignment reference a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=1/30; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=2/30; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.92321; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=3/30; ncol2=17; w=16; offset=0; strand=R; shift=1; score=0.923014; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=4/30; ncol2=17; w=16; offset=0; strand=D; shift=1; score=0.920197; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6

dyads_m36_shift1 (dyads_m36dyads_m36)
; oligos_7nt_mkv2_m2 versus dyads_m36 (dyads_m36dyads_m36); m=5/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.908563; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=6/30; ncol2=17; w=16; offset=0; strand=R; shift=1; score=0.899735; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; oligos_7nt_mkv2_m2 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=7/30; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.878388; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=8/30; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.875409; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=9/30; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.872015; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; oligos_7nt_mkv2_m2 versus dyads_m19 (dyads_m19dyads_m19); m=10/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.870809; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=11/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.859213; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=12/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.858805; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=13/30; ncol2=17; w=16; offset=0; strand=R; shift=1; score=0.836424; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=14/30; ncol2=17; w=16; offset=0; strand=D; shift=1; score=0.828917; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

dyads_m2_shift1 (dyads_m2dyads_m2)
; oligos_7nt_mkv2_m2 versus dyads_m2 (dyads_m2dyads_m2); m=15/30; ncol2=18; w=16; offset=0; strand=D; shift=1; score=0.821285; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=16/30; ncol2=16; w=15; offset=1; strand=D; shift=2; score=0.814765; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=17/30; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.810656; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0

oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=18/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.802487; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; oligos_7nt_mkv2_m2 versus dyads_m5 (dyads_m5dyads_m5); m=19/30; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.791809; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=20/30; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.790768; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; oligos_7nt_mkv2_m2 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=21/30; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.76997; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0

dyads_m1_shift1 (dyads_m1dyads_m1)
; oligos_7nt_mkv2_m2 versus dyads_m1 (dyads_m1dyads_m1); m=22/30; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.737151; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=23/30; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.737151; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=24/30; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.721423; -gmyGaCAGCTGtCrkc- ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0

dyads_m25_shift2 (dyads_m25dyads_m25)
; oligos_7nt_mkv2_m2 versus dyads_m25 (dyads_m25dyads_m25); m=25/30; ncol2=17; w=15; offset=1; strand=D; shift=2; score=0.714485; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8

dyads_m21_shift2 (dyads_m21dyads_m21)
; oligos_7nt_mkv2_m2 versus dyads_m21 (dyads_m21dyads_m21); m=26/30; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.704539; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0

oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=27/30; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.680013; --cwGaCAGCTGtCwg-- ; cor=; Ncor= a 0 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 c 0 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 t 0 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=28/30; ncol2=18; w=16; offset=-1; strand=D; shift=0; score=0.66825; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=29/30; ncol2=12; w=12; offset=1; strand=D; shift=2; score=0.554821; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0

oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=30/30; ncol2=12; w=12; offset=3; strand=R; shift=4; score=0.535119; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m8_shift8 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m8_shift8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)
; oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=0 (reference); ncol1=10; shift=8; ncol=23; --------rtGAGAAAha----- ; Alignment reference a 0 0 0 0 0 0 0 0 101 13 0 154 0 154 154 154 43 85 0 0 0 0 0 c 0 0 0 0 0 0 0 0 3 32 0 0 0 0 0 0 52 30 0 0 0 0 0 g 0 0 0 0 0 0 0 0 44 11 154 0 154 0 0 0 5 34 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 98 0 0 0 0 0 0 54 5 0 0 0 0 0

oligos_6nt_mkv2_m8_shift8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)
; oligos_6nt_mkv2_m8 versus oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=1/8; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 1; --------rtGAGAAAha----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 101 13 0 154 0 154 154 154 43 85 0 0 0 0 0 c 0 0 0 0 0 0 0 0 3 32 0 0 0 0 0 0 52 30 0 0 0 0 0 g 0 0 0 0 0 0 0 0 44 11 154 0 154 0 0 0 5 34 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 98 0 0 0 0 0 0 54 5 0 0 0 0 0

dyads_m29_shift7 (dyads_m29dyads_m29)
; oligos_6nt_mkv2_m8 versus dyads_m29 (dyads_m29dyads_m29); m=2/8; ncol2=12; w=10; offset=-1; strand=D; shift=7; score=0.784394; -------AmTGArAAAyry---- ; cor=; Ncor= a 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 c 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 g 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 t 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0

oligos_7nt_mkv2_m6_shift7 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; oligos_6nt_mkv2_m8 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=3/8; ncol2=11; w=10; offset=-1; strand=D; shift=7; score=0.655091; -------msTGAAAAAyr----- ; cor=; Ncor= a 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 0 0 0 0 0 c 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 0 0 0 0 0 g 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 0 0 0 0 0 t 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4 0 0 0 0 0

oligos_8nt_mkv2_m9_rc_shift7 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; oligos_6nt_mkv2_m8 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=4/8; ncol2=12; w=10; offset=-1; strand=R; shift=7; score=0.603326; -------MsTGAAAAACrt---- ; cor=; Ncor= a 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 c 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 g 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 t 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0

dyads_m39_shift10 (dyads_m39dyads_m39)
; oligos_6nt_mkv2_m8 versus dyads_m39 (dyads_m39dyads_m39); m=5/8; ncol2=10; w=8; offset=2; strand=D; shift=10; score=0.559766; ----------GwGAAATAyr--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 5 25 0 56 56 56 0 56 5 21 0 0 0 c 0 0 0 0 0 0 0 0 0 0 7 1 0 0 0 0 0 0 20 6 0 0 0 g 0 0 0 0 0 0 0 0 0 0 40 3 56 0 0 0 0 0 5 23 0 0 0 t 0 0 0 0 0 0 0 0 0 0 4 27 0 0 0 0 56 0 26 6 0 0 0

oligos_8nt_mkv2_m6_shift0 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_6nt_mkv2_m8 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=6/8; ncol2=18; w=10; offset=-8; strand=D; shift=0; score=0.530909; CrTGRAAAATGAGAAAwr----- ; cor=; Ncor= a 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 0 c 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 0 g 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 0 t 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0 0

dyads_m27_shift2 (dyads_m27dyads_m27)
; oligos_6nt_mkv2_m8 versus dyads_m27 (dyads_m27dyads_m27); m=7/8; ncol2=18; w=10; offset=-6; strand=D; shift=2; score=0.45369; --yGGAAAATkAdAAAAwsh--- ; cor=; Ncor= a 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 0 0 c 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 0 0 g 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 0 0 t 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0 0 0

dyads_m20_rc_shift7 (dyads_m20dyads_m20_rc)
; oligos_6nt_mkv2_m8 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=8/8; ncol2=23; w=10; offset=-1; strand=R; shift=7; score=0.407724; -------AATGAGAAAtrCACAC ; cor=; Ncor= a 0 0 0 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 c 0 0 0 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 g 0 0 0 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 t 0 0 0 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6

One-to-n matrix alignment; reference matrix: dyads_m34_shift11 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m34_shift11 (dyads_m34dyads_m34)
; dyads_m34 (dyads_m34dyads_m34); m=0 (reference); ncol1=15; shift=11; ncol=26; -----------ssACGcrsssCCGvs ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 1 4 15 0 0 3 8 2 2 2 3 0 0 6 2 c 0 0 0 0 0 0 0 0 0 0 0 6 7 3 21 1 11 4 7 7 7 15 19 0 6 8 g 0 0 0 0 0 0 0 0 0 0 0 10 7 2 0 20 5 7 9 11 9 3 2 21 7 8 t 0 0 0 0 0 0 0 0 0 0 0 4 3 1 0 0 2 2 3 1 3 0 0 0 2 3

dyads_m34_shift11 (dyads_m34dyads_m34)
; dyads_m34 versus dyads_m34 (dyads_m34dyads_m34); m=1/6; ncol2=15; w=15; offset=0; strand=D; shift=11; score= 1; -----------ssACGcrsssCCGvs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1 4 15 0 0 3 8 2 2 2 3 0 0 6 2 c 0 0 0 0 0 0 0 0 0 0 0 6 7 3 21 1 11 4 7 7 7 15 19 0 6 8 g 0 0 0 0 0 0 0 0 0 0 0 10 7 2 0 20 5 7 9 11 9 3 2 21 7 8 t 0 0 0 0 0 0 0 0 0 0 0 4 3 1 0 0 2 2 3 1 3 0 0 0 2 3

dyads_m15_rc_shift12 (dyads_m15dyads_m15_rc)
; dyads_m34 versus dyads_m15_rc (dyads_m15dyads_m15_rc); m=2/6; ncol2=15; w=14; offset=1; strand=R; shift=12; score=0.636357; ------------sccGCgrssACGGg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 0 0 1 3 1 0 7 0 0 1 2 c 0 0 0 0 0 0 0 0 0 0 0 0 4 3 6 0 9 1 2 3 4 1 9 0 0 2 g 0 0 0 0 0 0 0 0 0 0 0 0 3 2 1 9 0 6 3 4 4 1 0 9 8 3 t 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 1 1 1 0 0 0 0 2

dyads_m37_shift11 (dyads_m37dyads_m37)
; dyads_m34 versus dyads_m37 (dyads_m37dyads_m37); m=3/6; ncol2=11; w=11; offset=0; strand=D; shift=11; score=0.543919; -----------ksrCGyACGsv---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 1 1 7 0 0 0 10 0 0 1 3 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2 4 0 11 0 5 1 11 0 5 3 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 5 4 3 0 11 2 0 0 11 4 4 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 3 2 1 0 0 4 0 0 0 1 1 0 0 0 0

oligos_6nt_mkv2_m6_shift16 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)
; dyads_m34 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=4/6; ncol2=11; w=10; offset=5; strand=D; shift=16; score=0.442045; ----------------ssCCGCCGGG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 1 0 0 0 0 0 2 2 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 13 21 25 1 23 22 3 3 4 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 9 3 1 25 3 4 23 20 18 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 0 0 0 0 0 1 2

dyads_m31_rc_shift0 (dyads_m31dyads_m31_rc)
; dyads_m34 versus dyads_m31_rc (dyads_m31dyads_m31_rc); m=5/6; ncol2=26; w=15; offset=-11; strand=R; shift=0; score=0.440631; ysGCGssgbsscsscgsssssCCGsb ; cor=; Ncor= a 7 7 2 0 0 3 4 6 6 4 4 6 7 3 5 5 6 4 6 2 5 2 0 1 7 5 c 14 10 1 33 4 11 10 8 10 17 12 17 14 12 18 6 13 13 11 16 17 30 32 4 12 11 g 6 12 31 2 31 17 17 19 10 9 16 7 11 19 8 20 12 15 14 13 10 3 3 30 11 10 t 9 7 2 1 1 5 5 3 10 6 4 6 4 2 5 5 5 4 5 5 4 1 1 1 6 10

oligos_6nt_mkv2_m5_shift17 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; dyads_m34 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=6/6; ncol2=10; w=9; offset=6; strand=D; shift=17; score=0.407543; -----------------ssCCCCGCs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 7 23 21 23 24 0 25 8 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 9 2 4 2 1 25 0 9 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 6 0 0 0 0 0 0 6

One-to-n matrix alignment; reference matrix: dyads_m2_shift1 ; 28 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift1 (dyads_m2dyads_m2)
; dyads_m2 (dyads_m2dyads_m2); m=0 (reference); ncol1=18; shift=1; ncol=19; -krrrACAGCTGCTGtcta ; Alignment reference a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

dyads_m2_shift1 (dyads_m2dyads_m2)
; dyads_m2 versus dyads_m2 (dyads_m2dyads_m2); m=1/27; ncol2=18; w=18; offset=0; strand=D; shift=1; score= 1; -krrrACAGCTGCTGtcta ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; dyads_m2 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=2/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.904148; -drrGACAGCTGCTGhbb- ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; dyads_m2 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=3/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.895694; -rraGACAGCTGCTgyyy- ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

dyads_m25_shift2 (dyads_m25dyads_m25)
; dyads_m2 versus dyads_m25 (dyads_m25dyads_m25); m=4/27; ncol2=17; w=17; offset=1; strand=D; shift=2; score=0.88108; --dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; dyads_m2 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=5/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.88046; -krkGACAGCTGCTkhvb- ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; dyads_m2 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=6/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.833349; -bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; dyads_m2 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=7/27; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.821285; -gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; dyads_m2 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=8/27; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.819829; -grwGACAGCTGyTkyc-- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; dyads_m2 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=9/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.804693; -swsAACAGCTGCTGchm- ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; dyads_m2 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=10/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.800214; --rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; dyads_m2 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=11/27; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.771503; -rrwGACAGCTGyTky--- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; dyads_m2 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=12/27; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.762649; -kkwsACAGCTGTTsys-- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

dyads_m36_shift1 (dyads_m36dyads_m36)
; dyads_m2 versus dyads_m36 (dyads_m36dyads_m36); m=13/27; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.742126; -rvkGACAGCTGctks--- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; dyads_m2 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=14/27; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.720512; --grgACAGCTGCtkm--- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; dyads_m2 versus dyads_m19 (dyads_m19dyads_m19); m=15/27; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.710401; -rvdGACAGCTGvyks--- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; dyads_m2 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=16/27; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.688103; -rstGACAGCTGmhkg--- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; dyads_m2 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=17/27; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.686997; -rvtGACAGCTGmhkg--- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; dyads_m2 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=18/27; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.684101; --vwGACAGCTGytkd--- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; dyads_m2 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=19/27; ncol2=18; w=17; offset=-1; strand=D; shift=0; score=0.663081; sygCAGCAGCTGCTGcrs- ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 0 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 0 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 0 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; dyads_m2 versus dyads_m5 (dyads_m5dyads_m5); m=20/27; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.660354; -rvdGACAGCTGmsg---- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; dyads_m2 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=21/27; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.658408; -rswGACAGCTGmsg---- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; dyads_m2 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=22/27; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.650203; -rstGACAGCTGMskg--- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; dyads_m2 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=23/27; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.633431; -mvrGACAGCTGwGsv--- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0 0

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; dyads_m2 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=24/27; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.63008; -gmyGaCAGCTGtCrkc-- ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0 0

dyads_m21_shift2 (dyads_m21dyads_m21)
; dyads_m2 versus dyads_m21 (dyads_m21dyads_m21); m=25/27; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.624225; --ssAGCAGCTGCTss--- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0 0

oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)
; dyads_m2 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=26/27; ncol2=12; w=12; offset=3; strand=R; shift=4; score=0.506958; ----asCACCTGCTky--- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0 0

oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; dyads_m2 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=27/27; ncol2=12; w=12; offset=1; strand=D; shift=2; score=0.478767; --gvAACAGTTGcr----- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m14_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m14_shift0 (oligos_7nt_mkv2_m14oligos_7nt_mkv2_m14)
; oligos_7nt_mkv2_m14 (oligos_7nt_mkv2_m14oligos_7nt_mkv2_m14); m=0 (reference); ncol1=11; shift=0; ncol=12; tMACTCACTCA- ; Alignment reference a 1 17 24 0 0 0 24 0 0 2 21 0 c 5 7 0 24 0 24 0 24 0 20 1 0 g 2 0 0 0 0 0 0 0 0 2 1 0 t 16 0 0 0 24 0 0 0 24 0 1 0

oligos_7nt_mkv2_m14_shift0 (oligos_7nt_mkv2_m14oligos_7nt_mkv2_m14)
; oligos_7nt_mkv2_m14 versus oligos_7nt_mkv2_m14 (oligos_7nt_mkv2_m14oligos_7nt_mkv2_m14); m=1/2; ncol2=11; w=11; offset=0; strand=D; shift=0; score= 1; tMACTCACTCA- ; cor=; Ncor= a 1 17 24 0 0 0 24 0 0 2 21 0 c 5 7 0 24 0 24 0 24 0 20 1 0 g 2 0 0 0 0 0 0 0 0 2 1 0 t 16 0 0 0 24 0 0 0 24 0 1 0

oligos_8nt_mkv2_m19_shift0 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19)
; oligos_7nt_mkv2_m14 versus oligos_8nt_mkv2_m19 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19); m=2/2; ncol2=12; w=11; offset=0; strand=D; shift=0; score=0.909756; TMACTCACTCAy ; cor=; Ncor= a 3 17 23 0 1 0 23 0 1 0 23 1 c 3 6 0 24 0 24 0 24 0 24 0 6 g 0 0 0 0 0 0 1 0 1 0 0 1 t 18 1 1 0 23 0 0 0 22 0 1 16

One-to-n matrix alignment; reference matrix: dyads_m22_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m22_shift3 (dyads_m22dyads_m22)
; dyads_m22 (dyads_m22dyads_m22); m=0 (reference); ncol1=10; shift=3; ncol=13; ---wmCAAATGst ; Alignment reference a 0 0 0 11 9 0 21 21 21 0 0 1 5 c 0 0 0 3 7 21 0 0 0 0 0 10 5 g 0 0 0 1 2 0 0 0 0 0 21 6 5 t 0 0 0 6 3 0 0 0 0 21 0 4 6

dyads_m22_shift3 (dyads_m22dyads_m22)
; dyads_m22 versus dyads_m22 (dyads_m22dyads_m22); m=1/2; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 1; ---wmCAAATGst ; cor=; Ncor= a 0 0 0 11 9 0 21 21 21 0 0 1 5 c 0 0 0 3 7 21 0 0 0 0 0 10 5 g 0 0 0 1 2 0 0 0 0 0 21 6 5 t 0 0 0 6 3 0 0 0 0 21 0 4 6

oligos_8nt_mkv2_m18_rc_shift0 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18_rc)
; dyads_m22 versus oligos_8nt_mkv2_m18_rc (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18_rc); m=2/2; ncol2=12; w=9; offset=-3; strand=R; shift=0; score=0.526517; wTTTAsAAATsy- ; cor=; Ncor= a 18 1 0 0 28 1 28 27 28 0 1 2 0 c 2 1 5 0 0 12 0 0 0 0 7 10 0 g 1 2 0 0 0 15 0 0 0 0 17 0 0 t 7 24 23 28 0 0 0 1 0 28 3 16 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m16_shift9 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m16_shift9 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=0 (reference); ncol1=12; shift=9; ncol=21; ---------YkGAAAATsAyr ; Alignment reference a 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 c 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 g 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 t 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5

oligos_8nt_mkv2_m16_shift9 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; oligos_8nt_mkv2_m16 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=1/10; ncol2=12; w=12; offset=0; strand=D; shift=9; score= 1; ---------YkGAAAATsAyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 c 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 g 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 t 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5

oligos_7nt_mkv2_m10_shift10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; oligos_8nt_mkv2_m16 versus oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=2/10; ncol2=11; w=11; offset=1; strand=D; shift=10; score=0.757419; ----------GRAAAATGAGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3 34 112 112 110 112 0 0 112 1 92 c 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 16 2 g 0 0 0 0 0 0 0 0 0 0 105 77 0 0 0 0 0 112 0 77 17 t 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 112 0 0 18 1

oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; oligos_8nt_mkv2_m16 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=3/10; ncol2=12; w=11; offset=-1; strand=R; shift=8; score=0.604377; --------MsTGAAAAACrt- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0

dyads_m10_rc_shift7 (dyads_m10dyads_m10_rc)
; oligos_8nt_mkv2_m16 versus dyads_m10_rc (dyads_m10dyads_m10_rc); m=4/10; ncol2=15; w=12; offset=-2; strand=R; shift=7; score=0.591029; -------CAtGGAAAATGAGA ; cor=; Ncor= a 0 0 0 0 0 0 0 2 50 2 1 0 72 55 56 56 3 0 71 0 55 c 0 0 0 0 0 0 0 51 8 12 0 0 0 2 4 10 1 0 0 1 4 g 0 0 0 0 0 0 0 7 9 14 71 72 0 10 9 4 2 72 1 71 9 t 0 0 0 0 0 0 0 12 5 44 0 0 0 5 3 2 66 0 0 0 4

dyads_m27_shift9 (dyads_m27dyads_m27)
; oligos_8nt_mkv2_m16 versus dyads_m27 (dyads_m27dyads_m27); m=5/10; ncol2=18; w=12; offset=0; strand=D; shift=9; score=0.56598; ---------yGGAAAATkAdA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 6 3 65 66 66 64 6 4 45 20 53 c 0 0 0 0 0 0 0 0 0 17 4 0 0 0 0 0 6 3 2 1 0 g 0 0 0 0 0 0 0 0 0 7 48 63 0 0 0 0 0 41 8 27 13 t 0 0 0 0 0 0 0 0 0 39 8 0 1 0 0 2 54 18 11 18 0

dyads_m4_shift0 (dyads_m4dyads_m4)
; oligos_8nt_mkv2_m16 versus dyads_m4 (dyads_m4dyads_m4); m=6/10; ncol2=21; w=12; offset=-9; strand=D; shift=0; score=0.542879; gCkRRAAAACTGAAAATCAyR ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0

oligos_8nt_mkv2_m6_shift7 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_8nt_mkv2_m16 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=7/10; ncol2=18; w=12; offset=-2; strand=D; shift=7; score=0.505792; -------CrTGRAAAATGAGA ; cor=; Ncor= a 0 0 0 0 0 0 0 4 66 0 4 27 102 102 101 100 2 2 96 1 100 c 0 0 0 0 0 0 0 89 3 13 2 2 0 0 0 1 1 0 0 1 1 g 0 0 0 0 0 0 0 2 30 2 96 73 0 0 0 0 0 99 2 85 1 t 0 0 0 0 0 0 0 7 3 87 0 0 0 0 1 1 99 1 4 15 0

oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m16 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=8/10; ncol2=13; w=9; offset=-4; strand=D; shift=5; score=0.498435; -----WAmACTGAAAAwC--- ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0

oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; oligos_8nt_mkv2_m16 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=9/10; ncol2=11; w=8; offset=-3; strand=D; shift=6; score=0.467186; ------AmACTGAAAAw---- ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0

oligos_8nt_mkv2_m14_shift5 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14)
; oligos_8nt_mkv2_m16 versus oligos_8nt_mkv2_m14 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14); m=10/10; ncol2=12; w=8; offset=-4; strand=D; shift=5; score=0.430455; -----AwCATGGAAAAT---- ; cor=; Ncor= a 0 0 0 0 0 68 46 1 74 0 1 0 81 83 73 78 3 0 0 0 0 c 0 0 0 0 0 1 3 79 0 11 2 0 0 0 0 3 0 0 0 0 0 g 0 0 0 0 0 14 0 0 9 0 80 83 1 0 0 0 1 0 0 0 0 t 0 0 0 0 0 0 34 3 0 72 0 0 1 0 10 2 79 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m13_shift2 ; 30 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=0 (reference); ncol1=16; shift=2; ncol=18; --grmArCAGCTGTCwyc ; Alignment reference a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_7nt_mkv2_m13 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=1/29; ncol2=16; w=16; offset=0; strand=D; shift=2; score= 1; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m13 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=2/29; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.974887; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

dyads_m3_shift3 (dyads_m3dyads_m3)
; oligos_7nt_mkv2_m13 versus dyads_m3 (dyads_m3dyads_m3); m=3/29; ncol2=15; w=15; offset=1; strand=D; shift=3; score=0.936315; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m13 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=4/29; ncol2=16; w=16; offset=0; strand=R; shift=2; score=0.92321; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=5/29; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.886592; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=6/29; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.882741; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=7/29; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.871522; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m13 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=8/29; ncol2=14; w=14; offset=1; strand=D; shift=3; score=0.849814; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; oligos_7nt_mkv2_m13 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=9/29; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.844947; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; oligos_7nt_mkv2_m13 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=10/29; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.840281; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_7nt_mkv2_m13 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=11/29; ncol2=18; w=16; offset=-2; strand=R; shift=0; score=0.819829; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=12/29; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.806438; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m13 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=13/29; ncol2=14; w=14; offset=1; strand=R; shift=3; score=0.803906; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=14/29; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.803838; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

dyads_m8_shift3 (dyads_m8dyads_m8)
; oligos_7nt_mkv2_m13 versus dyads_m8 (dyads_m8dyads_m8); m=15/29; ncol2=15; w=15; offset=1; strand=D; shift=3; score=0.798818; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=16/29; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.784365; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=17/29; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.767952; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; oligos_7nt_mkv2_m13 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=18/29; ncol2=14; w=14; offset=2; strand=R; shift=4; score=0.765577; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m13 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=19/29; ncol2=14; w=14; offset=2; strand=R; shift=4; score=0.765491; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=20/29; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.760891; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=21/29; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.760802; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

dyads_m1_shift2 (dyads_m1dyads_m1)
; oligos_7nt_mkv2_m13 versus dyads_m1 (dyads_m1dyads_m1); m=22/29; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.756774; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m13 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=23/29; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.756774; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=24/29; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.751148; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m13 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=25/29; ncol2=14; w=14; offset=1; strand=D; shift=3; score=0.70475; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_7nt_mkv2_m13 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=26/29; ncol2=17; w=15; offset=-2; strand=R; shift=0; score=0.697775; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

dyads_m21_shift3 (dyads_m21dyads_m21)
; oligos_7nt_mkv2_m13 versus dyads_m21 (dyads_m21dyads_m21); m=27/29; ncol2=14; w=14; offset=1; strand=D; shift=3; score=0.645862; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

oligos_8nt_mkv2_m25_shift3 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_7nt_mkv2_m13 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=28/29; ncol2=12; w=12; offset=1; strand=D; shift=3; score=0.545307; ---gvAACAGTTGcr--- ; cor=; Ncor= a 0 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 c 0 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 g 0 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 t 0 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0

oligos_7nt_mkv2_m12_shift4 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_7nt_mkv2_m13 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=29/29; ncol2=11; w=11; offset=2; strand=D; shift=4; score=0.500221; ----smACAGTTGym--- ; cor=; Ncor= a 0 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 c 0 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 g 0 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 t 0 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m3_shift0 ; 24 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=0 (reference); ncol1=15; shift=0; ncol=18; rstGACAGCTGMskg--- ; Alignment reference a 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=1/23; ncol2=15; w=15; offset=0; strand=D; shift=0; score= 1; rstGACAGCTGMskg--- ; cor=; Ncor= a 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

oligos_8nt_mkv2_m17_shift0 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=2/23; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.974937; rstGACAGCTGmhkg--- ; cor=; Ncor= a 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m22_shift0 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=3/23; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.972007; rvtGACAGCTGmhkg--- ; cor=; Ncor= a 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

dyads_m19_shift0 (dyads_m19dyads_m19)
; oligos_8nt_mkv2_m3 versus dyads_m19 (dyads_m19dyads_m19); m=4/23; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.959398; rvdGACAGCTGvyks--- ; cor=; Ncor= a 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m3 versus dyads_m36 (dyads_m36dyads_m36); m=5/23; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.934337; rvkGACAGCTGctks--- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m3 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=6/23; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.911197; rswGACAGCTGmsg---- ; cor=; Ncor= a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

dyads_m5_shift0 (dyads_m5dyads_m5)
; oligos_8nt_mkv2_m3 versus dyads_m5 (dyads_m5dyads_m5); m=7/23; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.907814; rvdGACAGCTGmsg---- ; cor=; Ncor= a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

dyads_m8_rc_shift0 (dyads_m8dyads_m8_rc)
; oligos_8nt_mkv2_m3 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=8/23; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.888667; mvrGACAGCTGwGsv--- ; cor=; Ncor= a 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 0 c 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 0 g 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 0 t 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0 0

dyads_m3_rc_shift0 (dyads_m3dyads_m3_rc)
; oligos_8nt_mkv2_m3 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=9/23; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.85086; rrwGACAGCTGyTky--- ; cor=; Ncor= a 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m3 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=10/23; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.826277; -vwGACAGCTGytkd--- ; cor=; Ncor= a 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m3 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=11/23; ncol2=14; w=14; offset=1; strand=D; shift=1; score=0.80933; -grgACAGCTGCtkm--- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=12/23; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.808925; -cwGaCAGCTGtCwg--- ; cor=; Ncor= a 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 0 c 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 0 g 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 0 t 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m3 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=13/23; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.802487; gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

dyads_m1_shift0 (dyads_m1dyads_m1)
; oligos_8nt_mkv2_m3 versus dyads_m1 (dyads_m1dyads_m1); m=14/23; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.801669; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_8nt_mkv2_m3 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=15/23; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.801669; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_7nt_mkv2_m13_rc_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m3 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=16/23; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.784365; grwGACAGCTGyTkyc-- ; cor=; Ncor= a 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m3 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=17/23; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.771254; kkwsACAGCTGTTsys-- ; cor=; Ncor= a 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

oligos_8nt_mkv2_m12_shift0 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=18/23; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.769761; gmyGaCAGCTGtCrkc-- ; cor=; Ncor= a 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 0 c 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 0 g 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 0 t 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0 0

oligos_8nt_mkv2_m1_rc_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=19/23; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.753963; krkGACAGCTGCTkhvb- ; cor=; Ncor= a 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_8nt_mkv2_m10_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=20/23; ncol2=17; w=15; offset=0; strand=D; shift=0; score=0.740305; rraGACAGCTGCTgyyy- ; cor=; Ncor= a 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

oligos_8nt_mkv2_m27_rc_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=21/23; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.729624; drrGACAGCTGCTGhbb- ; cor=; Ncor= a 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

dyads_m2_shift0 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m3 versus dyads_m2 (dyads_m2dyads_m2); m=22/23; ncol2=18; w=15; offset=0; strand=D; shift=0; score=0.650203; krrrACAGCTGCTGtcta ; cor=; Ncor= a 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=23/23; ncol2=16; w=14; offset=1; strand=D; shift=1; score=0.594322; -rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

One-to-n matrix alignment; reference matrix: dyads_m27_shift2 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m27_shift2 (dyads_m27dyads_m27)
; dyads_m27 (dyads_m27dyads_m27); m=0 (reference); ncol1=18; shift=2; ncol=28; --yGGAAAATkAdAAAAwsh-------- ; Alignment reference a 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 0 0 0 0 0 0 0 c 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 0 0 0 0 0 0 0 g 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 0 0 0 0 0 0 0 t 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0 0 0 0 0 0 0 0

dyads_m27_shift2 (dyads_m27dyads_m27)
; dyads_m27 versus dyads_m27 (dyads_m27dyads_m27); m=1/10; ncol2=18; w=18; offset=0; strand=D; shift=2; score= 1; --yGGAAAATkAdAAAAwsh-------- ; cor=; Ncor= a 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 0 0 0 0 0 0 0 c 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 0 0 0 0 0 0 0 g 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 0 0 0 0 0 0 0 t 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m6_shift0 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; dyads_m27 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=2/10; ncol2=18; w=16; offset=-2; strand=D; shift=0; score=0.729546; CrTGRAAAATGAGAAAwr---------- ; cor=; Ncor= a 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 0 0 0 0 0 0 c 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 0 0 0 0 0 0 g 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 0 0 0 0 0 0 t 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0 0 0 0 0 0 0

dyads_m24_shift2 (dyads_m24dyads_m24)
; dyads_m27 versus dyads_m24 (dyads_m24dyads_m24); m=3/10; ncol2=18; w=18; offset=0; strand=D; shift=2; score=0.701163; --ygRRAAAmsTGAAAAwyr-------- ; cor=; Ncor= a 0 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 0 0 0 0 0 0 0 c 0 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 g 0 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 0 0 0 0 0 0 0 t 0 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0 0 0 0 0 0 0 0

dyads_m10_rc_shift0 (dyads_m10dyads_m10_rc)
; dyads_m27 versus dyads_m10_rc (dyads_m10dyads_m10_rc); m=4/10; ncol2=15; w=13; offset=-2; strand=R; shift=0; score=0.588429; CAtGGAAAATGAGAA------------- ; cor=; Ncor= a 2 50 2 1 0 72 55 56 56 3 0 71 0 55 56 0 0 0 0 0 0 0 0 0 0 0 0 0 c 51 8 12 0 0 0 2 4 10 1 0 0 1 4 9 0 0 0 0 0 0 0 0 0 0 0 0 0 g 7 9 14 71 72 0 10 9 4 2 72 1 71 9 2 0 0 0 0 0 0 0 0 0 0 0 0 0 t 12 5 44 0 0 0 5 3 2 66 0 0 0 4 5 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv2_m10_shift3 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; dyads_m27 versus oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=5/10; ncol2=11; w=11; offset=1; strand=D; shift=3; score=0.575015; ---GRAAAATGAGA-------------- ; cor=; Ncor= a 0 0 0 3 34 112 112 110 112 0 0 112 1 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 2 1 0 0 0 0 0 0 0 16 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 105 77 0 0 0 0 0 112 0 77 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 2 0 0 0 2 0 112 0 0 18 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m16_shift2 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; dyads_m27 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=6/10; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.56598; --YkGAAAATsAyr-------------- ; cor=; Ncor= a 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m29_shift7 (dyads_m29dyads_m29)
; dyads_m27 versus dyads_m29 (dyads_m29dyads_m29); m=7/10; ncol2=12; w=12; offset=5; strand=D; shift=7; score=0.539564; -------AmTGArAAAyry--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0 0 0 0 0 0

dyads_m9_shift3 (dyads_m9dyads_m9)
; dyads_m27 versus dyads_m9 (dyads_m9dyads_m9); m=8/10; ncol2=26; w=17; offset=1; strand=D; shift=3; score=0.512151; ---GrAAAwtrarAAAtgcaCAcTGTAG ; cor=; Ncor= a 0 0 0 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 c 0 0 0 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 g 0 0 0 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 t 0 0 0 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13

oligos_6nt_mkv2_m8_shift8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)
; dyads_m27 versus oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=9/10; ncol2=10; w=10; offset=6; strand=D; shift=8; score=0.45369; --------rtGAGAAAha---------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 101 13 0 154 0 154 154 154 43 85 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 3 32 0 0 0 0 0 0 52 30 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 44 11 154 0 154 0 0 0 5 34 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 98 0 0 0 0 0 0 54 5 0 0 0 0 0 0 0 0 0 0

dyads_m40_shift5 (dyads_m40dyads_m40)
; dyads_m27 versus dyads_m40 (dyads_m40dyads_m40); m=10/10; ncol2=25; w=15; offset=3; strand=D; shift=5; score=0.440949; -----AAAATGAGAAATrCACAcTkTAG ; cor=; Ncor= a 0 0 0 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 c 0 0 0 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 g 0 0 0 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 t 0 0 0 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m15_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m15_shift2 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)
; oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=0 (reference); ncol1=12; shift=2; ncol=14; --vcCCGCCGcGss ; Alignment reference a 0 0 4 0 0 1 0 1 0 0 2 0 1 1 c 0 0 6 9 14 13 0 12 12 1 9 0 5 4 g 0 0 4 3 0 0 14 1 2 13 2 14 8 7 t 0 0 0 2 0 0 0 0 0 0 1 0 0 2

oligos_8nt_mkv2_m15_shift2 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)
; oligos_8nt_mkv2_m15 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=1/8; ncol2=12; w=12; offset=0; strand=D; shift=2; score= 1; --vcCCGCCGcGss ; cor=; Ncor= a 0 0 4 0 0 1 0 1 0 0 2 0 1 1 c 0 0 6 9 14 13 0 12 12 1 9 0 5 4 g 0 0 4 3 0 0 14 1 2 13 2 14 8 7 t 0 0 0 2 0 0 0 0 0 0 1 0 0 2

dyads_m26_shift2 (dyads_m26dyads_m26)
; oligos_8nt_mkv2_m15 versus dyads_m26 (dyads_m26dyads_m26); m=2/8; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.931423; --csCCGcsGCGss ; cor=; Ncor= a 0 0 1 0 1 0 1 4 3 0 1 0 3 2 c 0 0 19 15 25 27 1 15 13 2 24 3 10 8 g 0 0 6 10 2 1 26 6 11 24 2 25 12 16 t 0 0 2 3 0 0 0 3 1 2 1 0 3 2

oligos_6nt_mkv2_m6_shift2 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)
; oligos_8nt_mkv2_m15 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=3/8; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.823855; --ssCCGCCGGGs- ; cor=; Ncor= a 0 0 3 2 1 0 0 0 0 0 2 2 4 0 c 0 0 11 13 21 25 1 23 22 3 3 4 10 0 g 0 0 10 9 3 1 25 3 4 23 20 18 11 0 t 0 0 2 2 1 0 0 0 0 0 1 2 1 0

oligos_7nt_mkv2_m7_rc_shift3 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc)
; oligos_8nt_mkv2_m15 versus oligos_7nt_mkv2_m7_rc (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc); m=4/8; ncol2=11; w=11; offset=1; strand=R; shift=3; score=0.787447; ---ssCGCCGGGss ; cor=; Ncor= a 0 0 0 2 4 3 0 0 0 0 3 0 6 4 c 0 0 0 16 17 33 1 28 32 4 3 1 14 11 g 0 0 0 14 11 0 33 5 4 32 29 34 11 17 t 0 0 0 4 4 0 2 3 0 0 1 1 5 4

oligos_7nt_mkv2_m15_shift1 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; oligos_8nt_mkv2_m15 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=5/8; ncol2=11; w=10; offset=-1; strand=D; shift=1; score=0.732153; -ssCCCGCCGsg-- ; cor=; Ncor= a 0 4 4 0 1 0 0 3 0 0 3 3 0 0 c 0 7 11 23 24 26 0 19 23 2 10 5 0 0 g 0 11 8 3 2 1 27 5 4 25 11 18 0 0 t 0 5 4 1 0 0 0 0 0 0 3 1 0 0

dyads_m12_rc_shift2 (dyads_m12dyads_m12_rc)
; oligos_8nt_mkv2_m15 versus dyads_m12_rc (dyads_m12dyads_m12_rc); m=6/8; ncol2=14; w=12; offset=0; strand=R; shift=2; score=0.651999; --ssCCSGCGSGGs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 4 7 8 10 3 1 11 0 3 2 1 4 g 0 0 6 3 2 1 8 10 0 11 8 9 9 6 t 0 0 1 1 1 0 0 0 0 0 0 0 1 1

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; oligos_8nt_mkv2_m15 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=7/8; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=0.499164; ssCCCCGCsg---- ; cor=; Ncor= a 0 3 0 0 0 0 0 0 2 1 0 0 0 0 c 10 7 23 21 23 24 0 25 8 6 0 0 0 0 g 11 9 2 4 2 1 25 0 9 15 0 0 0 0 t 4 6 0 0 0 0 0 0 6 3 0 0 0 0

dyads_m30_shift0 (dyads_m30dyads_m30)
; oligos_8nt_mkv2_m15 versus dyads_m30 (dyads_m30dyads_m30); m=8/8; ncol2=11; w=9; offset=-2; strand=D; shift=0; score=0.457706; ymCCCMGCCyr--- ; cor=; Ncor= a 2 4 0 0 0 8 0 0 0 2 3 0 0 0 c 3 3 11 11 11 3 0 11 11 4 2 0 0 0 g 2 2 0 0 0 0 11 0 0 2 4 0 0 0 t 4 2 0 0 0 0 0 0 0 3 2 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 28 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5dyads_m5)
; dyads_m5 (dyads_m5dyads_m5); m=0 (reference); ncol1=14; shift=0; ncol=18; rvdGACAGCTGmsg---- ; Alignment reference a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

dyads_m5_shift0 (dyads_m5dyads_m5)
; dyads_m5 versus dyads_m5 (dyads_m5dyads_m5); m=1/27; ncol2=14; w=14; offset=0; strand=D; shift=0; score= 1; rvdGACAGCTGmsg---- ; cor=; Ncor= a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; dyads_m5 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=2/27; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.999419; rswGACAGCTGmsg---- ; cor=; Ncor= a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

dyads_m19_shift0 (dyads_m19dyads_m19)
; dyads_m5 versus dyads_m19 (dyads_m19dyads_m19); m=3/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.916223; rvdGACAGCTGvyks--- ; cor=; Ncor= a 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; dyads_m5 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=4/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.907814; rstGACAGCTGMskg--- ; cor=; Ncor= a 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; dyads_m5 versus dyads_m36 (dyads_m36dyads_m36); m=5/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.906945; rvkGACAGCTGctks--- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

oligos_8nt_mkv2_m22_shift0 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; dyads_m5 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=6/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.899671; rvtGACAGCTGmhkg--- ; cor=; Ncor= a 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m17_shift0 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; dyads_m5 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=7/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.899145; rstGACAGCTGmhkg--- ; cor=; Ncor= a 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

dyads_m8_rc_shift0 (dyads_m8dyads_m8_rc)
; dyads_m5 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=8/27; ncol2=15; w=14; offset=0; strand=R; shift=0; score=0.853287; mvrGACAGCTGwGsv--- ; cor=; Ncor= a 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 0 c 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 0 g 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 0 t 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0 0

dyads_m3_rc_shift0 (dyads_m3dyads_m3_rc)
; dyads_m5 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=9/27; ncol2=15; w=14; offset=0; strand=R; shift=0; score=0.828376; rrwGACAGCTGyTky--- ; cor=; Ncor= a 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; dyads_m5 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=10/27; ncol2=14; w=13; offset=1; strand=R; shift=1; score=0.799789; -vwGACAGCTGytkd--- ; cor=; Ncor= a 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; dyads_m5 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=11/27; ncol2=14; w=13; offset=1; strand=D; shift=1; score=0.79754; -grgACAGCTGCtkm--- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; dyads_m5 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=12/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.791809; gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; dyads_m5 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=13/27; ncol2=14; w=13; offset=1; strand=D; shift=1; score=0.771828; -cwGaCAGCTGtCwg--- ; cor=; Ncor= a 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 0 0 c 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 0 0 g 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 0 0 t 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0 0 0

oligos_7nt_mkv2_m13_rc_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; dyads_m5 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/27; ncol2=16; w=14; offset=0; strand=R; shift=0; score=0.765577; grwGACAGCTGyTkyc-- ; cor=; Ncor= a 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

dyads_m1_shift0 (dyads_m1dyads_m1)
; dyads_m5 versus dyads_m1 (dyads_m1dyads_m1); m=15/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.760426; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; dyads_m5 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=16/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.760426; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; dyads_m5 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=17/27; ncol2=16; w=14; offset=0; strand=R; shift=0; score=0.74244; kkwsACAGCTGTTsys-- ; cor=; Ncor= a 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

oligos_8nt_mkv2_m12_shift0 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; dyads_m5 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=18/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.740617; gmyGaCAGCTGtCrkc-- ; cor=; Ncor= a 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 0 c 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 0 g 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 0 t 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0 0

oligos_8nt_mkv2_m1_rc_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; dyads_m5 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=19/27; ncol2=17; w=14; offset=0; strand=R; shift=0; score=0.732454; krkGACAGCTGCTkhvb- ; cor=; Ncor= a 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_8nt_mkv2_m10_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; dyads_m5 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=20/27; ncol2=17; w=14; offset=0; strand=D; shift=0; score=0.728933; rraGACAGCTGCTgyyy- ; cor=; Ncor= a 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

oligos_8nt_mkv2_m27_rc_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; dyads_m5 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=21/27; ncol2=17; w=14; offset=0; strand=R; shift=0; score=0.723541; drrGACAGCTGCTGhbb- ; cor=; Ncor= a 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

dyads_m2_shift0 (dyads_m2dyads_m2)
; dyads_m5 versus dyads_m2 (dyads_m2dyads_m2); m=22/27; ncol2=18; w=14; offset=0; strand=D; shift=0; score=0.660354; krrrACAGCTGCTGtcta ; cor=; Ncor= a 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m13_rc_shift0 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; dyads_m5 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=23/27; ncol2=17; w=14; offset=0; strand=R; shift=0; score=0.630006; bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; dyads_m5 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=24/27; ncol2=17; w=14; offset=0; strand=D; shift=0; score=0.624237; swsAACAGCTGCTGchm- ; cor=; Ncor= a 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; dyads_m5 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=25/27; ncol2=16; w=13; offset=1; strand=D; shift=1; score=0.620177; -rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

oligos_8nt_mkv2_m25_shift1 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; dyads_m5 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=26/27; ncol2=12; w=12; offset=1; strand=D; shift=1; score=0.600963; -gvAACAGTTGcr----- ; cor=; Ncor= a 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 0 c 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 0 g 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 0 t 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0 0

dyads_m25_shift1 (dyads_m25dyads_m25)
; dyads_m5 versus dyads_m25 (dyads_m25dyads_m25); m=27/27; ncol2=17; w=13; offset=1; strand=D; shift=1; score=0.561534; -dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

One-to-n matrix alignment; reference matrix: dyads_m33_shift12 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m33_shift12 (dyads_m33dyads_m33)
; dyads_m33 (dyads_m33dyads_m33); m=0 (reference); ncol1=10; shift=12; ncol=23; ------------ACACTGTAGr- ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 54 1 76 0 0 0 0 76 5 21 0 c 0 0 0 0 0 0 0 0 0 0 0 0 17 68 0 76 0 0 0 0 3 6 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1 76 0 0 66 48 0 t 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 75 0 76 0 2 1 0

dyads_m33_shift12 (dyads_m33dyads_m33)
; dyads_m33 versus dyads_m33 (dyads_m33dyads_m33); m=1/5; ncol2=10; w=10; offset=0; strand=D; shift=12; score= 1; ------------ACACTGTAGr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 54 1 76 0 0 0 0 76 5 21 0 c 0 0 0 0 0 0 0 0 0 0 0 0 17 68 0 76 0 0 0 0 3 6 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1 76 0 0 66 48 0 t 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 75 0 76 0 2 1 0

dyads_m23_shift10 (dyads_m23dyads_m23)
; dyads_m33 versus dyads_m23 (dyads_m23dyads_m23); m=2/5; ncol2=12; w=10; offset=-2; strand=D; shift=10; score=0.794922; ----------gMACAcTGTAGr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 0 c 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 0 g 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 0 t 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1 0

dyads_m6_shift9 (dyads_m6dyads_m6)
; dyads_m33 versus dyads_m6 (dyads_m6dyads_m6); m=3/5; ncol2=14; w=10; offset=-3; strand=D; shift=9; score=0.686708; ---------trCACACTgTAGrA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 78 c 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 5 g 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 1 t 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1 8

oligos_8nt_mkv2_m26_rc_shift9 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)
; dyads_m33 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=4/5; ncol2=12; w=9; offset=-3; strand=R; shift=9; score=0.671399; ---------trCACACTGTAG-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 19 40 0 87 0 87 1 4 5 0 65 8 0 0 c 0 0 0 0 0 0 0 0 0 9 18 79 0 86 0 85 0 1 0 1 10 0 0 g 0 0 0 0 0 0 0 0 0 3 24 0 0 0 0 0 1 69 0 7 63 0 0 t 0 0 0 0 0 0 0 0 0 56 5 8 0 1 0 1 82 12 87 14 6 0 0

dyads_m20_rc_shift0 (dyads_m20dyads_m20_rc)
; dyads_m33 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=5/5; ncol2=23; w=10; offset=-12; strand=R; shift=0; score=0.414113; AATGAGAAAtrCACACTkTAGGA ; cor=; Ncor= a 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 4 0 60 0 10 48 c 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 3 0 0 0 3 4 g 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 35 0 0 60 44 0 t 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46 18 60 0 0 3 8

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m19_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m19_shift0 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19)
; oligos_8nt_mkv2_m19 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19); m=0 (reference); ncol1=12; shift=0; ncol=12; TMACTCACTCAy ; Alignment reference a 3 17 23 0 1 0 23 0 1 0 23 1 c 3 6 0 24 0 24 0 24 0 24 0 6 g 0 0 0 0 0 0 1 0 1 0 0 1 t 18 1 1 0 23 0 0 0 22 0 1 16

oligos_8nt_mkv2_m19_shift0 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19)
; oligos_8nt_mkv2_m19 versus oligos_8nt_mkv2_m19 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19); m=1/2; ncol2=12; w=12; offset=0; strand=D; shift=0; score= 1; TMACTCACTCAy ; cor=; Ncor= a 3 17 23 0 1 0 23 0 1 0 23 1 c 3 6 0 24 0 24 0 24 0 24 0 6 g 0 0 0 0 0 0 1 0 1 0 0 1 t 18 1 1 0 23 0 0 0 22 0 1 16

oligos_7nt_mkv2_m14_shift0 (oligos_7nt_mkv2_m14oligos_7nt_mkv2_m14)
; oligos_8nt_mkv2_m19 versus oligos_7nt_mkv2_m14 (oligos_7nt_mkv2_m14oligos_7nt_mkv2_m14); m=2/2; ncol2=11; w=11; offset=0; strand=D; shift=0; score=0.909756; tMACTCACTCA- ; cor=; Ncor= a 1 17 24 0 0 0 24 0 0 2 21 0 c 5 7 0 24 0 24 0 24 0 20 1 0 g 2 0 0 0 0 0 0 0 0 2 1 0 t 16 0 0 0 24 0 0 0 24 0 1 0

One-to-n matrix alignment; reference matrix: dyads_m29_shift8 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m29_shift8 (dyads_m29dyads_m29)
; dyads_m29 (dyads_m29dyads_m29); m=0 (reference); ncol1=12; shift=8; ncol=25; --------AmTGArAAAyry----- ; Alignment reference a 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 0 c 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0 0

dyads_m29_shift8 (dyads_m29dyads_m29)
; dyads_m29 versus dyads_m29 (dyads_m29dyads_m29); m=1/15; ncol2=12; w=12; offset=0; strand=D; shift=8; score= 1; --------AmTGArAAAyry----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 0 c 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0 0

oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; dyads_m29 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=2/15; ncol2=12; w=12; offset=0; strand=R; shift=8; score=0.872856; --------MsTGAAAAACrt----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0 0

oligos_6nt_mkv2_m8_shift9 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)
; dyads_m29 versus oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=3/15; ncol2=10; w=10; offset=1; strand=D; shift=9; score=0.784394; ---------rtGAGAAAha------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 101 13 0 154 0 154 154 154 43 85 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3 32 0 0 0 0 0 0 52 30 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 44 11 154 0 154 0 0 0 5 34 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 6 98 0 0 0 0 0 0 54 5 0 0 0 0 0 0

oligos_7nt_mkv2_m6_shift8 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; dyads_m29 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=4/15; ncol2=11; w=11; offset=0; strand=D; shift=8; score=0.778169; --------msTGAAAAAyr------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4 0 0 0 0 0 0

oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; dyads_m29 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=5/15; ncol2=13; w=10; offset=-3; strand=D; shift=5; score=0.555704; -----WAmACTGAAAAwC------- ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0 0

oligos_8nt_mkv2_m6_shift1 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; dyads_m29 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=6/15; ncol2=18; w=11; offset=-7; strand=D; shift=1; score=0.548376; -CrTGRAAAATGAGAAAwr------ ; cor=; Ncor= a 0 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 0 0 c 0 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 0 0 g 0 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 0 0 t 0 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0 0 0

dyads_m39_shift11 (dyads_m39dyads_m39)
; dyads_m29 versus dyads_m39 (dyads_m39dyads_m39); m=7/15; ncol2=10; w=9; offset=3; strand=D; shift=11; score=0.547389; -----------GwGAAATAyr---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 5 25 0 56 56 56 0 56 5 21 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 7 1 0 0 0 0 0 0 20 6 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 40 3 56 0 0 0 0 0 5 23 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 4 27 0 0 0 0 56 0 26 6 0 0 0 0

dyads_m27_shift3 (dyads_m27dyads_m27)
; dyads_m29 versus dyads_m27 (dyads_m27dyads_m27); m=8/15; ncol2=18; w=12; offset=-5; strand=D; shift=3; score=0.539564; ---yGGAAAATkAdAAAAwsh---- ; cor=; Ncor= a 0 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 0 0 0 c 0 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 0 0 0 g 0 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 0 0 0 t 0 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0 0 0 0

oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; dyads_m29 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=9/15; ncol2=11; w=9; offset=-2; strand=D; shift=6; score=0.524527; ------AmACTGAAAAw-------- ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0 0 0

dyads_m20_rc_shift8 (dyads_m20dyads_m20_rc)
; dyads_m29 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=10/15; ncol2=23; w=12; offset=0; strand=R; shift=8; score=0.483333; --------AATGAGAAAtrCACACT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 c 0 0 0 0 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 g 0 0 0 0 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 t 0 0 0 0 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46

dyads_m24_shift1 (dyads_m24dyads_m24)
; dyads_m29 versus dyads_m24 (dyads_m24dyads_m24); m=11/15; ncol2=18; w=11; offset=-7; strand=D; shift=1; score=0.449941; -ygRRAAAmsTGAAAAwyr------ ; cor=; Ncor= a 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 0 0 0 0 0 c 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 g 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 0 0 0 0 0 t 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0 0 0 0 0 0

dyads_m40_shift6 (dyads_m40dyads_m40)
; dyads_m29 versus dyads_m40 (dyads_m40dyads_m40); m=12/15; ncol2=25; w=12; offset=-2; strand=D; shift=6; score=0.427977; ------AAAATGAGAAATrCACAcT ; cor=; Ncor= a 0 0 0 0 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 c 0 0 0 0 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 g 0 0 0 0 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 t 0 0 0 0 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51

oligos_7nt_mkv2_m10_shift4 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; dyads_m29 versus oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=13/15; ncol2=11; w=7; offset=-4; strand=D; shift=4; score=0.412941; ----GRAAAATGAGA---------- ; cor=; Ncor= a 0 0 0 0 3 34 112 112 110 112 0 0 112 1 92 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 2 1 0 0 0 0 0 0 0 16 2 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 105 77 0 0 0 0 0 112 0 77 17 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 2 0 0 0 2 0 112 0 0 18 1 0 0 0 0 0 0 0 0 0 0

dyads_m4_shift0 (dyads_m4dyads_m4)
; dyads_m29 versus dyads_m4 (dyads_m4dyads_m4); m=14/15; ncol2=21; w=12; offset=-8; strand=D; shift=0; score=0.409592; gCkRRAAAACTGAAAATCAyR---- ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0 0

dyads_m10_rc_shift1 (dyads_m10dyads_m10_rc)
; dyads_m29 versus dyads_m10_rc (dyads_m10dyads_m10_rc); m=15/15; ncol2=15; w=8; offset=-7; strand=R; shift=1; score=0.400944; -CAtGGAAAATGAGAA--------- ; cor=; Ncor= a 0 2 50 2 1 0 72 55 56 56 3 0 71 0 55 56 0 0 0 0 0 0 0 0 0 c 0 51 8 12 0 0 0 2 4 10 1 0 0 1 4 9 0 0 0 0 0 0 0 0 0 g 0 7 9 14 71 72 0 10 9 4 2 72 1 71 9 2 0 0 0 0 0 0 0 0 0 t 0 12 5 44 0 0 0 5 3 2 66 0 0 0 4 5 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m9_shift3 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift3 (dyads_m9dyads_m9)
; dyads_m9 (dyads_m9dyads_m9); m=0 (reference); ncol1=26; shift=3; ncol=29; ---GrAAAwtrarAAAtgcaCAcTGTAGr ; Alignment reference a 0 0 0 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 24 c 0 0 0 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 6 g 0 0 0 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 47 t 0 0 0 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13 10

dyads_m9_shift3 (dyads_m9dyads_m9)
; dyads_m9 versus dyads_m9 (dyads_m9dyads_m9); m=1/9; ncol2=26; w=26; offset=0; strand=D; shift=3; score= 1; ---GrAAAwtrarAAAtgcaCAcTGTAGr ; cor=; Ncor= a 0 0 0 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 24 c 0 0 0 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 6 g 0 0 0 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 47 t 0 0 0 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13 10

dyads_m40_shift5 (dyads_m40dyads_m40)
; dyads_m9 versus dyads_m40 (dyads_m40dyads_m40); m=2/9; ncol2=25; w=24; offset=2; strand=D; shift=5; score=0.819302; -----AAAATGAGAAATrCACAcTkTAGG ; cor=; Ncor= a 0 0 0 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 14 c 0 0 0 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 3 g 0 0 0 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 45 t 0 0 0 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0 2

dyads_m20_rc_shift7 (dyads_m20dyads_m20_rc)
; dyads_m9 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=3/9; ncol2=23; w=22; offset=4; strand=R; shift=7; score=0.737463; -------AATGAGAAAtrCACACTkTAGG ; cor=; Ncor= a 0 0 0 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 4 0 60 0 10 c 0 0 0 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 3 0 0 0 3 g 0 0 0 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 35 0 0 60 44 t 0 0 0 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46 18 60 0 0 3

dyads_m27_shift2 (dyads_m27dyads_m27)
; dyads_m9 versus dyads_m27 (dyads_m27dyads_m27); m=4/9; ncol2=18; w=17; offset=-1; strand=D; shift=2; score=0.512151; --yGGAAAATkAdAAAAwsh--------- ; cor=; Ncor= a 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 0 0 0 0 0 0 0 0 c 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 0 0 0 0 0 0 0 0 g 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 0 0 0 0 0 0 0 0 t 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m11_shift11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11)
; dyads_m9 versus oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=5/9; ncol2=13; w=13; offset=8; strand=D; shift=11; score=0.483973; -----------AGAAATRCACACT----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 59 4 71 72 71 0 18 0 68 0 72 1 3 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 2 2 71 1 72 0 52 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 3 63 0 0 0 1 50 0 1 0 0 9 3 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 10 3 0 0 1 69 2 1 2 0 0 10 66 0 0 0 0 0

oligos_8nt_mkv2_m6_shift0 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; dyads_m9 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=6/9; ncol2=18; w=15; offset=-3; strand=D; shift=0; score=0.464877; CrTGRAAAATGAGAAAwr----------- ; cor=; Ncor= a 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 0 0 0 0 0 0 0 c 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 0 0 0 0 0 0 0 g 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 0 0 0 0 0 0 0 t 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0 0 0 0 0 0 0 0

dyads_m6_shift16 (dyads_m6dyads_m6)
; dyads_m9 versus dyads_m6 (dyads_m6dyads_m6); m=7/9; ncol2=14; w=13; offset=13; strand=D; shift=16; score=0.455525; ----------------trCACACTgTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1

dyads_m23_shift17 (dyads_m23dyads_m23)
; dyads_m9 versus dyads_m23 (dyads_m23dyads_m23); m=8/9; ncol2=12; w=12; offset=14; strand=D; shift=17; score=0.447898; -----------------gMACAcTGTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1

oligos_8nt_mkv2_m26_rc_shift16 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)
; dyads_m9 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=9/9; ncol2=12; w=12; offset=13; strand=R; shift=16; score=0.431592; ----------------trCACACTGTAG- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 40 0 87 0 87 1 4 5 0 65 8 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 79 0 86 0 85 0 1 0 1 10 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 24 0 0 0 0 0 1 69 0 7 63 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 5 8 0 1 0 1 82 12 87 14 6 0

One-to-n matrix alignment; reference matrix: dyads_m13_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m13_shift0 (dyads_m13dyads_m13)
; dyads_m13 (dyads_m13dyads_m13); m=0 (reference); ncol1=17; shift=0; ncol=17; mkGAGwkmsrwGCACwg ; Alignment reference a 7 1 0 13 0 6 2 6 1 5 4 0 0 14 0 5 3 c 4 3 0 0 1 2 3 6 4 3 2 1 15 1 15 3 3 g 1 5 15 1 14 3 6 2 8 4 3 14 0 0 0 3 6 t 3 6 0 1 0 4 4 1 2 3 6 0 0 0 0 4 3

dyads_m13_shift0 (dyads_m13dyads_m13)
; dyads_m13 versus dyads_m13 (dyads_m13dyads_m13); m=1/1; ncol2=17; w=17; offset=0; strand=D; shift=0; score= 1; mkGAGwkmsrwGCACwg ; cor=; Ncor= a 7 1 0 13 0 6 2 6 1 5 4 0 0 14 0 5 3 c 4 3 0 0 1 2 3 6 4 3 2 1 15 1 15 3 3 g 1 5 15 1 14 3 6 2 8 4 3 14 0 0 0 3 6 t 3 6 0 1 0 4 4 1 2 3 6 0 0 0 0 4 3

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m10_shift5 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m10_shift5 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=0 (reference); ncol1=11; shift=5; ncol=18; -----GRAAAATGAGA-- ; Alignment reference a 0 0 0 0 0 3 34 112 112 110 112 0 0 112 1 92 0 0 c 0 0 0 0 0 2 1 0 0 0 0 0 0 0 16 2 0 0 g 0 0 0 0 0 105 77 0 0 0 0 0 112 0 77 17 0 0 t 0 0 0 0 0 2 0 0 0 2 0 112 0 0 18 1 0 0

oligos_7nt_mkv2_m10_shift5 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; oligos_7nt_mkv2_m10 versus oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=1/8; ncol2=11; w=11; offset=0; strand=D; shift=5; score= 1; -----GRAAAATGAGA-- ; cor=; Ncor= a 0 0 0 0 0 3 34 112 112 110 112 0 0 112 1 92 0 0 c 0 0 0 0 0 2 1 0 0 0 0 0 0 0 16 2 0 0 g 0 0 0 0 0 105 77 0 0 0 0 0 112 0 77 17 0 0 t 0 0 0 0 0 2 0 0 0 2 0 112 0 0 18 1 0 0

oligos_8nt_mkv2_m16_shift4 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; oligos_7nt_mkv2_m10 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=2/8; ncol2=12; w=11; offset=-1; strand=D; shift=4; score=0.757419; ----YkGAAAATsAyr-- ; cor=; Ncor= a 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 c 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 g 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 t 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0

dyads_m10_rc_shift2 (dyads_m10dyads_m10_rc)
; oligos_7nt_mkv2_m10 versus dyads_m10_rc (dyads_m10dyads_m10_rc); m=3/8; ncol2=15; w=11; offset=-3; strand=R; shift=2; score=0.703083; --CAtGGAAAATGAGAA- ; cor=; Ncor= a 0 0 2 50 2 1 0 72 55 56 56 3 0 71 0 55 56 0 c 0 0 51 8 12 0 0 0 2 4 10 1 0 0 1 4 9 0 g 0 0 7 9 14 71 72 0 10 9 4 2 72 1 71 9 2 0 t 0 0 12 5 44 0 0 0 5 3 2 66 0 0 0 4 5 0

oligos_8nt_mkv2_m6_shift2 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_7nt_mkv2_m10 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=4/8; ncol2=18; w=11; offset=-3; strand=D; shift=2; score=0.606985; --CrTGRAAAATGAGAAA ; cor=; Ncor= a 0 0 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 c 0 0 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 g 0 0 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 t 0 0 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2

dyads_m27_shift4 (dyads_m27dyads_m27)
; oligos_7nt_mkv2_m10 versus dyads_m27 (dyads_m27dyads_m27); m=5/8; ncol2=18; w=11; offset=-1; strand=D; shift=4; score=0.575015; ----yGGAAAATkAdAAA ; cor=; Ncor= a 0 0 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 c 0 0 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 g 0 0 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 t 0 0 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1

oligos_7nt_mkv2_m6_shift2 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; oligos_7nt_mkv2_m10 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=6/8; ncol2=11; w=8; offset=-3; strand=D; shift=2; score=0.477376; --msTGAAAAAyr----- ; cor=; Ncor= a 0 0 78 23 0 1 138 138 138 124 139 6 38 0 0 0 0 0 c 0 0 58 59 0 0 0 0 0 0 0 59 4 0 0 0 0 0 g 0 0 1 41 0 138 1 1 0 0 0 16 93 0 0 0 0 0 t 0 0 2 16 139 0 0 0 1 15 0 58 4 0 0 0 0 0

oligos_8nt_mkv2_m14_shift0 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14)
; oligos_7nt_mkv2_m10 versus oligos_8nt_mkv2_m14 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14); m=7/8; ncol2=12; w=7; offset=-5; strand=D; shift=0; score=0.427127; AwCATGGAAAAT------ ; cor=; Ncor= a 68 46 1 74 0 1 0 81 83 73 78 3 0 0 0 0 0 0 c 1 3 79 0 11 2 0 0 0 0 3 0 0 0 0 0 0 0 g 14 0 0 9 0 80 83 1 0 0 0 1 0 0 0 0 0 0 t 0 34 3 0 72 0 0 1 0 10 2 79 0 0 0 0 0 0

dyads_m29_shift9 (dyads_m29dyads_m29)
; oligos_7nt_mkv2_m10 versus dyads_m29 (dyads_m29dyads_m29); m=8/8; ncol2=12; w=7; offset=4; strand=D; shift=9; score=0.412941; ---------AmTGArAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 c 0 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 t 0 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0

One-to-n matrix alignment; reference matrix: dyads_m19_shift0 ; 27 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m19_shift0 (dyads_m19dyads_m19)
; dyads_m19 (dyads_m19dyads_m19); m=0 (reference); ncol1=15; shift=0; ncol=18; rvdGACAGCTGvyks--- ; Alignment reference a 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

dyads_m19_shift0 (dyads_m19dyads_m19)
; dyads_m19 versus dyads_m19 (dyads_m19dyads_m19); m=1/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score= 1; rvdGACAGCTGvyks--- ; cor=; Ncor= a 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; dyads_m19 versus dyads_m36 (dyads_m36dyads_m36); m=2/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score= 0.9759; rvkGACAGCTGctks--- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

oligos_8nt_mkv2_m17_shift0 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; dyads_m19 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=3/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.967761; rstGACAGCTGmhkg--- ; cor=; Ncor= a 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m22_shift0 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; dyads_m19 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=4/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.967611; rvtGACAGCTGmhkg--- ; cor=; Ncor= a 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; dyads_m19 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=5/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.959398; rstGACAGCTGMskg--- ; cor=; Ncor= a 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

dyads_m5_shift0 (dyads_m5dyads_m5)
; dyads_m19 versus dyads_m5 (dyads_m5dyads_m5); m=6/26; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.916223; rvdGACAGCTGmsg---- ; cor=; Ncor= a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; dyads_m19 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=7/26; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.915403; rswGACAGCTGmsg---- ; cor=; Ncor= a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

dyads_m3_rc_shift0 (dyads_m3dyads_m3_rc)
; dyads_m19 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=8/26; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.914462; rrwGACAGCTGyTky--- ; cor=; Ncor= a 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

dyads_m8_rc_shift0 (dyads_m8dyads_m8_rc)
; dyads_m19 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=9/26; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.909851; mvrGACAGCTGwGsv--- ; cor=; Ncor= a 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 0 c 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 0 g 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 0 t 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; dyads_m19 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=10/26; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.872415; -vwGACAGCTGytkd--- ; cor=; Ncor= a 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; dyads_m19 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=11/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.870809; gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; dyads_m19 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=12/26; ncol2=14; w=14; offset=1; strand=D; shift=1; score=0.870723; -grgACAGCTGCtkm--- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

oligos_7nt_mkv2_m13_rc_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; dyads_m19 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=13/26; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.844947; grwGACAGCTGyTkyc-- ; cor=; Ncor= a 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; dyads_m19 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=14/26; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.824628; -cwGaCAGCTGtCwg--- ; cor=; Ncor= a 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 0 c 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 0 g 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 0 t 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; dyads_m19 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=15/26; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.813747; kkwsACAGCTGTTsys-- ; cor=; Ncor= a 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; dyads_m19 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=16/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.812212; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

dyads_m1_shift0 (dyads_m1dyads_m1)
; dyads_m19 versus dyads_m1 (dyads_m1dyads_m1); m=17/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.812212; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_8nt_mkv2_m10_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; dyads_m19 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=18/26; ncol2=17; w=15; offset=0; strand=D; shift=0; score=0.808446; rraGACAGCTGCTgyyy- ; cor=; Ncor= a 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

oligos_8nt_mkv2_m1_rc_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; dyads_m19 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=19/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.798678; krkGACAGCTGCTkhvb- ; cor=; Ncor= a 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_8nt_mkv2_m27_rc_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; dyads_m19 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=20/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.792794; drrGACAGCTGCTGhbb- ; cor=; Ncor= a 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

oligos_8nt_mkv2_m12_shift0 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; dyads_m19 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=21/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.772473; gmyGaCAGCTGtCrkc-- ; cor=; Ncor= a 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 0 c 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 0 g 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 0 t 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0 0

dyads_m2_shift0 (dyads_m2dyads_m2)
; dyads_m19 versus dyads_m2 (dyads_m2dyads_m2); m=22/26; ncol2=18; w=15; offset=0; strand=D; shift=0; score=0.710401; krrrACAGCTGCTGtcta ; cor=; Ncor= a 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m13_rc_shift0 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; dyads_m19 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=23/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.669005; bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; dyads_m19 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=24/26; ncol2=16; w=14; offset=1; strand=D; shift=1; score=0.662736; -rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; dyads_m19 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=25/26; ncol2=17; w=15; offset=0; strand=D; shift=0; score=0.653747; swsAACAGCTGCTGchm- ; cor=; Ncor= a 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

dyads_m25_shift1 (dyads_m25dyads_m25)
; dyads_m19 versus dyads_m25 (dyads_m25dyads_m25); m=26/26; ncol2=17; w=14; offset=1; strand=D; shift=1; score=0.595154; -dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

One-to-n matrix alignment; reference matrix: dyads_m31_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m31_shift0 (dyads_m31dyads_m31)
; dyads_m31 (dyads_m31dyads_m31); m=0 (reference); ncol1=26; shift=0; ncol=26; vsCGGssssscgssgssvcssCGCsr ; Alignment reference a 10 6 1 1 1 4 5 5 4 5 5 5 2 4 6 4 6 10 3 5 5 1 1 2 7 9 c 10 11 30 3 3 10 13 14 15 12 20 8 19 11 7 16 9 10 19 17 17 31 2 31 12 6 g 11 12 4 32 30 17 16 11 13 13 6 18 12 14 17 12 17 10 8 10 11 4 33 1 10 14 t 5 7 1 0 2 5 2 6 4 6 5 5 3 7 6 4 4 6 6 4 3 0 0 2 7 7

dyads_m31_shift0 (dyads_m31dyads_m31)
; dyads_m31 versus dyads_m31 (dyads_m31dyads_m31); m=1/3; ncol2=26; w=26; offset=0; strand=D; shift=0; score= 1; vsCGGssssscgssgssvcssCGCsr ; cor=; Ncor= a 10 6 1 1 1 4 5 5 4 5 5 5 2 4 6 4 6 10 3 5 5 1 1 2 7 9 c 10 11 30 3 3 10 13 14 15 12 20 8 19 11 7 16 9 10 19 17 17 31 2 31 12 6 g 11 12 4 32 30 17 16 11 13 13 6 18 12 14 17 12 17 10 8 10 11 4 33 1 10 14 t 5 7 1 0 2 5 2 6 4 6 5 5 3 7 6 4 4 6 6 4 3 0 0 2 7 7

dyads_m28_rc_shift2 (dyads_m28dyads_m28_rc)
; dyads_m31 versus dyads_m28_rc (dyads_m28dyads_m28_rc); m=2/3; ncol2=24; w=24; offset=2; strand=R; shift=2; score=0.727254; --ssGCGssssssssssssssCGCss ; cor=; Ncor= a 0 0 4 5 1 1 1 6 3 5 5 4 4 2 8 4 2 3 3 4 6 0 1 1 2 4 c 0 0 18 16 3 32 1 12 18 10 21 16 16 11 17 15 16 10 20 14 15 37 6 34 16 14 g 0 0 14 17 34 5 37 15 14 21 10 16 15 18 11 16 17 21 11 18 12 1 31 3 16 17 t 0 0 3 1 1 1 0 6 4 3 3 3 4 8 3 4 4 5 5 3 6 1 1 1 5 4

dyads_m34_rc_shift0 (dyads_m34dyads_m34_rc)
; dyads_m31 versus dyads_m34_rc (dyads_m34dyads_m34_rc); m=3/3; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.440631; sbCGGsssygCGTss----------- ; cor=; Ncor= a 3 2 0 0 0 3 1 3 2 2 0 0 1 3 4 0 0 0 0 0 0 0 0 0 0 0 c 8 7 21 2 3 9 11 9 7 5 20 0 2 7 10 0 0 0 0 0 0 0 0 0 0 0 g 8 6 0 19 15 7 7 7 4 11 1 21 3 7 6 0 0 0 0 0 0 0 0 0 0 0 t 2 6 0 0 3 2 2 2 8 3 0 0 15 4 1 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m25_shift1 ; 18 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m25_shift1 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=0 (reference); ncol1=12; shift=1; ncol=18; -gvAACAGTTGcr----- ; Alignment reference a 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 0 c 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 0 g 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 0 t 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0 0

oligos_8nt_mkv2_m25_shift1 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_8nt_mkv2_m25 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=1/17; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 1; -gvAACAGTTGcr----- ; cor=; Ncor= a 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 0 c 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 0 g 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 0 t 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0 0

oligos_7nt_mkv2_m12_shift2 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_8nt_mkv2_m25 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=2/17; ncol2=11; w=11; offset=1; strand=D; shift=2; score=0.84999; --smACAGTTGym----- ; cor=; Ncor= a 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 0 c 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 0 g 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 0 t 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m25 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=3/17; ncol2=14; w=12; offset=0; strand=D; shift=1; score=0.651707; -grgACAGCTGCtkm--- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m25 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=4/17; ncol2=14; w=12; offset=0; strand=R; shift=1; score=0.607784; -vwGACAGCTGytkd--- ; cor=; Ncor= a 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

dyads_m5_shift0 (dyads_m5dyads_m5)
; oligos_8nt_mkv2_m25 versus dyads_m5 (dyads_m5dyads_m5); m=5/17; ncol2=14; w=12; offset=-1; strand=D; shift=0; score=0.600963; rvdGACAGCTGmsg---- ; cor=; Ncor= a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m25 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=6/17; ncol2=14; w=12; offset=-1; strand=D; shift=0; score=0.600448; rswGACAGCTGmsg---- ; cor=; Ncor= a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m25 versus dyads_m36 (dyads_m36dyads_m36); m=7/17; ncol2=15; w=12; offset=-1; strand=D; shift=0; score=0.596803; rvkGACAGCTGctks--- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

dyads_m3_shift1 (dyads_m3dyads_m3)
; oligos_8nt_mkv2_m25 versus dyads_m3 (dyads_m3dyads_m3); m=8/17; ncol2=15; w=12; offset=0; strand=D; shift=1; score=0.574341; -rmArCAGCTGTCwyy-- ; cor=; Ncor= a 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 0 0 c 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 0 0 g 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 0 0 t 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m25 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=9/17; ncol2=16; w=12; offset=-1; strand=D; shift=0; score=0.554821; gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_8nt_mkv2_m25 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=10/17; ncol2=16; w=12; offset=-1; strand=D; shift=0; score=0.553665; srsAACAGCTGTswmm-- ; cor=; Ncor= a 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 0 0 c 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 0 0 g 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 0 0 t 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3 0 0

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m25 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=11/17; ncol2=17; w=12; offset=-1; strand=D; shift=0; score=0.553124; swsAACAGCTGCTGchm- ; cor=; Ncor= a 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m25 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=12/17; ncol2=16; w=12; offset=0; strand=D; shift=1; score=0.547171; -rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

dyads_m25_shift1 (dyads_m25dyads_m25)
; oligos_8nt_mkv2_m25 versus dyads_m25 (dyads_m25dyads_m25); m=13/17; ncol2=17; w=12; offset=0; strand=D; shift=1; score=0.547102; -dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

oligos_8nt_mkv2_m13_rc_shift0 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m25 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=14/17; ncol2=17; w=12; offset=-1; strand=R; shift=0; score=0.546616; bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_7nt_mkv2_m13_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_8nt_mkv2_m25 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=15/17; ncol2=16; w=12; offset=-1; strand=D; shift=0; score=0.545307; grmArCAGCTGTCwyc-- ; cor=; Ncor= a 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 0 0 c 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 0 0 g 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 0 0 t 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5 0 0

oligos_8nt_mkv2_m27_rc_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m25 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=16/17; ncol2=17; w=12; offset=-1; strand=R; shift=0; score=0.510146; drrGACAGCTGCTGhbb- ; cor=; Ncor= a 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

dyads_m2_shift0 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m25 versus dyads_m2 (dyads_m2dyads_m2); m=17/17; ncol2=18; w=12; offset=-1; strand=D; shift=0; score=0.478767; krrrACAGCTGCTGtcta ; cor=; Ncor= a 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m24_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m24_shift1 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24)
; oligos_8nt_mkv2_m24 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24); m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTAAATAAAaw ; Alignment reference a 0 11 13 1 31 31 23 1 29 29 28 16 11 c 0 4 1 1 0 0 1 0 0 2 0 4 6 g 0 3 6 2 0 0 1 1 2 1 2 5 2 t 0 14 12 28 1 1 7 30 1 0 2 7 13

oligos_8nt_mkv2_m24_shift1 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24)
; oligos_8nt_mkv2_m24 versus oligos_8nt_mkv2_m24 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24); m=1/4; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 1; -wwTAAATAAAaw ; cor=; Ncor= a 0 11 13 1 31 31 23 1 29 29 28 16 11 c 0 4 1 1 0 0 1 0 0 2 0 4 6 g 0 3 6 2 0 0 1 1 2 1 2 5 2 t 0 14 12 28 1 1 7 30 1 0 2 7 13

oligos_7nt_mkv2_m9_shift1 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9)
; oligos_8nt_mkv2_m24 versus oligos_7nt_mkv2_m9 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9); m=2/4; ncol2=11; w=11; offset=0; strand=D; shift=1; score=0.851868; -wtTAAATAAag- ; cor=; Ncor= a 0 4 3 0 12 12 13 1 13 12 6 3 0 c 0 3 3 0 0 0 0 0 0 1 3 1 0 g 0 1 3 0 1 0 0 0 0 0 2 6 0 t 0 5 4 13 0 1 0 12 0 0 2 3 0

dyads_m38_shift0 (dyads_m38dyads_m38)
; oligos_8nt_mkv2_m24 versus dyads_m38 (dyads_m38dyads_m38); m=3/4; ncol2=12; w=11; offset=-1; strand=D; shift=0; score=0.783514; twTTAAATAAww- ; cor=; Ncor= a 6 9 3 0 27 27 22 3 26 27 12 8 0 c 7 5 1 0 0 1 1 0 0 0 3 6 0 g 5 3 2 1 0 1 2 0 1 1 5 6 0 t 11 12 23 28 2 0 4 26 2 1 9 9 0

dyads_m16_shift0 (dyads_m16dyads_m16)
; oligos_8nt_mkv2_m24 versus dyads_m16 (dyads_m16dyads_m16); m=4/4; ncol2=12; w=11; offset=-1; strand=D; shift=0; score=0.708821; ttTTAATTAAaa- ; cor=; Ncor= a 6 6 0 1 24 23 3 1 27 26 14 12 0 c 4 4 0 0 3 1 1 0 0 2 4 6 0 g 6 4 2 0 0 1 1 3 0 0 4 4 0 t 12 14 26 27 1 3 23 24 1 0 6 6 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m12_shift2 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m12_shift2 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=0 (reference); ncol1=11; shift=2; ncol=17; --smACAGTTGym---- ; Alignment reference a 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

oligos_7nt_mkv2_m12_shift2 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_7nt_mkv2_m12 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=1/12; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 1; --smACAGTTGym---- ; cor=; Ncor= a 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

oligos_8nt_mkv2_m25_shift1 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_7nt_mkv2_m12 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=2/12; ncol2=12; w=11; offset=-1; strand=D; shift=1; score=0.84999; -gvAACAGTTGcr---- ; cor=; Ncor= a 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m12 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=3/12; ncol2=14; w=11; offset=-1; strand=D; shift=1; score=0.583235; -hmarCAGCTGTCwb-- ; cor=; Ncor= a 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 0 c 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 0 g 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 0 t 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m12 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=4/12; ncol2=14; w=11; offset=-1; strand=D; shift=1; score=0.561346; -grgACAGCTGCtkm-- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

dyads_m3_shift1 (dyads_m3dyads_m3)
; oligos_7nt_mkv2_m12 versus dyads_m3 (dyads_m3dyads_m3); m=5/12; ncol2=15; w=11; offset=-1; strand=D; shift=1; score=0.532562; -rmArCAGCTGTCwyy- ; cor=; Ncor= a 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 0 c 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 0 g 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 0 t 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6 0

dyads_m8_shift1 (dyads_m8dyads_m8)
; oligos_7nt_mkv2_m12 versus dyads_m8 (dyads_m8dyads_m8); m=6/12; ncol2=15; w=11; offset=-1; strand=D; shift=1; score=0.530588; -bsCwCAGCTGTCybk- ; cor=; Ncor= a 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 0 c 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 0 g 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 0 t 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; oligos_7nt_mkv2_m12 versus dyads_m36 (dyads_m36dyads_m36); m=7/12; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=0.525172; rvkGACAGCTGctks-- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m12 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=8/12; ncol2=16; w=11; offset=-2; strand=D; shift=0; score=0.516408; srsAACAGCTGTswmm- ; cor=; Ncor= a 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 0 c 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 0 g 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 0 t 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3 0

oligos_7nt_mkv2_m13_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_7nt_mkv2_m12 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=9/12; ncol2=16; w=11; offset=-2; strand=D; shift=0; score=0.500221; grmArCAGCTGTCwyc- ; cor=; Ncor= a 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 0 c 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 0 g 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 0 t 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5 0

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_7nt_mkv2_m12 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=10/12; ncol2=16; w=11; offset=-1; strand=D; shift=1; score=0.491725; -rgmACAGCTGCTGcws ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_7nt_mkv2_m12 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=11/12; ncol2=17; w=11; offset=-2; strand=D; shift=0; score=0.468748; swsAACAGCTGCTGchm ; cor=; Ncor= a 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

oligos_8nt_mkv2_m13_rc_shift0 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_7nt_mkv2_m12 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=12/12; ncol2=17; w=11; offset=-2; strand=R; shift=0; score=0.46688; bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6

One-to-n matrix alignment; reference matrix: dyads_m32_shift1 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m32_shift1 (dyads_m32dyads_m32)
; dyads_m32 (dyads_m32dyads_m32); m=0 (reference); ncol1=25; shift=1; ncol=26; -rCACAcTGTAGGACcTGrAATATGg ; Alignment reference a 0 30 7 83 1 84 8 4 5 10 72 8 19 66 4 13 5 14 22 68 60 0 84 0 4 14 c 0 6 64 0 82 0 56 5 3 3 4 9 3 4 65 37 10 3 6 3 7 0 0 0 4 6 g 0 42 4 1 1 0 14 5 58 6 5 63 60 5 4 17 3 58 49 3 11 0 0 0 68 50 t 0 6 9 0 0 0 6 70 18 65 3 4 2 9 11 17 66 9 7 10 6 84 0 84 8 14

dyads_m32_shift1 (dyads_m32dyads_m32)
; dyads_m32 versus dyads_m32 (dyads_m32dyads_m32); m=1/6; ncol2=25; w=25; offset=0; strand=D; shift=1; score= 1; -rCACAcTGTAGGACcTGrAATATGg ; cor=; Ncor= a 0 30 7 83 1 84 8 4 5 10 72 8 19 66 4 13 5 14 22 68 60 0 84 0 4 14 c 0 6 64 0 82 0 56 5 3 3 4 9 3 4 65 37 10 3 6 3 7 0 0 0 4 6 g 0 42 4 1 1 0 14 5 58 6 5 63 60 5 4 17 3 58 49 3 11 0 0 0 68 50 t 0 6 9 0 0 0 6 70 18 65 3 4 2 9 11 17 66 9 7 10 6 84 0 84 8 14

dyads_m14_rc_shift5 (dyads_m14dyads_m14_rc)
; dyads_m32 versus dyads_m14_rc (dyads_m14dyads_m14_rc); m=2/6; ncol2=21; w=21; offset=4; strand=R; shift=5; score=0.805402; -----AcTGTAGgACmtgGwaTATGg ; cor=; Ncor= a 0 0 0 0 0 68 13 0 1 0 66 6 20 69 4 27 6 13 8 57 60 0 90 0 5 18 c 0 0 0 0 0 2 54 0 0 0 2 9 5 3 67 36 10 5 9 2 11 0 0 0 14 1 g 0 0 0 0 0 4 7 0 89 0 14 64 58 3 5 9 16 51 67 3 16 1 0 0 64 52 t 0 0 0 0 0 16 16 90 0 90 8 11 7 15 14 18 58 21 6 28 3 89 0 90 7 19

dyads_m18_rc_shift7 (dyads_m18dyads_m18_rc)
; dyads_m32 versus dyads_m18_rc (dyads_m18dyads_m18_rc); m=3/6; ncol2=19; w=19; offset=6; strand=R; shift=7; score=0.745917; -------TGTAGGACmTGGAATATGG ; cor=; Ncor= a 0 0 0 0 0 0 0 6 6 1 93 0 15 79 10 24 4 5 20 72 76 1 94 0 3 20 c 0 0 0 0 0 0 0 3 3 0 1 0 8 8 78 37 1 3 4 4 6 0 0 0 17 1 g 0 0 0 0 0 0 0 6 67 0 0 95 69 6 4 18 16 65 65 3 10 0 0 0 72 65 t 0 0 0 0 0 0 0 80 19 94 1 0 3 2 3 16 74 22 6 16 3 94 1 95 3 9

dyads_m6_shift0 (dyads_m6dyads_m6)
; dyads_m32 versus dyads_m6 (dyads_m6dyads_m6); m=4/6; ncol2=14; w=13; offset=-1; strand=D; shift=0; score=0.488819; trCACACTgTAGrA------------ ; cor=; Ncor= a 16 34 0 92 0 80 5 4 5 0 92 0 25 78 0 0 0 0 0 0 0 0 0 0 0 0 c 15 19 91 0 92 1 72 7 6 0 0 0 7 5 0 0 0 0 0 0 0 0 0 0 0 0 g 10 36 0 0 0 3 8 5 62 1 0 92 59 1 0 0 0 0 0 0 0 0 0 0 0 0 t 51 3 1 0 0 8 7 76 19 91 0 0 1 8 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m23_shift1 (dyads_m23dyads_m23)
; dyads_m32 versus dyads_m23 (dyads_m23dyads_m23); m=5/6; ncol2=12; w=12; offset=0; strand=D; shift=1; score=0.45898; -gMACAcTGTAGr------------- ; cor=; Ncor= a 0 21 26 95 0 95 5 6 0 0 95 10 47 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 21 67 0 95 0 55 1 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 50 0 0 0 0 14 4 95 0 0 67 44 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 3 2 0 0 0 21 84 0 95 0 16 1 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m26_rc_shift0 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)
; dyads_m32 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=6/6; ncol2=12; w=11; offset=-1; strand=R; shift=0; score=0.41068; trCACACTGTAG-------------- ; cor=; Ncor= a 19 40 0 87 0 87 1 4 5 0 65 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 9 18 79 0 86 0 85 0 1 0 1 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 3 24 0 0 0 0 0 1 69 0 7 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 56 5 8 0 1 0 1 82 12 87 14 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift13 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift13 (dyads_m6dyads_m6)
; dyads_m6 (dyads_m6dyads_m6); m=0 (reference); ncol1=14; shift=13; ncol=27; -------------trCACACTgTAGrA ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 78 c 0 0 0 0 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 5 g 0 0 0 0 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1 8

dyads_m6_shift13 (dyads_m6dyads_m6)
; dyads_m6 versus dyads_m6 (dyads_m6dyads_m6); m=1/9; ncol2=14; w=14; offset=0; strand=D; shift=13; score= 1; -------------trCACACTgTAGrA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 78 c 0 0 0 0 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 5 g 0 0 0 0 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1 8

oligos_8nt_mkv2_m26_rc_shift13 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)
; dyads_m6 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=2/9; ncol2=12; w=12; offset=0; strand=R; shift=13; score=0.831536; -------------trCACACTGTAG-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 19 40 0 87 0 87 1 4 5 0 65 8 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 79 0 86 0 85 0 1 0 1 10 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 3 24 0 0 0 0 0 1 69 0 7 63 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 56 5 8 0 1 0 1 82 12 87 14 6 0 0

dyads_m23_shift14 (dyads_m23dyads_m23)
; dyads_m6 versus dyads_m23 (dyads_m23dyads_m23); m=3/9; ncol2=12; w=12; offset=1; strand=D; shift=14; score=0.811881; --------------gMACAcTGTAGr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1 0

dyads_m33_shift16 (dyads_m33dyads_m33)
; dyads_m6 versus dyads_m33 (dyads_m33dyads_m33); m=4/9; ncol2=10; w=10; offset=3; strand=D; shift=16; score=0.686708; ----------------ACACTGTAGr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 1 76 0 0 0 0 76 5 21 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 68 0 76 0 0 0 0 3 6 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1 76 0 0 66 48 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 75 0 76 0 2 1 0

dyads_m20_rc_shift4 (dyads_m20dyads_m20_rc)
; dyads_m6 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=5/9; ncol2=23; w=14; offset=-9; strand=R; shift=4; score=0.596039; ----AATGAGAAAtrCACACTkTAGGA ; cor=; Ncor= a 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 4 0 60 0 10 48 c 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 3 0 0 0 3 4 g 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 35 0 0 60 44 0 t 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46 18 60 0 0 3 8

dyads_m40_shift2 (dyads_m40dyads_m40)
; dyads_m6 versus dyads_m40 (dyads_m40dyads_m40); m=6/9; ncol2=25; w=14; offset=-11; strand=D; shift=2; score=0.548362; --AAAATGAGAAATrCACAcTkTAGGA ; cor=; Ncor= a 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 14 54 c 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 3 5 g 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 45 2 t 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0 2 3

dyads_m32_shift14 (dyads_m32dyads_m32)
; dyads_m6 versus dyads_m32 (dyads_m32dyads_m32); m=7/9; ncol2=25; w=13; offset=1; strand=D; shift=14; score=0.488819; --------------rCACAcTGTAGGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 7 83 1 84 8 4 5 10 72 8 19 66 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 64 0 82 0 56 5 3 3 4 9 3 4 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 4 1 1 0 14 5 58 6 5 63 60 5 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 9 0 0 0 6 70 18 65 3 4 2 9

dyads_m9_shift0 (dyads_m9dyads_m9)
; dyads_m6 versus dyads_m9 (dyads_m9dyads_m9); m=8/9; ncol2=26; w=13; offset=-13; strand=D; shift=0; score=0.455525; GrAAAwtrarAAAtgcaCAcTGTAGr- ; cor=; Ncor= a 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 24 0 c 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 6 0 g 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 47 0 t 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13 10 0

oligos_8nt_mkv2_m11_shift8 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11)
; dyads_m6 versus oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=9/9; ncol2=13; w=8; offset=-5; strand=D; shift=8; score=0.403134; --------AGAAATRCACACT------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 59 4 71 72 71 0 18 0 68 0 72 1 3 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 2 1 0 0 2 2 71 1 72 0 52 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 63 0 0 0 1 50 0 1 0 0 9 3 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 10 3 0 0 1 69 2 1 2 0 0 10 66 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m10_shift1 ; 29 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=0 (reference); ncol1=17; shift=1; ncol=18; -rraGACAGCTGCTgyyy ; Alignment reference a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6

oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=1/28; ncol2=17; w=17; offset=0; strand=D; shift=1; score= 1; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6

oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=2/28; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.979057; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7

oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=3/28; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.969232; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m10 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=4/28; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.920197; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0

dyads_m2_shift1 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m10 versus dyads_m2 (dyads_m2dyads_m2); m=5/28; ncol2=18; w=17; offset=0; strand=D; shift=1; score=0.895694; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m10 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=6/28; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.886592; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0

oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=7/28; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.866139; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4

oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=8/28; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.86254; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6

oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=9/28; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.848932; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; oligos_8nt_mkv2_m10 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=10/28; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.836515; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0

oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m10 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=11/28; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.832416; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0

dyads_m36_shift1 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m10 versus dyads_m36 (dyads_m36dyads_m36); m=12/28; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.827072; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; oligos_8nt_mkv2_m10 versus dyads_m19 (dyads_m19dyads_m19); m=13/28; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.808446; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m10 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=14/28; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.799103; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=15/28; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.784719; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=16/28; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.783611; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0

dyads_m25_shift2 (dyads_m25dyads_m25)
; oligos_8nt_mkv2_m10 versus dyads_m25 (dyads_m25dyads_m25); m=17/28; ncol2=17; w=16; offset=1; strand=D; shift=2; score=0.758892; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8

oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m10 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=18/28; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.752153; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0

oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=19/28; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.740305; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0

dyads_m5_shift1 (dyads_m5dyads_m5)
; oligos_8nt_mkv2_m10 versus dyads_m5 (dyads_m5dyads_m5); m=20/28; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.728933; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m10 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=21/28; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.727971; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; oligos_8nt_mkv2_m10 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=22/28; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.714878; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=23/28; ncol2=18; w=17; offset=-1; strand=D; shift=0; score=0.670588; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2

dyads_m1_shift1 (dyads_m1dyads_m1)
; oligos_8nt_mkv2_m10 versus dyads_m1 (dyads_m1dyads_m1); m=24/28; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.662618; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_8nt_mkv2_m10 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=25/28; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.662618; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

dyads_m21_shift2 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m10 versus dyads_m21 (dyads_m21dyads_m21); m=26/28; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.627824; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0

oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m10 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=27/28; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.609995; --cwGaCAGCTGtCwg-- ; cor=; Ncor= a 0 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 c 0 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 t 0 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0

oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)
; oligos_8nt_mkv2_m10 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=28/28; ncol2=12; w=12; offset=3; strand=R; shift=4; score=0.50397; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m18_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m18_shift5 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18)
; oligos_8nt_mkv2_m18 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18); m=0 (reference); ncol1=12; shift=5; ncol=17; -----rsATTTsTAAAw ; Alignment reference a 0 0 0 0 0 16 3 28 0 1 0 0 0 28 23 24 7 c 0 0 0 0 0 0 17 0 0 0 0 15 0 0 0 2 1 g 0 0 0 0 0 10 7 0 0 0 0 12 0 0 5 1 2 t 0 0 0 0 0 2 1 0 28 27 28 1 28 0 0 1 18

oligos_8nt_mkv2_m18_shift5 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18)
; oligos_8nt_mkv2_m18 versus oligos_8nt_mkv2_m18 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18); m=1/3; ncol2=12; w=12; offset=0; strand=D; shift=5; score= 1; -----rsATTTsTAAAw ; cor=; Ncor= a 0 0 0 0 0 16 3 28 0 1 0 0 0 28 23 24 7 c 0 0 0 0 0 0 17 0 0 0 0 15 0 0 0 2 1 g 0 0 0 0 0 10 7 0 0 0 0 12 0 0 5 1 2 t 0 0 0 0 0 2 1 0 28 27 28 1 28 0 0 1 18

dyads_m22_rc_shift4 (dyads_m22dyads_m22_rc)
; oligos_8nt_mkv2_m18 versus dyads_m22_rc (dyads_m22dyads_m22_rc); m=2/3; ncol2=10; w=9; offset=-1; strand=R; shift=4; score=0.526517; ----asCATTTGkw--- ; cor=; Ncor= a 0 0 0 0 6 4 0 21 0 0 0 0 3 6 0 0 0 c 0 0 0 0 5 6 21 0 0 0 0 0 2 1 0 0 0 g 0 0 0 0 5 10 0 0 0 0 0 21 7 3 0 0 0 t 0 0 0 0 5 1 0 0 21 21 21 0 9 11 0 0 0

oligos_8nt_mkv2_m11_rc_shift0 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc)
; oligos_8nt_mkv2_m18 versus oligos_8nt_mkv2_m11_rc (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc); m=3/3; ncol2=13; w=8; offset=-5; strand=R; shift=0; score=0.411758; AGTGTGYATTTCT---- ; cor=; Ncor= a 66 10 0 0 2 1 2 69 1 0 0 3 10 0 0 0 0 c 3 9 0 0 1 0 50 1 0 0 0 63 3 0 0 0 0 g 0 52 0 72 1 71 2 2 0 0 1 2 0 0 0 0 0 t 3 1 72 0 68 0 18 0 71 72 71 4 59 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 28 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=0 (reference); ncol1=14; shift=0; ncol=18; rswGACAGCTGmsg---- ; Alignment reference a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=1/27; ncol2=14; w=14; offset=0; strand=D; shift=0; score= 1; rswGACAGCTGmsg---- ; cor=; Ncor= a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

dyads_m5_shift0 (dyads_m5dyads_m5)
; oligos_7nt_mkv2_m4 versus dyads_m5 (dyads_m5dyads_m5); m=2/27; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.999419; rvdGACAGCTGmsg---- ; cor=; Ncor= a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

dyads_m19_shift0 (dyads_m19dyads_m19)
; oligos_7nt_mkv2_m4 versus dyads_m19 (dyads_m19dyads_m19); m=3/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.915403; rvdGACAGCTGvyks--- ; cor=; Ncor= a 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=4/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.911197; rstGACAGCTGMskg--- ; cor=; Ncor= a 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; oligos_7nt_mkv2_m4 versus dyads_m36 (dyads_m36dyads_m36); m=5/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.905622; rvkGACAGCTGctks--- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

oligos_8nt_mkv2_m22_shift0 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=6/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.901383; rvtGACAGCTGmhkg--- ; cor=; Ncor= a 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m17_shift0 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=7/27; ncol2=15; w=14; offset=0; strand=D; shift=0; score=0.901244; rstGACAGCTGmhkg--- ; cor=; Ncor= a 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

dyads_m8_rc_shift0 (dyads_m8dyads_m8_rc)
; oligos_7nt_mkv2_m4 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=8/27; ncol2=15; w=14; offset=0; strand=R; shift=0; score=0.852935; mvrGACAGCTGwGsv--- ; cor=; Ncor= a 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 0 c 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 0 g 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 0 t 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0 0

dyads_m3_rc_shift0 (dyads_m3dyads_m3_rc)
; oligos_7nt_mkv2_m4 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=9/27; ncol2=15; w=14; offset=0; strand=R; shift=0; score=0.828216; rrwGACAGCTGyTky--- ; cor=; Ncor= a 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=10/27; ncol2=14; w=13; offset=1; strand=R; shift=1; score=0.80045; -vwGACAGCTGytkd--- ; cor=; Ncor= a 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=11/27; ncol2=14; w=13; offset=1; strand=D; shift=1; score=0.796612; -grgACAGCTGCtkm--- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=12/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.790768; gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=13/27; ncol2=14; w=13; offset=1; strand=D; shift=1; score=0.771906; -cwGaCAGCTGtCwg--- ; cor=; Ncor= a 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 0 0 c 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 0 0 g 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 0 0 t 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0 0 0

oligos_7nt_mkv2_m13_rc_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/27; ncol2=16; w=14; offset=0; strand=R; shift=0; score=0.765491; grwGACAGCTGyTkyc-- ; cor=; Ncor= a 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

dyads_m1_shift0 (dyads_m1dyads_m1)
; oligos_7nt_mkv2_m4 versus dyads_m1 (dyads_m1dyads_m1); m=15/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.759761; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=16/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.759761; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=17/27; ncol2=16; w=14; offset=0; strand=R; shift=0; score=0.744923; kkwsACAGCTGTTsys-- ; cor=; Ncor= a 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

oligos_8nt_mkv2_m12_shift0 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=18/27; ncol2=16; w=14; offset=0; strand=D; shift=0; score=0.740561; gmyGaCAGCTGtCrkc-- ; cor=; Ncor= a 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 0 c 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 0 g 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 0 t 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0 0

oligos_8nt_mkv2_m1_rc_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=19/27; ncol2=17; w=14; offset=0; strand=R; shift=0; score=0.732546; krkGACAGCTGCTkhvb- ; cor=; Ncor= a 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_8nt_mkv2_m10_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=20/27; ncol2=17; w=14; offset=0; strand=D; shift=0; score=0.727971; rraGACAGCTGCTgyyy- ; cor=; Ncor= a 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

oligos_8nt_mkv2_m27_rc_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=21/27; ncol2=17; w=14; offset=0; strand=R; shift=0; score=0.721739; drrGACAGCTGCTGhbb- ; cor=; Ncor= a 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

dyads_m2_shift0 (dyads_m2dyads_m2)
; oligos_7nt_mkv2_m4 versus dyads_m2 (dyads_m2dyads_m2); m=22/27; ncol2=18; w=14; offset=0; strand=D; shift=0; score=0.658408; krrrACAGCTGCTGtcta ; cor=; Ncor= a 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m13_rc_shift0 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=23/27; ncol2=17; w=14; offset=0; strand=R; shift=0; score=0.625014; bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=24/27; ncol2=17; w=14; offset=0; strand=D; shift=0; score=0.621102; swsAACAGCTGCTGchm- ; cor=; Ncor= a 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=25/27; ncol2=16; w=13; offset=1; strand=D; shift=1; score=0.618683; -rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

oligos_8nt_mkv2_m25_shift1 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=26/27; ncol2=12; w=12; offset=1; strand=D; shift=1; score=0.600448; -gvAACAGTTGcr----- ; cor=; Ncor= a 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 0 c 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 0 g 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 0 t 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0 0

dyads_m25_shift1 (dyads_m25dyads_m25)
; oligos_7nt_mkv2_m4 versus dyads_m25 (dyads_m25dyads_m25); m=27/27; ncol2=17; w=13; offset=1; strand=D; shift=1; score=0.560227; -dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

One-to-n matrix alignment; reference matrix: dyads_m12_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m12_shift0 (dyads_m12dyads_m12)
; dyads_m12 (dyads_m12dyads_m12); m=0 (reference); ncol1=14; shift=0; ncol=14; vssCCSCGCSGGss ; Alignment reference a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m12_shift0 (dyads_m12dyads_m12)
; dyads_m12 versus dyads_m12 (dyads_m12dyads_m12); m=1/8; ncol2=14; w=14; offset=0; strand=D; shift=0; score= 1; vssCCSCGCSGGss ; cor=; Ncor= a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0

oligos_6nt_mkv2_m6_shift3 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)
; dyads_m12 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=2/8; ncol2=11; w=11; offset=3; strand=D; shift=3; score=0.743492; ---ssCCGCCGGGs ; cor=; Ncor= a 0 0 0 3 2 1 0 0 0 0 0 2 2 4 c 0 0 0 11 13 21 25 1 23 22 3 3 4 10 g 0 0 0 10 9 3 1 25 3 4 23 20 18 11 t 0 0 0 2 2 1 0 0 0 0 0 1 2 1

oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; dyads_m12 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=3/8; ncol2=11; w=11; offset=2; strand=D; shift=2; score=0.729556; --ssCCCGCCGsg- ; cor=; Ncor= a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; dyads_m12 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=4/8; ncol2=10; w=10; offset=1; strand=D; shift=1; score=0.664288; -ssCCCCGCsg--- ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 2 1 0 0 0 c 0 10 7 23 21 23 24 0 25 8 6 0 0 0 g 0 11 9 2 4 2 1 25 0 9 15 0 0 0 t 0 4 6 0 0 0 0 0 0 6 3 0 0 0

oligos_8nt_mkv2_m15_rc_shift2 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15_rc)
; dyads_m12 versus oligos_8nt_mkv2_m15_rc (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15_rc); m=5/8; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.651999; --ssCgCGGCGGgb ; cor=; Ncor= a 0 0 2 0 0 1 0 0 0 0 0 0 2 0 c 0 0 7 8 14 2 13 2 1 14 0 0 3 4 g 0 0 4 5 0 9 1 12 12 0 13 14 9 6 t 0 0 1 1 0 2 0 0 1 0 1 0 0 4

oligos_7nt_mkv2_m7_shift2 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)
; dyads_m12 versus oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=6/8; ncol2=11; w=11; offset=2; strand=D; shift=2; score=0.626799; --ssCCCGGCGss- ; cor=; Ncor= a 0 0 4 5 1 1 0 0 3 2 0 4 4 0 c 0 0 17 11 34 29 32 4 5 33 0 11 14 0 g 0 0 11 14 1 3 4 32 28 1 33 17 16 0 t 0 0 4 6 0 3 0 0 0 0 3 4 2 0

dyads_m26_rc_shift2 (dyads_m26dyads_m26_rc)
; dyads_m12 versus dyads_m26_rc (dyads_m26dyads_m26_rc); m=7/8; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.62499; --ssCGCsgCGGsg ; cor=; Ncor= a 0 0 2 3 0 1 2 1 3 0 0 0 3 2 c 0 0 16 12 25 2 24 11 6 26 1 2 10 6 g 0 0 8 10 3 24 2 13 15 1 27 25 15 19 t 0 0 2 3 0 1 0 3 4 1 0 1 0 1

dyads_m30_shift1 (dyads_m30dyads_m30)
; dyads_m12 versus dyads_m30 (dyads_m30dyads_m30); m=8/8; ncol2=11; w=11; offset=1; strand=D; shift=1; score=0.566606; -ymCCCMGCCyr-- ; cor=; Ncor= a 0 2 4 0 0 0 8 0 0 0 2 3 0 0 c 0 3 3 11 11 11 3 0 11 11 4 2 0 0 g 0 2 2 0 0 0 0 11 0 0 2 4 0 0 t 0 4 2 0 0 0 0 0 0 0 3 2 0 0

One-to-n matrix alignment; reference matrix: dyads_m1_shift1 ; 20 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift1 (dyads_m1dyads_m1)
; dyads_m1 (dyads_m1dyads_m1); m=0 (reference); ncol1=16; shift=1; ncol=17; -vmwGaCAGCTGtCwkb ; Alignment reference a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; dyads_m1 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=1/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m1_shift1 (dyads_m1dyads_m1)
; dyads_m1 versus dyads_m1 (dyads_m1dyads_m1); m=2/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; dyads_m1 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=3/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.928003; -gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; dyads_m1 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=4/19; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.868996; --cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; dyads_m1 versus dyads_m19 (dyads_m19dyads_m19); m=5/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.812212; -rvdGACAGCTGvyks- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; dyads_m1 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=6/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.808909; -rvtGACAGCTGmhkg- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0

oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; dyads_m1 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=7/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.805464; -rstGACAGCTGmhkg- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0

oligos_8nt_mkv2_m3_rc_shift2 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; dyads_m1 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=8/19; ncol2=15; w=15; offset=1; strand=R; shift=2; score=0.801669; --cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

dyads_m36_shift1 (dyads_m36dyads_m36)
; dyads_m1 versus dyads_m36 (dyads_m36dyads_m36); m=9/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.774901; -rvkGACAGCTGctks- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; dyads_m1 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=10/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.764901; -srsAACAGCTGTswmm ; cor=; Ncor= a 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

dyads_m8_shift2 (dyads_m8dyads_m8)
; dyads_m1 versus dyads_m8 (dyads_m8dyads_m8); m=11/19; ncol2=15; w=15; offset=1; strand=D; shift=2; score=0.763334; --bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

dyads_m5_rc_shift3 (dyads_m5dyads_m5_rc)
; dyads_m1 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=12/19; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.760426; ---cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; dyads_m1 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=13/19; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.759761; ---cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; dyads_m1 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/19; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.756774; -grwGACAGCTGyTkyc ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; dyads_m1 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=15/19; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.748158; --hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; dyads_m1 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=16/19; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.737151; -akmAGCAGCTGTCysc ; cor=; Ncor= a 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)
; dyads_m1 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=17/19; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.726765; -rrwGACAGCTGyTky- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0

oligos_8nt_mkv2_m10_rc_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; dyads_m1 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=18/19; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.662618; rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; dyads_m1 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=19/19; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.655261; --kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

One-to-n matrix alignment; reference matrix: dyads_m37_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m37_shift0 (dyads_m37dyads_m37)
; dyads_m37 (dyads_m37dyads_m37); m=0 (reference); ncol1=11; shift=0; ncol=15; ksrCGyACGsv---- ; Alignment reference a 1 1 7 0 0 0 10 0 0 1 3 0 0 0 0 c 2 4 0 11 0 5 1 11 0 5 3 0 0 0 0 g 5 4 3 0 11 2 0 0 11 4 4 0 0 0 0 t 3 2 1 0 0 4 0 0 0 1 1 0 0 0 0

dyads_m37_shift0 (dyads_m37dyads_m37)
; dyads_m37 versus dyads_m37 (dyads_m37dyads_m37); m=1/2; ncol2=11; w=11; offset=0; strand=D; shift=0; score= 1; ksrCGyACGsv---- ; cor=; Ncor= a 1 1 7 0 0 0 10 0 0 1 3 0 0 0 0 c 2 4 0 11 0 5 1 11 0 5 3 0 0 0 0 g 5 4 3 0 11 2 0 0 11 4 4 0 0 0 0 t 3 2 1 0 0 4 0 0 0 1 1 0 0 0 0

dyads_m34_shift0 (dyads_m34dyads_m34)
; dyads_m37 versus dyads_m34 (dyads_m34dyads_m34); m=2/2; ncol2=15; w=11; offset=0; strand=D; shift=0; score=0.543919; ssACGcrsssCCGvs ; cor=; Ncor= a 1 4 15 0 0 3 8 2 2 2 3 0 0 6 2 c 6 7 3 21 1 11 4 7 7 7 15 19 0 6 8 g 10 7 2 0 20 5 7 9 11 9 3 2 21 7 8 t 4 3 1 0 0 2 2 3 1 3 0 0 0 2 3

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m21_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m21_shift1 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21)
; oligos_8nt_mkv2_m21 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21); m=0 (reference); ncol1=12; shift=1; ncol=21; -yTGTAGAACAkw-------- ; Alignment reference a 0 1 0 0 0 32 0 32 32 0 32 2 14 0 0 0 0 0 0 0 0 c 0 16 0 0 0 0 1 0 0 30 0 0 1 0 0 0 0 0 0 0 0 g 0 4 1 32 0 0 31 0 0 0 0 10 1 0 0 0 0 0 0 0 0 t 0 11 31 0 32 0 0 0 0 2 0 20 16 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m21_shift1 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21)
; oligos_8nt_mkv2_m21 versus oligos_8nt_mkv2_m21 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21); m=1/3; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 1; -yTGTAGAACAkw-------- ; cor=; Ncor= a 0 1 0 0 0 32 0 32 32 0 32 2 14 0 0 0 0 0 0 0 0 c 0 16 0 0 0 0 1 0 0 30 0 0 1 0 0 0 0 0 0 0 0 g 0 4 1 32 0 0 31 0 0 0 0 10 1 0 0 0 0 0 0 0 0 t 0 11 31 0 32 0 0 0 0 2 0 20 16 0 0 0 0 0 0 0 0

dyads_m14_rc_shift0 (dyads_m14dyads_m14_rc)
; oligos_8nt_mkv2_m21 versus dyads_m14_rc (dyads_m14dyads_m14_rc); m=2/3; ncol2=21; w=12; offset=-1; strand=R; shift=0; score=0.455219; AcTGTAGgACmtgGwaTATGg ; cor=; Ncor= a 68 13 0 1 0 66 6 20 69 4 27 6 13 8 57 60 0 90 0 5 18 c 2 54 0 0 0 2 9 5 3 67 36 10 5 9 2 11 0 0 0 14 1 g 4 7 0 89 0 14 64 58 3 5 9 16 51 67 3 16 1 0 0 64 52 t 16 16 90 0 90 8 11 7 15 14 18 58 21 6 28 3 89 0 90 7 19

dyads_m18_rc_shift2 (dyads_m18dyads_m18_rc)
; oligos_8nt_mkv2_m21 versus dyads_m18_rc (dyads_m18dyads_m18_rc); m=3/3; ncol2=19; w=11; offset=1; strand=R; shift=2; score=0.419833; --TGTAGGACmTGGAATATGG ; cor=; Ncor= a 0 0 6 6 1 93 0 15 79 10 24 4 5 20 72 76 1 94 0 3 20 c 0 0 3 3 0 1 0 8 8 78 37 1 3 4 4 6 0 0 0 17 1 g 0 0 6 67 0 0 95 69 6 4 18 16 65 65 3 10 0 0 0 72 65 t 0 0 80 19 94 1 0 3 2 3 16 74 22 6 16 3 94 1 95 3 9

One-to-n matrix alignment; reference matrix: dyads_m35_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m35_shift0 (dyads_m35dyads_m35)
; dyads_m35 (dyads_m35dyads_m35); m=0 (reference); ncol1=21; shift=0; ncol=21; hmACCyvsvmmcymhrACCcb ; Alignment reference a 7 11 27 0 0 6 7 6 9 10 7 4 1 10 9 14 26 0 0 6 6 c 11 13 0 28 28 10 11 7 8 10 12 16 11 12 7 6 1 28 27 14 7 g 2 2 1 0 0 5 7 11 7 6 5 2 6 4 4 8 1 0 1 5 7 t 8 2 0 0 0 7 3 4 4 2 4 6 10 2 8 0 0 0 0 3 8

dyads_m35_shift0 (dyads_m35dyads_m35)
; dyads_m35 versus dyads_m35 (dyads_m35dyads_m35); m=1/1; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 1; hmACCyvsvmmcymhrACCcb ; cor=; Ncor= a 7 11 27 0 0 6 7 6 9 10 7 4 1 10 9 14 26 0 0 6 6 c 11 13 0 28 28 10 11 7 8 10 12 16 11 12 7 6 1 28 27 14 7 g 2 2 1 0 0 5 7 11 7 6 5 2 6 4 4 8 1 0 1 5 7 t 8 2 0 0 0 7 3 4 4 2 4 6 10 2 8 0 0 0 0 3 8

One-to-n matrix alignment; reference matrix: dyads_m7_shift6 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift6 (dyads_m7dyads_m7)
; dyads_m7 (dyads_m7dyads_m7); m=0 (reference); ncol1=23; shift=6; ncol=29; ------mmACTkrAAAwcdTGrAAAATgA ; Alignment reference a 0 0 0 0 0 0 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 107 107 0 7 81 c 0 0 0 0 0 0 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 0 0 0 15 2 g 0 0 0 0 0 0 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 0 0 0 71 6 t 0 0 0 0 0 0 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4 0 0 107 14 18

dyads_m7_shift6 (dyads_m7dyads_m7)
; dyads_m7 versus dyads_m7 (dyads_m7dyads_m7); m=1/8; ncol2=23; w=23; offset=0; strand=D; shift=6; score= 1; ------mmACTkrAAAwcdTGrAAAATgA ; cor=; Ncor= a 0 0 0 0 0 0 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 107 107 0 7 81 c 0 0 0 0 0 0 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 0 0 0 15 2 g 0 0 0 0 0 0 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 0 0 0 71 6 t 0 0 0 0 0 0 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4 0 0 107 14 18

dyads_m24_shift10 (dyads_m24dyads_m24)
; dyads_m7 versus dyads_m24 (dyads_m24dyads_m24); m=2/8; ncol2=18; w=18; offset=4; strand=D; shift=10; score=0.638194; ----------ygRRAAAmsTGAAAAwyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 c 0 0 0 0 0 0 0 0 0 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 g 0 0 0 0 0 0 0 0 0 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 t 0 0 0 0 0 0 0 0 0 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0

oligos_8nt_mkv2_m14_shift15 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14)
; dyads_m7 versus oligos_8nt_mkv2_m14 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14); m=3/8; ncol2=12; w=12; offset=9; strand=D; shift=15; score=0.47877; ---------------AwCATGGAAAAT-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 68 46 1 74 0 1 0 81 83 73 78 3 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 79 0 11 2 0 0 0 0 3 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 9 0 80 83 1 0 0 0 1 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 3 0 72 0 0 1 0 10 2 79 0 0

oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; dyads_m7 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=4/8; ncol2=13; w=12; offset=-1; strand=D; shift=5; score=0.472281; -----WAmACTGAAAAwC----------- ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; dyads_m7 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=5/8; ncol2=11; w=11; offset=0; strand=D; shift=6; score=0.456224; ------AmACTGAAAAw------------ ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; dyads_m7 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=6/8; ncol2=12; w=12; offset=2; strand=R; shift=8; score= 0.4461; --------MsTGAAAAACrt--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0 0 0 0 0 0

dyads_m4_shift0 (dyads_m4dyads_m4)
; dyads_m7 versus dyads_m4 (dyads_m4dyads_m4); m=7/8; ncol2=21; w=15; offset=-6; strand=D; shift=0; score=0.432109; gCkRRAAAACTGAAAATCAyR-------- ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 0 0 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 0 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 0 0 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0 0 0 0 0 0

dyads_m10_rc_shift17 (dyads_m10dyads_m10_rc)
; dyads_m7 versus dyads_m10_rc (dyads_m10dyads_m10_rc); m=8/8; ncol2=15; w=12; offset=11; strand=R; shift=17; score=0.414247; -----------------CAtGGAAAATGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 50 2 1 0 72 55 56 56 3 0 71 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 8 12 0 0 0 2 4 10 1 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 9 14 71 72 0 10 9 4 2 72 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 5 44 0 0 0 5 3 2 66 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m17_shift0 ; 27 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m17_shift0 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=0 (reference); ncol1=15; shift=0; ncol=18; rstGACAGCTGmhkg--- ; Alignment reference a 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m17_shift0 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=1/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score= 1; rstGACAGCTGmhkg--- ; cor=; Ncor= a 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m22_shift0 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=2/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.999291; rvtGACAGCTGmhkg--- ; cor=; Ncor= a 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=3/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.974937; rstGACAGCTGMskg--- ; cor=; Ncor= a 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m17 versus dyads_m36 (dyads_m36dyads_m36); m=4/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.969149; rvkGACAGCTGctks--- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

dyads_m19_shift0 (dyads_m19dyads_m19)
; oligos_8nt_mkv2_m17 versus dyads_m19 (dyads_m19dyads_m19); m=5/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.967761; rvdGACAGCTGvyks--- ; cor=; Ncor= a 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m17 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=6/26; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.901244; rswGACAGCTGmsg---- ; cor=; Ncor= a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

dyads_m5_shift0 (dyads_m5dyads_m5)
; oligos_8nt_mkv2_m17 versus dyads_m5 (dyads_m5dyads_m5); m=7/26; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.899145; rvdGACAGCTGmsg---- ; cor=; Ncor= a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

dyads_m3_rc_shift0 (dyads_m3dyads_m3_rc)
; oligos_8nt_mkv2_m17 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=8/26; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.87481; rrwGACAGCTGyTky--- ; cor=; Ncor= a 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m17 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=9/26; ncol2=14; w=14; offset=1; strand=D; shift=1; score=0.861474; -grgACAGCTGCtkm--- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m17 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=10/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.858805; gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

dyads_m8_rc_shift0 (dyads_m8dyads_m8_rc)
; oligos_8nt_mkv2_m17 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=11/26; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.855746; mvrGACAGCTGwGsv--- ; cor=; Ncor= a 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 0 c 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 0 g 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 0 t 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m17 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=12/26; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.843736; -vwGACAGCTGytkd--- ; cor=; Ncor= a 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m17 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=13/26; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.814029; -cwGaCAGCTGtCwg--- ; cor=; Ncor= a 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 0 c 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 0 g 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 0 t 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0 0

oligos_7nt_mkv2_m13_rc_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m17 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/26; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.806438; grwGACAGCTGyTkyc-- ; cor=; Ncor= a 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_8nt_mkv2_m17 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=15/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.805464; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

dyads_m1_shift0 (dyads_m1dyads_m1)
; oligos_8nt_mkv2_m17 versus dyads_m1 (dyads_m1dyads_m1); m=16/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.805464; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_8nt_mkv2_m1_rc_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=17/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.792927; krkGACAGCTGCTkhvb- ; cor=; Ncor= a 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m17 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=18/26; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.788812; kkwsACAGCTGTTsys-- ; cor=; Ncor= a 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

oligos_8nt_mkv2_m10_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=19/26; ncol2=17; w=15; offset=0; strand=D; shift=0; score=0.784719; rraGACAGCTGCTgyyy- ; cor=; Ncor= a 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

oligos_8nt_mkv2_m12_shift0 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=20/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.783569; gmyGaCAGCTGtCrkc-- ; cor=; Ncor= a 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 0 c 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 0 g 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 0 t 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0 0

oligos_8nt_mkv2_m27_rc_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=21/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.778514; drrGACAGCTGCTGhbb- ; cor=; Ncor= a 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

dyads_m2_shift0 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m17 versus dyads_m2 (dyads_m2dyads_m2); m=22/26; ncol2=18; w=15; offset=0; strand=D; shift=0; score=0.688103; krrrACAGCTGCTGtcta ; cor=; Ncor= a 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=23/26; ncol2=16; w=14; offset=1; strand=D; shift=1; score=0.646746; -rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

oligos_8nt_mkv2_m13_rc_shift0 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=24/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.632354; bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m17 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=25/26; ncol2=17; w=15; offset=0; strand=D; shift=0; score=0.627706; swsAACAGCTGCTGchm- ; cor=; Ncor= a 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

dyads_m25_shift1 (dyads_m25dyads_m25)
; oligos_8nt_mkv2_m17 versus dyads_m25 (dyads_m25dyads_m25); m=26/26; ncol2=17; w=14; offset=1; strand=D; shift=1; score=0.584481; -dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

One-to-n matrix alignment; reference matrix: dyads_m8_shift3 ; 25 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift3 (dyads_m8dyads_m8)
; dyads_m8 (dyads_m8dyads_m8); m=0 (reference); ncol1=15; shift=3; ncol=18; ---bsCwCAGCTGTCybk ; Alignment reference a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

dyads_m8_shift3 (dyads_m8dyads_m8)
; dyads_m8 versus dyads_m8 (dyads_m8dyads_m8); m=1/24; ncol2=15; w=15; offset=0; strand=D; shift=3; score= 1; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; dyads_m8 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=2/24; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.909851; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; dyads_m8 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=3/24; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.888667; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; dyads_m8 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=4/24; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.886652; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

dyads_m3_shift3 (dyads_m3dyads_m3)
; dyads_m8 versus dyads_m3 (dyads_m3dyads_m3); m=5/24; ncol2=15; w=15; offset=0; strand=D; shift=3; score=0.868842; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; dyads_m8 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=6/24; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.863931; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; dyads_m8 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=7/24; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.855746; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; dyads_m8 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=8/24; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.854612; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; dyads_m8 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=9/24; ncol2=14; w=14; offset=1; strand=R; shift=4; score=0.853287; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; dyads_m8 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=10/24; ncol2=14; w=14; offset=1; strand=R; shift=4; score=0.852935; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; dyads_m8 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=11/24; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.798818; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

oligos_6nt_mkv2_m1_rc_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; dyads_m8 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=12/24; ncol2=14; w=14; offset=0; strand=R; shift=3; score=0.79691; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 c 0 0 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 t 0 0 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; dyads_m8 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=13/24; ncol2=14; w=14; offset=0; strand=R; shift=3; score=0.788588; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; dyads_m8 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=14/24; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.773248; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; dyads_m8 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=15/24; ncol2=16; w=15; offset=-1; strand=R; shift=2; score=0.76997; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; dyads_m8 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=16/24; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.763334; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m1_shift2 (dyads_m1dyads_m1)
; dyads_m8 versus dyads_m1 (dyads_m1dyads_m1); m=17/24; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.763334; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; dyads_m8 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=18/24; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.716809; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; dyads_m8 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=19/24; ncol2=17; w=15; offset=-2; strand=R; shift=1; score=0.714878; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; dyads_m8 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=20/24; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.70366; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; dyads_m8 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=21/24; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.695913; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; dyads_m8 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=22/24; ncol2=18; w=15; offset=-3; strand=R; shift=0; score=0.633431; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; dyads_m8 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=23/24; ncol2=16; w=14; offset=-2; strand=R; shift=1; score=0.587616; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_7nt_mkv2_m12_shift4 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; dyads_m8 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=24/24; ncol2=11; w=11; offset=1; strand=D; shift=4; score=0.530588; ----smACAGTTGym--- ; cor=; Ncor= a 0 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 c 0 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 g 0 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 t 0 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m14_shift9 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m14_shift9 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14)
; oligos_8nt_mkv2_m14 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14); m=0 (reference); ncol1=12; shift=9; ncol=23; ---------AwCATGGAAAAT-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 68 46 1 74 0 1 0 81 83 73 78 3 0 0 c 0 0 0 0 0 0 0 0 0 1 3 79 0 11 2 0 0 0 0 3 0 0 0 g 0 0 0 0 0 0 0 0 0 14 0 0 9 0 80 83 1 0 0 0 1 0 0 t 0 0 0 0 0 0 0 0 0 0 34 3 0 72 0 0 1 0 10 2 79 0 0

oligos_8nt_mkv2_m14_shift9 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14)
; oligos_8nt_mkv2_m14 versus oligos_8nt_mkv2_m14 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14); m=1/8; ncol2=12; w=12; offset=0; strand=D; shift=9; score= 1; ---------AwCATGGAAAAT-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 68 46 1 74 0 1 0 81 83 73 78 3 0 0 c 0 0 0 0 0 0 0 0 0 1 3 79 0 11 2 0 0 0 0 3 0 0 0 g 0 0 0 0 0 0 0 0 0 14 0 0 9 0 80 83 1 0 0 0 1 0 0 t 0 0 0 0 0 0 0 0 0 0 34 3 0 72 0 0 1 0 10 2 79 0 0

dyads_m10_rc_shift11 (dyads_m10dyads_m10_rc)
; oligos_8nt_mkv2_m14 versus dyads_m10_rc (dyads_m10dyads_m10_rc); m=2/8; ncol2=15; w=10; offset=2; strand=R; shift=11; score=0.574052; -----------CAtGGAAAATGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 2 50 2 1 0 72 55 56 56 3 0 71 c 0 0 0 0 0 0 0 0 0 0 0 51 8 12 0 0 0 2 4 10 1 0 0 g 0 0 0 0 0 0 0 0 0 0 0 7 9 14 71 72 0 10 9 4 2 72 1 t 0 0 0 0 0 0 0 0 0 0 0 12 5 44 0 0 0 5 3 2 66 0 0

oligos_8nt_mkv2_m6_shift11 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_8nt_mkv2_m14 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=3/8; ncol2=18; w=10; offset=2; strand=D; shift=11; score=0.488906; -----------CrTGRAAAATGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 4 66 0 4 27 102 102 101 100 2 2 96 c 0 0 0 0 0 0 0 0 0 0 0 89 3 13 2 2 0 0 0 1 1 0 0 g 0 0 0 0 0 0 0 0 0 0 0 2 30 2 96 73 0 0 0 0 0 99 2 t 0 0 0 0 0 0 0 0 0 0 0 7 3 87 0 0 0 0 1 1 99 1 4

dyads_m7_shift0 (dyads_m7dyads_m7)
; oligos_8nt_mkv2_m14 versus dyads_m7 (dyads_m7dyads_m7); m=4/8; ncol2=23; w=12; offset=-9; strand=D; shift=0; score=0.47877; mmACTkrAAAwcdTGrAAAATgA ; cor=; Ncor= a 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 107 107 0 7 81 c 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 0 0 0 15 2 g 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 0 0 0 71 6 t 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4 0 0 107 14 18

dyads_m18_rc_shift4 (dyads_m18dyads_m18_rc)
; oligos_8nt_mkv2_m14 versus dyads_m18_rc (dyads_m18dyads_m18_rc); m=5/8; ncol2=19; w=12; offset=-5; strand=R; shift=4; score=0.452281; ----TGTAGGACmTGGAATATGG ; cor=; Ncor= a 0 0 0 0 6 6 1 93 0 15 79 10 24 4 5 20 72 76 1 94 0 3 20 c 0 0 0 0 3 3 0 1 0 8 8 78 37 1 3 4 4 6 0 0 0 17 1 g 0 0 0 0 6 67 0 0 95 69 6 4 18 16 65 65 3 10 0 0 0 72 65 t 0 0 0 0 80 19 94 1 0 3 2 3 16 74 22 6 16 3 94 1 95 3 9

oligos_8nt_mkv2_m16_shift13 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; oligos_8nt_mkv2_m14 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=6/8; ncol2=12; w=8; offset=4; strand=D; shift=13; score=0.430455; -------------YkGAAAATsA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 c 0 0 0 0 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0

oligos_7nt_mkv2_m10_shift14 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; oligos_8nt_mkv2_m14 versus oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=7/8; ncol2=11; w=7; offset=5; strand=D; shift=14; score=0.427127; --------------GRAAAATGA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 34 112 112 110 112 0 0 112 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 105 77 0 0 0 0 0 112 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 112 0 0

dyads_m14_rc_shift2 (dyads_m14dyads_m14_rc)
; oligos_8nt_mkv2_m14 versus dyads_m14_rc (dyads_m14dyads_m14_rc); m=8/8; ncol2=21; w=12; offset=-7; strand=R; shift=2; score=0.403477; --AcTGTAGgACmtgGwaTATGg ; cor=; Ncor= a 0 0 68 13 0 1 0 66 6 20 69 4 27 6 13 8 57 60 0 90 0 5 18 c 0 0 2 54 0 0 0 2 9 5 3 67 36 10 5 9 2 11 0 0 0 14 1 g 0 0 4 7 0 89 0 14 64 58 3 5 9 16 51 67 3 16 1 0 0 64 52 t 0 0 16 16 90 0 90 8 11 7 15 14 18 58 21 6 28 3 89 0 90 7 19

One-to-n matrix alignment; reference matrix: dyads_m17_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m17_shift0 (dyads_m17dyads_m17)
; dyads_m17 (dyads_m17dyads_m17); m=0 (reference); ncol1=10; shift=0; ncol=11; sdGCCACCwm- ; Alignment reference a 4 8 0 0 0 26 0 0 10 7 0 c 11 1 0 27 27 0 27 27 5 11 0 g 10 9 27 0 0 1 0 0 1 5 0 t 2 9 0 0 0 0 0 0 11 4 0

dyads_m17_shift0 (dyads_m17dyads_m17)
; dyads_m17 versus dyads_m17 (dyads_m17dyads_m17); m=1/2; ncol2=10; w=10; offset=0; strand=D; shift=0; score= 1; sdGCCACCwm- ; cor=; Ncor= a 4 8 0 0 0 26 0 0 10 7 0 c 11 1 0 27 27 0 27 27 5 11 0 g 10 9 27 0 0 1 0 0 1 5 0 t 2 9 0 0 0 0 0 0 11 4 0

oligos_6nt_mkv2_m9_rc_shift1 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9_rc)
; dyads_m17 versus oligos_6nt_mkv2_m9_rc (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9_rc); m=2/2; ncol2=10; w=9; offset=1; strand=R; shift=1; score=0.679742; -ttCCACCTyy ; cor=; Ncor= a 0 6 7 0 0 41 0 0 0 4 1 c 0 5 7 41 41 0 41 41 0 11 12 g 0 5 10 0 0 0 0 0 0 10 4 t 0 25 17 0 0 0 0 0 41 16 24

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m27_shift1 ; 28 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=0 (reference); ncol1=17; shift=1; ncol=18; -vvdCAGCAGCTGTCyyh ; Alignment reference a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=1/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score= 1; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=2/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.979057; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=3/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.969442; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m27 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=4/27; ncol2=16; w=16; offset=1; strand=R; shift=2; score=0.923014; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_8nt_mkv2_m27 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=5/27; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=0.904148; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=6/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.900447; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=7/27; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.883572; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_8nt_mkv2_m27 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=8/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.871522; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=9/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.86851; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; oligos_8nt_mkv2_m27 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=10/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.830296; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

dyads_m3_shift3 (dyads_m3dyads_m3)
; oligos_8nt_mkv2_m27 versus dyads_m3 (dyads_m3dyads_m3); m=11/27; ncol2=15; w=15; offset=2; strand=D; shift=3; score=0.82507; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_8nt_mkv2_m27 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=12/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.814862; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m27 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=13/27; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.803149; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; oligos_8nt_mkv2_m27 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=14/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.792794; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_8nt_mkv2_m27 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=15/27; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.788345; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=16/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.778514; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=17/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.777366; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_8nt_mkv2_m27 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=18/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.740136; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=19/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.729624; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; oligos_8nt_mkv2_m27 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=20/27; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.723541; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_8nt_mkv2_m27 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=21/27; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.721739; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

dyads_m8_shift3 (dyads_m8dyads_m8)
; oligos_8nt_mkv2_m27 versus dyads_m8 (dyads_m8dyads_m8); m=22/27; ncol2=15; w=15; offset=2; strand=D; shift=3; score=0.70366; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=23/27; ncol2=18; w=17; offset=0; strand=D; shift=1; score=0.701806; -sygCAGCAGCTGCTGcr ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4

dyads_m21_shift3 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m27 versus dyads_m21 (dyads_m21dyads_m21); m=24/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.651207; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_8nt_mkv2_m27 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=25/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.587165; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

oligos_8nt_mkv2_m25_rc_shift5 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25_rc)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m25_rc (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25_rc); m=26/27; ncol2=12; w=12; offset=4; strand=R; shift=5; score=0.510146; -----ygCAACTGTTbc- ; cor=; Ncor= a 0 0 0 0 0 1 1 0 6 5 0 0 0 0 0 0 1 0 c 0 0 0 0 0 2 1 6 0 0 6 0 0 0 0 2 3 0 g 0 0 0 0 0 0 4 0 0 1 0 0 6 0 0 2 1 0 t 0 0 0 0 0 3 0 0 0 0 0 6 0 6 6 2 1 0

oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; oligos_8nt_mkv2_m27 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=27/27; ncol2=12; w=12; offset=2; strand=D; shift=3; score=0.506454; ---rmAGCAGGTGst--- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m6_shift7 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m6_shift7 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=0 (reference); ncol1=11; shift=7; ncol=18; -------msTGAAAAAyr ; Alignment reference a 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 c 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 g 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 t 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4

oligos_7nt_mkv2_m6_shift7 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; oligos_7nt_mkv2_m6 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=1/10; ncol2=11; w=11; offset=0; strand=D; shift=7; score= 1; -------msTGAAAAAyr ; cor=; Ncor= a 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 c 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 g 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 t 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4

oligos_8nt_mkv2_m9_rc_shift7 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; oligos_7nt_mkv2_m6 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=2/10; ncol2=12; w=11; offset=0; strand=R; shift=7; score=0.894083; -------MsTGAAAAACr ; cor=; Ncor= a 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 c 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 g 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 t 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4

dyads_m29_shift7 (dyads_m29dyads_m29)
; oligos_7nt_mkv2_m6 versus dyads_m29 (dyads_m29dyads_m29); m=3/10; ncol2=12; w=11; offset=0; strand=D; shift=7; score=0.778169; -------AmTGArAAAyr ; cor=; Ncor= a 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 c 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 g 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 t 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5

dyads_m39_shift8 (dyads_m39dyads_m39)
; oligos_7nt_mkv2_m6 versus dyads_m39 (dyads_m39dyads_m39); m=4/10; ncol2=10; w=10; offset=1; strand=D; shift=8; score=0.700857; --------GwGAAATAyr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 5 25 0 56 56 56 0 56 5 21 c 0 0 0 0 0 0 0 0 7 1 0 0 0 0 0 0 20 6 g 0 0 0 0 0 0 0 0 40 3 56 0 0 0 0 0 5 23 t 0 0 0 0 0 0 0 0 4 27 0 0 0 0 56 0 26 6

oligos_6nt_mkv2_m8_shift8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)
; oligos_7nt_mkv2_m6 versus oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=5/10; ncol2=10; w=10; offset=1; strand=D; shift=8; score=0.655091; --------rtGAGAAAha ; cor=; Ncor= a 0 0 0 0 0 0 0 0 101 13 0 154 0 154 154 154 43 85 c 0 0 0 0 0 0 0 0 3 32 0 0 0 0 0 0 52 30 g 0 0 0 0 0 0 0 0 44 11 154 0 154 0 0 0 5 34 t 0 0 0 0 0 0 0 0 6 98 0 0 0 0 0 0 54 5

oligos_8nt_mkv2_m4_shift4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; oligos_7nt_mkv2_m6 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=6/10; ncol2=13; w=10; offset=-3; strand=D; shift=4; score=0.639996; ----WAmACTGAAAAwC- ; cor=; Ncor= a 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 c 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 g 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 t 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0

oligos_7nt_mkv2_m5_shift5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m6 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=7/10; ncol2=11; w=9; offset=-2; strand=D; shift=5; score=0.625742; -----AmACTGAAAAw-- ; cor=; Ncor= a 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 c 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 g 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 t 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0

dyads_m24_shift0 (dyads_m24dyads_m24)
; oligos_7nt_mkv2_m6 versus dyads_m24 (dyads_m24dyads_m24); m=8/10; ncol2=18; w=11; offset=-7; strand=D; shift=0; score=0.583076; ygRRAAAmsTGAAAAwyr ; cor=; Ncor= a 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 c 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 g 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 t 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1

oligos_8nt_mkv2_m6_shift7 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_7nt_mkv2_m6 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=9/10; ncol2=18; w=11; offset=0; strand=D; shift=7; score=0.481647; -------CrTGRAAAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 4 66 0 4 27 102 102 101 100 2 2 c 0 0 0 0 0 0 0 89 3 13 2 2 0 0 0 1 1 0 g 0 0 0 0 0 0 0 2 30 2 96 73 0 0 0 0 0 99 t 0 0 0 0 0 0 0 7 3 87 0 0 0 0 1 1 99 1

oligos_7nt_mkv2_m10_shift10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; oligos_7nt_mkv2_m6 versus oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=10/10; ncol2=11; w=8; offset=3; strand=D; shift=10; score=0.477376; ----------GRAAAATG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 3 34 112 112 110 112 0 0 c 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 105 77 0 0 0 0 0 112 t 0 0 0 0 0 0 0 0 0 0 2 0 0 0 2 0 112 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift2 ; 29 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=0 (reference); ncol1=16; shift=2; ncol=18; --srsAACAGCTGTswmm ; Alignment reference a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=1/28; ncol2=16; w=16; offset=0; strand=D; shift=2; score= 1; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=2/28; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.974887; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

dyads_m3_shift3 (dyads_m3dyads_m3)
; oligos_7nt_mkv2_m3 versus dyads_m3 (dyads_m3dyads_m3); m=3/28; ncol2=15; w=15; offset=1; strand=D; shift=3; score=0.91171; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=4/28; ncol2=16; w=16; offset=0; strand=R; shift=2; score=0.875409; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=5/28; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.840343; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=6/28; ncol2=14; w=14; offset=1; strand=D; shift=3; score=0.837399; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=7/28; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.832416; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=8/28; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.814862; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; oligos_7nt_mkv2_m3 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=9/28; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.813747; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; oligos_7nt_mkv2_m3 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=10/28; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.802625; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=11/28; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.788812; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=12/28; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.785602; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

dyads_m8_shift3 (dyads_m8dyads_m8)
; oligos_7nt_mkv2_m3 versus dyads_m8 (dyads_m8dyads_m8); m=13/28; ncol2=15; w=15; offset=1; strand=D; shift=3; score=0.773248; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=14/28; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.771647; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=15/28; ncol2=15; w=15; offset=1; strand=R; shift=3; score=0.771254; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=16/28; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.764901; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m1_shift2 (dyads_m1dyads_m1)
; oligos_7nt_mkv2_m3 versus dyads_m1 (dyads_m1dyads_m1); m=17/28; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.764901; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=18/28; ncol2=14; w=14; offset=1; strand=R; shift=3; score=0.764672; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_7nt_mkv2_m3 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=19/28; ncol2=18; w=16; offset=-2; strand=R; shift=0; score=0.762649; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=20/28; ncol2=14; w=14; offset=2; strand=R; shift=4; score=0.744923; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; oligos_7nt_mkv2_m3 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=21/28; ncol2=14; w=14; offset=2; strand=R; shift=4; score=0.74244; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=22/28; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.722913; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=23/28; ncol2=14; w=14; offset=1; strand=D; shift=3; score=0.716528; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=24/28; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.711793; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=25/28; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.703385; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_7nt_mkv2_m3 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=26/28; ncol2=17; w=15; offset=-2; strand=R; shift=0; score=0.652721; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

oligos_8nt_mkv2_m25_shift3 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=27/28; ncol2=12; w=12; offset=1; strand=D; shift=3; score=0.553665; ---gvAACAGTTGcr--- ; cor=; Ncor= a 0 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 c 0 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 g 0 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 t 0 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0

oligos_7nt_mkv2_m12_shift4 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=28/28; ncol2=11; w=11; offset=2; strand=D; shift=4; score=0.516408; ----smACAGTTGym--- ; cor=; Ncor= a 0 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 c 0 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 g 0 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 t 0 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m22_shift0 ; 27 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m22_shift0 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=0 (reference); ncol1=15; shift=0; ncol=18; rvtGACAGCTGmhkg--- ; Alignment reference a 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m22_shift0 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=1/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score= 1; rvtGACAGCTGmhkg--- ; cor=; Ncor= a 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m17_shift0 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=2/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.999291; rstGACAGCTGmhkg--- ; cor=; Ncor= a 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=3/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.972007; rstGACAGCTGMskg--- ; cor=; Ncor= a 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 0 c 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 0 g 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 0 t 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0 0

dyads_m36_shift0 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m22 versus dyads_m36 (dyads_m36dyads_m36); m=4/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.970708; rvkGACAGCTGctks--- ; cor=; Ncor= a 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0

dyads_m19_shift0 (dyads_m19dyads_m19)
; oligos_8nt_mkv2_m22 versus dyads_m19 (dyads_m19dyads_m19); m=5/26; ncol2=15; w=15; offset=0; strand=D; shift=0; score=0.967611; rvdGACAGCTGvyks--- ; cor=; Ncor= a 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m22 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=6/26; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.901383; rswGACAGCTGmsg---- ; cor=; Ncor= a 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0

dyads_m5_shift0 (dyads_m5dyads_m5)
; oligos_8nt_mkv2_m22 versus dyads_m5 (dyads_m5dyads_m5); m=7/26; ncol2=14; w=14; offset=0; strand=D; shift=0; score=0.899671; rvdGACAGCTGmsg---- ; cor=; Ncor= a 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0

dyads_m3_rc_shift0 (dyads_m3dyads_m3_rc)
; oligos_8nt_mkv2_m22 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=8/26; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.872422; rrwGACAGCTGyTky--- ; cor=; Ncor= a 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m22 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=9/26; ncol2=14; w=14; offset=1; strand=D; shift=1; score=0.862061; -grgACAGCTGCtkm--- ; cor=; Ncor= a 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m22 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=10/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.859213; gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0

dyads_m8_rc_shift0 (dyads_m8dyads_m8_rc)
; oligos_8nt_mkv2_m22 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=11/26; ncol2=15; w=15; offset=0; strand=R; shift=0; score=0.854612; mvrGACAGCTGwGsv--- ; cor=; Ncor= a 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 0 c 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 0 g 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 0 t 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0 0

oligos_6nt_mkv2_m3_rc_shift1 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m22 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=12/26; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.842779; -vwGACAGCTGytkd--- ; cor=; Ncor= a 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0

oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m22 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=13/26; ncol2=14; w=14; offset=1; strand=R; shift=1; score=0.816836; -cwGaCAGCTGtCwg--- ; cor=; Ncor= a 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 0 c 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 0 g 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 0 t 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_8nt_mkv2_m22 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=14/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.808909; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

dyads_m1_shift0 (dyads_m1dyads_m1)
; oligos_8nt_mkv2_m22 versus dyads_m1 (dyads_m1dyads_m1); m=15/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.808909; vmwGaCAGCTGtCwkb-- ; cor=; Ncor= a 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 0 c 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 0 g 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 0 t 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0 0

oligos_7nt_mkv2_m13_rc_shift0 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m22 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=16/26; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.803838; grwGACAGCTGyTkyc-- ; cor=; Ncor= a 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0

oligos_8nt_mkv2_m1_rc_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=17/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.791251; krkGACAGCTGCTkhvb- ; cor=; Ncor= a 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0

oligos_8nt_mkv2_m12_shift0 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=18/26; ncol2=16; w=15; offset=0; strand=D; shift=0; score=0.78905; gmyGaCAGCTGtCrkc-- ; cor=; Ncor= a 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 0 c 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 0 g 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 0 t 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0 0

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m22 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=19/26; ncol2=16; w=15; offset=0; strand=R; shift=0; score=0.785602; kkwsACAGCTGTTsys-- ; cor=; Ncor= a 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0

oligos_8nt_mkv2_m10_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=20/26; ncol2=17; w=15; offset=0; strand=D; shift=0; score=0.783611; rraGACAGCTGCTgyyy- ; cor=; Ncor= a 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0

oligos_8nt_mkv2_m27_rc_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=21/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.777366; drrGACAGCTGCTGhbb- ; cor=; Ncor= a 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0

dyads_m2_shift0 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m22 versus dyads_m2 (dyads_m2dyads_m2); m=22/26; ncol2=18; w=15; offset=0; strand=D; shift=0; score=0.686997; krrrACAGCTGCTGtcta ; cor=; Ncor= a 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3

oligos_8nt_mkv2_m8_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=23/26; ncol2=16; w=14; offset=1; strand=D; shift=1; score=0.645441; -rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0

oligos_8nt_mkv2_m13_rc_shift0 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=24/26; ncol2=17; w=15; offset=0; strand=R; shift=0; score=0.633314; bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m22 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=25/26; ncol2=17; w=15; offset=0; strand=D; shift=0; score=0.629598; swsAACAGCTGCTGchm- ; cor=; Ncor= a 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0

dyads_m25_shift1 (dyads_m25dyads_m25)
; oligos_8nt_mkv2_m22 versus dyads_m25 (dyads_m25dyads_m25); m=26/26; ncol2=17; w=14; offset=1; strand=D; shift=1; score=0.582771; -dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift3 ; 30 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=0 (reference); ncol1=14; shift=3; ncol=18; ---hmarCAGCTGTCwb- ; Alignment reference a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=1/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score= 1; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=2/29; ncol2=14; w=14; offset=0; strand=R; shift=3; score=0.930869; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

dyads_m3_shift3 (dyads_m3dyads_m3)
; oligos_6nt_mkv2_m3 versus dyads_m3 (dyads_m3dyads_m3); m=3/29; ncol2=15; w=14; offset=0; strand=D; shift=3; score=0.911546; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=4/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.894525; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; oligos_6nt_mkv2_m3 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=5/29; ncol2=15; w=14; offset=0; strand=R; shift=3; score=0.872768; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; oligos_6nt_mkv2_m3 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=6/29; ncol2=15; w=14; offset=0; strand=R; shift=3; score=0.872415; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

dyads_m8_shift3 (dyads_m8dyads_m8)
; oligos_6nt_mkv2_m3 versus dyads_m8 (dyads_m8dyads_m8); m=7/29; ncol2=15; w=14; offset=0; strand=D; shift=3; score=0.863931; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=8/29; ncol2=16; w=14; offset=-1; strand=D; shift=2; score=0.849814; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=9/29; ncol2=15; w=14; offset=0; strand=R; shift=3; score=0.843736; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=10/29; ncol2=15; w=14; offset=0; strand=R; shift=3; score=0.842779; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=11/29; ncol2=16; w=14; offset=-1; strand=D; shift=2; score=0.837399; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=12/29; ncol2=15; w=14; offset=0; strand=R; shift=3; score=0.826277; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=13/29; ncol2=16; w=14; offset=-1; strand=R; shift=2; score=0.810656; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=14/29; ncol2=14; w=13; offset=1; strand=R; shift=4; score=0.80045; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; oligos_6nt_mkv2_m3 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=15/29; ncol2=14; w=13; offset=1; strand=R; shift=4; score=0.799789; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=16/29; ncol2=17; w=14; offset=-2; strand=R; shift=1; score=0.752153; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=17/29; ncol2=16; w=14; offset=-1; strand=D; shift=2; score=0.748158; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m1_shift2 (dyads_m1dyads_m1)
; oligos_6nt_mkv2_m3 versus dyads_m1 (dyads_m1dyads_m1); m=18/29; ncol2=16; w=14; offset=-1; strand=D; shift=2; score=0.748158; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10

dyads_m21_shift3 (dyads_m21dyads_m21)
; oligos_6nt_mkv2_m3 versus dyads_m21 (dyads_m21dyads_m21); m=19/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.745137; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=20/29; ncol2=17; w=14; offset=-2; strand=D; shift=1; score=0.742298; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=21/29; ncol2=17; w=14; offset=-2; strand=D; shift=1; score=0.740136; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=22/29; ncol2=16; w=14; offset=-1; strand=D; shift=2; score=0.737378; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=23/29; ncol2=16; w=14; offset=-2; strand=R; shift=1; score=0.725047; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_6nt_mkv2_m3 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=24/29; ncol2=18; w=14; offset=-3; strand=R; shift=0; score=0.684101; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_6nt_mkv2_m3 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=25/29; ncol2=17; w=14; offset=-3; strand=R; shift=0; score=0.670975; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=26/29; ncol2=17; w=14; offset=-2; strand=D; shift=1; score=0.653771; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=27/29; ncol2=17; w=14; offset=-2; strand=R; shift=1; score=0.652231; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

oligos_8nt_mkv2_m25_rc_shift5 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25_rc)
; oligos_6nt_mkv2_m3 versus oligos_8nt_mkv2_m25_rc (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25_rc); m=28/29; ncol2=12; w=12; offset=2; strand=R; shift=5; score=0.607784; -----ygCAACTGTTbc- ; cor=; Ncor= a 0 0 0 0 0 1 1 0 6 5 0 0 0 0 0 0 1 0 c 0 0 0 0 0 2 1 6 0 0 6 0 0 0 0 2 3 0 g 0 0 0 0 0 0 4 0 0 1 0 0 6 0 0 2 1 0 t 0 0 0 0 0 3 0 0 0 0 0 6 0 6 6 2 1 0

oligos_7nt_mkv2_m12_shift4 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=29/29; ncol2=11; w=11; offset=1; strand=D; shift=4; score=0.583235; ----smACAGTTGym--- ; cor=; Ncor= a 0 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 c 0 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 g 0 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 t 0 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m6_shift2 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m6_shift2 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=0 (reference); ncol1=18; shift=2; ncol=30; --CrTGRAAAATGAGAAAwr---------- ; Alignment reference a 0 0 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 0 0 0 0 0 0 c 0 0 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 0 0 0 0 0 0 g 0 0 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 0 0 0 0 0 0 t 0 0 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m6_shift2 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_8nt_mkv2_m6 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=1/13; ncol2=18; w=18; offset=0; strand=D; shift=2; score= 1; --CrTGRAAAATGAGAAAwr---------- ; cor=; Ncor= a 0 0 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 0 0 0 0 0 0 c 0 0 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 0 0 0 0 0 0 g 0 0 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 0 0 0 0 0 0 t 0 0 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0 0 0 0 0 0 0

dyads_m10_rc_shift2 (dyads_m10dyads_m10_rc)
; oligos_8nt_mkv2_m6 versus dyads_m10_rc (dyads_m10dyads_m10_rc); m=2/13; ncol2=15; w=15; offset=0; strand=R; shift=2; score=0.800837; --CAtGGAAAATGAGAA------------- ; cor=; Ncor= a 0 0 2 50 2 1 0 72 55 56 56 3 0 71 0 55 56 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 51 8 12 0 0 0 2 4 10 1 0 0 1 4 9 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 7 9 14 71 72 0 10 9 4 2 72 1 71 9 2 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 12 5 44 0 0 0 5 3 2 66 0 0 0 4 5 0 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m27_shift4 (dyads_m27dyads_m27)
; oligos_8nt_mkv2_m6 versus dyads_m27 (dyads_m27dyads_m27); m=3/13; ncol2=18; w=16; offset=2; strand=D; shift=4; score=0.729546; ----yGGAAAATkAdAAAAwsh-------- ; cor=; Ncor= a 0 0 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 0 0 0 0 0 0 0 c 0 0 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 0 0 0 0 0 0 0 g 0 0 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 0 0 0 0 0 0 0 t 0 0 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0 0 0 0 0 0 0 0

oligos_7nt_mkv2_m10_shift5 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10)
; oligos_8nt_mkv2_m6 versus oligos_7nt_mkv2_m10 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10); m=4/13; ncol2=11; w=11; offset=3; strand=D; shift=5; score=0.606985; -----GRAAAATGAGA-------------- ; cor=; Ncor= a 0 0 0 0 0 3 34 112 112 110 112 0 0 112 1 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 2 1 0 0 0 0 0 0 0 16 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 105 77 0 0 0 0 0 112 0 77 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 2 0 0 0 2 0 112 0 0 18 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m29_shift9 (dyads_m29dyads_m29)
; oligos_8nt_mkv2_m6 versus dyads_m29 (dyads_m29dyads_m29); m=5/13; ncol2=12; w=11; offset=7; strand=D; shift=9; score=0.548376; ---------AmTGArAAAyry--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0 0 0 0 0 0

oligos_6nt_mkv2_m8_shift10 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)
; oligos_8nt_mkv2_m6 versus oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=6/13; ncol2=10; w=10; offset=8; strand=D; shift=10; score=0.530909; ----------rtGAGAAAha---------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 101 13 0 154 0 154 154 154 43 85 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 3 32 0 0 0 0 0 0 52 30 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 44 11 154 0 154 0 0 0 5 34 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 6 98 0 0 0 0 0 0 54 5 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m16_shift4 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; oligos_8nt_mkv2_m6 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=7/13; ncol2=12; w=12; offset=2; strand=D; shift=4; score=0.505792; ----YkGAAAATsAyr-------------- ; cor=; Ncor= a 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m14_shift0 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14)
; oligos_8nt_mkv2_m6 versus oligos_8nt_mkv2_m14 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14); m=8/13; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=0.488906; AwCATGGAAAAT------------------ ; cor=; Ncor= a 68 46 1 74 0 1 0 81 83 73 78 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 1 3 79 0 11 2 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 14 0 0 9 0 80 83 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 34 3 0 72 0 0 1 0 10 2 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv2_m6_shift2 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; oligos_8nt_mkv2_m6 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=9/13; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.481647; --msTGAAAAAyr----------------- ; cor=; Ncor= a 0 0 78 23 0 1 138 138 138 124 139 6 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 58 59 0 0 0 0 0 0 0 59 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 1 41 0 138 1 1 0 0 0 16 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 2 16 139 0 0 0 1 15 0 58 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m9_shift5 (dyads_m9dyads_m9)
; oligos_8nt_mkv2_m6 versus dyads_m9 (dyads_m9dyads_m9); m=10/13; ncol2=26; w=15; offset=3; strand=D; shift=5; score=0.464877; -----GrAAAwtrarAAAtgcaCAcTGTAG ; cor=; Ncor= a 0 0 0 0 0 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 c 0 0 0 0 0 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 g 0 0 0 0 0 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 t 0 0 0 0 0 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13

oligos_7nt_mkv2_m5_shift7 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; oligos_8nt_mkv2_m6 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=11/13; ncol2=11; w=11; offset=5; strand=D; shift=7; score=0.427826; -------AmACTGAAAAw------------ ; cor=; Ncor= a 0 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0 0 0 0 0 0 0

dyads_m40_shift7 (dyads_m40dyads_m40)
; oligos_8nt_mkv2_m6 versus dyads_m40 (dyads_m40dyads_m40); m=12/13; ncol2=25; w=13; offset=5; strand=D; shift=7; score=0.422638; -------AAAATGAGAAATrCACAcTkTAG ; cor=; Ncor= a 0 0 0 0 0 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 c 0 0 0 0 0 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 g 0 0 0 0 0 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 t 0 0 0 0 0 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0

oligos_8nt_mkv2_m9_rc_shift9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; oligos_8nt_mkv2_m6 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=13/13; ncol2=12; w=11; offset=7; strand=R; shift=9; score=0.422138; ---------MsTGAAAAACrt--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m11_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m11_shift0 (dyads_m11dyads_m11)
; dyads_m11 (dyads_m11dyads_m11); m=0 (reference); ncol1=12; shift=0; ncol=13; ccCCCTGCCwct- ; Alignment reference a 2 7 0 0 0 0 0 1 0 9 5 7 0 c 19 15 28 29 29 0 0 28 29 2 16 6 0 g 7 3 1 0 0 0 29 0 0 0 5 3 0 t 1 4 0 0 0 29 0 0 0 18 3 13 0

dyads_m11_shift0 (dyads_m11dyads_m11)
; dyads_m11 versus dyads_m11 (dyads_m11dyads_m11); m=1/6; ncol2=12; w=12; offset=0; strand=D; shift=0; score= 1; ccCCCTGCCwct- ; cor=; Ncor= a 2 7 0 0 0 0 0 1 0 9 5 7 0 c 19 15 28 29 29 0 0 28 29 2 16 6 0 g 7 3 1 0 0 0 29 0 0 0 5 3 0 t 1 4 0 0 0 29 0 0 0 18 3 13 0

oligos_7nt_mkv2_m8_shift0 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8)
; dyads_m11 versus oligos_7nt_mkv2_m8 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8); m=2/6; ncol2=11; w=11; offset=0; strand=D; shift=0; score=0.908767; smCCCTGCCwc-- ; cor=; Ncor= a 4 10 0 0 0 0 2 0 0 9 6 0 0 c 20 15 34 33 34 3 0 34 34 4 16 0 0 g 9 5 0 1 0 0 32 0 0 5 6 0 0 t 1 4 0 0 0 31 0 0 0 16 6 0 0

oligos_8nt_mkv2_m20_rc_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc)
; dyads_m11 versus oligos_8nt_mkv2_m20_rc (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc); m=3/6; ncol2=13; w=12; offset=0; strand=R; shift=0; score= 0.8834; CyCCCTGCCTCws ; cor=; Ncor= a 2 3 0 0 0 1 0 1 0 1 0 7 0 c 19 14 26 20 26 0 0 25 26 0 23 6 11 g 3 1 0 0 0 0 25 0 0 0 2 2 13 t 2 8 0 6 0 25 1 0 0 25 1 11 2

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc)
; dyads_m11 versus oligos_6nt_mkv2_m4_rc (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc); m=4/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score=0.749262; --cyCTGCCTsh- ; cor=; Ncor= a 0 0 8 6 0 0 0 0 0 0 4 16 0 c 0 0 32 23 59 0 0 59 59 0 33 16 0 g 0 0 6 12 0 0 59 0 0 0 15 10 0 t 0 0 13 18 0 59 0 0 0 59 7 17 0

dyads_m30_shift0 (dyads_m30dyads_m30)
; dyads_m11 versus dyads_m30 (dyads_m30dyads_m30); m=5/6; ncol2=11; w=11; offset=0; strand=D; shift=0; score=0.714061; ymCCCMGCCyr-- ; cor=; Ncor= a 2 4 0 0 0 8 0 0 0 2 3 0 0 c 3 3 11 11 11 3 0 11 11 4 2 0 0 g 2 2 0 0 0 0 11 0 0 2 4 0 0 t 4 2 0 0 0 0 0 0 0 3 2 0 0

oligos_7nt_mkv2_m11_shift2 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11)
; dyads_m11 versus oligos_7nt_mkv2_m11 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11); m=6/6; ncol2=11; w=10; offset=2; strand=D; shift=2; score=0.699274; --CyCTGCCTChs ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 0 0 10 0 c 0 0 27 18 34 0 0 35 35 0 35 11 15 g 0 0 1 2 1 1 35 0 0 0 0 2 17 t 0 0 4 15 0 34 0 0 0 35 0 12 3

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m23_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m23_shift1 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23)
; oligos_8nt_mkv2_m23 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23); m=0 (reference); ncol1=12; shift=1; ncol=14; -hkCCTTCCTCyb- ; Alignment reference a 0 3 1 0 0 0 0 0 0 0 0 0 0 0 c 0 2 1 8 8 0 0 8 8 0 8 3 3 0 g 0 0 2 0 0 1 0 0 0 0 0 1 2 0 t 0 3 4 0 0 7 8 0 0 8 0 4 3 0

oligos_8nt_mkv2_m23_shift1 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23)
; oligos_8nt_mkv2_m23 versus oligos_8nt_mkv2_m23 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23); m=1/5; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 1; -hkCCTTCCTCyb- ; cor=; Ncor= a 0 3 1 0 0 0 0 0 0 0 0 0 0 0 c 0 2 1 8 8 0 0 8 8 0 8 3 3 0 g 0 0 2 0 0 1 0 0 0 0 0 1 2 0 t 0 3 4 0 0 7 8 0 0 8 0 4 3 0

oligos_7nt_mkv2_m11_shift2 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11)
; oligos_8nt_mkv2_m23 versus oligos_7nt_mkv2_m11 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11); m=2/5; ncol2=11; w=11; offset=1; strand=D; shift=2; score=0.664623; --CyCTGCCTChs- ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 0 0 10 0 0 c 0 0 27 18 34 0 0 35 35 0 35 11 15 0 g 0 0 1 2 1 1 35 0 0 0 0 2 17 0 t 0 0 4 15 0 34 0 0 0 35 0 12 3 0

oligos_8nt_mkv2_m20_rc_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc)
; oligos_8nt_mkv2_m23 versus oligos_8nt_mkv2_m20_rc (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc); m=3/5; ncol2=13; w=12; offset=-1; strand=R; shift=0; score=0.663767; CyCCCTGCCTCws- ; cor=; Ncor= a 2 3 0 0 0 1 0 1 0 1 0 7 0 0 c 19 14 26 20 26 0 0 25 26 0 23 6 11 0 g 3 1 0 0 0 0 25 0 0 0 2 2 13 0 t 2 8 0 6 0 25 1 0 0 25 1 11 2 0

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc)
; oligos_8nt_mkv2_m23 versus oligos_6nt_mkv2_m4_rc (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc); m=4/5; ncol2=10; w=10; offset=1; strand=R; shift=2; score=0.588894; --cyCTGCCTsh-- ; cor=; Ncor= a 0 0 8 6 0 0 0 0 0 0 4 16 0 0 c 0 0 32 23 59 0 0 59 59 0 33 16 0 0 g 0 0 6 12 0 0 59 0 0 0 15 10 0 0 t 0 0 13 18 0 59 0 0 0 59 7 17 0 0

oligos_6nt_mkv2_m7_shift5 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7)
; oligos_8nt_mkv2_m23 versus oligos_6nt_mkv2_m7 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7); m=5/5; ncol2=10; w=8; offset=4; strand=D; shift=5; score=0.412254; -----hgCCTCCCw ; cor=; Ncor= a 0 0 0 0 0 10 6 0 0 0 0 0 0 17 c 0 0 0 0 0 10 7 40 40 0 40 40 40 6 g 0 0 0 0 0 5 19 0 0 0 0 0 0 5 t 0 0 0 0 0 15 8 0 0 40 0 0 0 12

One-to-n matrix alignment; reference matrix: dyads_m38_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m38_shift0 (dyads_m38dyads_m38)
; dyads_m38 (dyads_m38dyads_m38); m=0 (reference); ncol1=12; shift=0; ncol=13; twTTAAATAAww- ; Alignment reference a 6 9 3 0 27 27 22 3 26 27 12 8 0 c 7 5 1 0 0 1 1 0 0 0 3 6 0 g 5 3 2 1 0 1 2 0 1 1 5 6 0 t 11 12 23 28 2 0 4 26 2 1 9 9 0

dyads_m38_shift0 (dyads_m38dyads_m38)
; dyads_m38 versus dyads_m38 (dyads_m38dyads_m38); m=1/4; ncol2=12; w=12; offset=0; strand=D; shift=0; score= 1; twTTAAATAAww- ; cor=; Ncor= a 6 9 3 0 27 27 22 3 26 27 12 8 0 c 7 5 1 0 0 1 1 0 0 0 3 6 0 g 5 3 2 1 0 1 2 0 1 1 5 6 0 t 11 12 23 28 2 0 4 26 2 1 9 9 0

dyads_m16_shift0 (dyads_m16dyads_m16)
; dyads_m38 versus dyads_m16 (dyads_m16dyads_m16); m=2/4; ncol2=12; w=12; offset=0; strand=D; shift=0; score=0.883152; ttTTAATTAAaa- ; cor=; Ncor= a 6 6 0 1 24 23 3 1 27 26 14 12 0 c 4 4 0 0 3 1 1 0 0 2 4 6 0 g 6 4 2 0 0 1 1 3 0 0 4 4 0 t 12 14 26 27 1 3 23 24 1 0 6 6 0

oligos_7nt_mkv2_m9_shift1 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9)
; dyads_m38 versus oligos_7nt_mkv2_m9 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9); m=3/4; ncol2=11; w=11; offset=1; strand=D; shift=1; score=0.860166; -wtTAAATAAag- ; cor=; Ncor= a 0 4 3 0 12 12 13 1 13 12 6 3 0 c 0 3 3 0 0 0 0 0 0 1 3 1 0 g 0 1 3 0 1 0 0 0 0 0 2 6 0 t 0 5 4 13 0 1 0 12 0 0 2 3 0

oligos_8nt_mkv2_m24_shift1 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24)
; dyads_m38 versus oligos_8nt_mkv2_m24 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24); m=4/4; ncol2=12; w=11; offset=1; strand=D; shift=1; score=0.783514; -wwTAAATAAAaw ; cor=; Ncor= a 0 11 13 1 31 31 23 1 29 29 28 16 11 c 0 4 1 1 0 0 1 0 0 2 0 4 6 g 0 3 6 2 0 0 1 1 2 1 2 5 2 t 0 14 12 28 1 1 7 30 1 0 2 7 13

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m7_shift3 ; 15 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=0 (reference); ncol1=12; shift=3; ncol=18; ---rmAGCAGGTGst--- ; Alignment reference a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0

oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=1/14; ncol2=12; w=12; offset=0; strand=D; shift=3; score= 1; ---rmAGCAGGTGst--- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0

dyads_m21_shift3 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m7 versus dyads_m21 (dyads_m21dyads_m21); m=2/14; ncol2=14; w=12; offset=0; strand=D; shift=3; score=0.684465; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m7 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=3/14; ncol2=14; w=12; offset=0; strand=R; shift=3; score=0.60547; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_8nt_mkv2_m7 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=4/14; ncol2=17; w=12; offset=-3; strand=R; shift=0; score=0.549659; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=5/14; ncol2=17; w=12; offset=-2; strand=D; shift=1; score=0.54338; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=6/14; ncol2=16; w=12; offset=-2; strand=R; shift=1; score=0.541527; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m7 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=7/14; ncol2=16; w=12; offset=-1; strand=R; shift=2; score=0.535119; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=8/14; ncol2=17; w=12; offset=-2; strand=R; shift=1; score=0.535045; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=9/14; ncol2=18; w=12; offset=-2; strand=D; shift=1; score=0.532923; -sygCAGCAGCTGCTGcr ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=10/14; ncol2=17; w=12; offset=-2; strand=D; shift=1; score=0.511066; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_6nt_mkv2_m9_shift6 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9)
; oligos_8nt_mkv2_m7 versus oligos_6nt_mkv2_m9 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9); m=11/14; ncol2=10; w=9; offset=3; strand=D; shift=6; score=0.507586; ------rrAGGTGGaa-- ; cor=; Ncor= a 0 0 0 0 0 0 24 16 41 0 0 0 0 0 17 25 0 0 c 0 0 0 0 0 0 4 10 0 0 0 0 0 0 10 5 0 0 g 0 0 0 0 0 0 12 11 0 41 41 0 41 41 7 5 0 0 t 0 0 0 0 0 0 1 4 0 0 0 41 0 0 7 6 0 0

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_8nt_mkv2_m7 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=12/14; ncol2=18; w=12; offset=-3; strand=R; shift=0; score=0.506958; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=13/14; ncol2=17; w=12; offset=-2; strand=D; shift=1; score=0.506454; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_8nt_mkv2_m7 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=14/14; ncol2=17; w=12; offset=-2; strand=R; shift=1; score=0.50397; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m11_shift8 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m11_shift8 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11)
; oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=0 (reference); ncol1=13; shift=8; ncol=26; --------AGAAATRCACACT----- ; Alignment reference a 0 0 0 0 0 0 0 0 59 4 71 72 71 0 18 0 68 0 72 1 3 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 2 1 0 0 2 2 71 1 72 0 52 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 63 0 0 0 1 50 0 1 0 0 9 3 0 0 0 0 0 t 0 0 0 0 0 0 0 0 10 3 0 0 1 69 2 1 2 0 0 10 66 0 0 0 0 0

oligos_8nt_mkv2_m11_shift8 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11)
; oligos_8nt_mkv2_m11 versus oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=1/8; ncol2=13; w=13; offset=0; strand=D; shift=8; score= 1; --------AGAAATRCACACT----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 59 4 71 72 71 0 18 0 68 0 72 1 3 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 2 1 0 0 2 2 71 1 72 0 52 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 63 0 0 0 1 50 0 1 0 0 9 3 0 0 0 0 0 t 0 0 0 0 0 0 0 0 10 3 0 0 1 69 2 1 2 0 0 10 66 0 0 0 0 0

dyads_m20_rc_shift4 (dyads_m20dyads_m20_rc)
; oligos_8nt_mkv2_m11 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=2/8; ncol2=23; w=13; offset=-4; strand=R; shift=4; score=0.547874; ----AATGAGAAAtrCACACTkTAGG ; cor=; Ncor= a 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 4 0 60 0 10 c 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 3 0 0 0 3 g 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 35 0 0 60 44 t 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46 18 60 0 0 3

dyads_m40_shift2 (dyads_m40dyads_m40)
; oligos_8nt_mkv2_m11 versus dyads_m40 (dyads_m40dyads_m40); m=3/8; ncol2=25; w=13; offset=-6; strand=D; shift=2; score=0.50842; --AAAATGAGAAATrCACAcTkTAGG ; cor=; Ncor= a 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 14 c 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 3 g 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 45 t 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0 2

dyads_m39_shift7 (dyads_m39dyads_m39)
; oligos_8nt_mkv2_m11 versus dyads_m39 (dyads_m39dyads_m39); m=4/8; ncol2=10; w=9; offset=-1; strand=D; shift=7; score=0.49244; -------GwGAAATAyr--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 5 25 0 56 56 56 0 56 5 21 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 7 1 0 0 0 0 0 0 20 6 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 40 3 56 0 0 0 0 0 5 23 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 4 27 0 0 0 0 56 0 26 6 0 0 0 0 0 0 0 0 0

dyads_m9_shift0 (dyads_m9dyads_m9)
; oligos_8nt_mkv2_m11 versus dyads_m9 (dyads_m9dyads_m9); m=5/8; ncol2=26; w=13; offset=-8; strand=D; shift=0; score=0.483973; GrAAAwtrarAAAtgcaCAcTGTAGr ; cor=; Ncor= a 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 24 c 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 6 g 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 47 t 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13 10

oligos_8nt_mkv2_m26_rc_shift13 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)
; oligos_8nt_mkv2_m11 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=6/8; ncol2=12; w=8; offset=5; strand=R; shift=13; score=0.44416; -------------trCACACTGTAG- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 19 40 0 87 0 87 1 4 5 0 65 8 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 79 0 86 0 85 0 1 0 1 10 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 3 24 0 0 0 0 0 1 69 0 7 63 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 56 5 8 0 1 0 1 82 12 87 14 6 0

oligos_8nt_mkv2_m18_rc_shift4 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18_rc)
; oligos_8nt_mkv2_m11 versus oligos_8nt_mkv2_m18_rc (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18_rc); m=7/8; ncol2=12; w=8; offset=-4; strand=R; shift=4; score=0.411758; ----wTTTAsAAATsy---------- ; cor=; Ncor= a 0 0 0 0 18 1 0 0 28 1 28 27 28 0 1 2 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 2 1 5 0 0 12 0 0 0 0 7 10 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 1 2 0 0 0 15 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 7 24 23 28 0 0 0 1 0 28 3 16 0 0 0 0 0 0 0 0 0 0

dyads_m6_shift13 (dyads_m6dyads_m6)
; oligos_8nt_mkv2_m11 versus dyads_m6 (dyads_m6dyads_m6); m=8/8; ncol2=14; w=8; offset=5; strand=D; shift=13; score=0.403134; -------------trCACACTgTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 c 0 0 0 0 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 g 0 0 0 0 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 t 0 0 0 0 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m8_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m8_shift0 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8)
; oligos_7nt_mkv2_m8 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8); m=0 (reference); ncol1=11; shift=0; ncol=13; smCCCTGCCwc-- ; Alignment reference a 4 10 0 0 0 0 2 0 0 9 6 0 0 c 20 15 34 33 34 3 0 34 34 4 16 0 0 g 9 5 0 1 0 0 32 0 0 5 6 0 0 t 1 4 0 0 0 31 0 0 0 16 6 0 0

oligos_7nt_mkv2_m8_shift0 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8)
; oligos_7nt_mkv2_m8 versus oligos_7nt_mkv2_m8 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8); m=1/6; ncol2=11; w=11; offset=0; strand=D; shift=0; score= 1; smCCCTGCCwc-- ; cor=; Ncor= a 4 10 0 0 0 0 2 0 0 9 6 0 0 c 20 15 34 33 34 3 0 34 34 4 16 0 0 g 9 5 0 1 0 0 32 0 0 5 6 0 0 t 1 4 0 0 0 31 0 0 0 16 6 0 0

dyads_m11_shift0 (dyads_m11dyads_m11)
; oligos_7nt_mkv2_m8 versus dyads_m11 (dyads_m11dyads_m11); m=2/6; ncol2=12; w=11; offset=0; strand=D; shift=0; score=0.908767; ccCCCTGCCwct- ; cor=; Ncor= a 2 7 0 0 0 0 0 1 0 9 5 7 0 c 19 15 28 29 29 0 0 28 29 2 16 6 0 g 7 3 1 0 0 0 29 0 0 0 5 3 0 t 1 4 0 0 0 29 0 0 0 18 3 13 0

dyads_m30_shift0 (dyads_m30dyads_m30)
; oligos_7nt_mkv2_m8 versus dyads_m30 (dyads_m30dyads_m30); m=3/6; ncol2=11; w=11; offset=0; strand=D; shift=0; score=0.815323; ymCCCMGCCyr-- ; cor=; Ncor= a 2 4 0 0 0 8 0 0 0 2 3 0 0 c 3 3 11 11 11 3 0 11 11 4 2 0 0 g 2 2 0 0 0 0 11 0 0 2 4 0 0 t 4 2 0 0 0 0 0 0 0 3 2 0 0

oligos_8nt_mkv2_m20_rc_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc)
; oligos_7nt_mkv2_m8 versus oligos_8nt_mkv2_m20_rc (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc); m=4/6; ncol2=13; w=11; offset=0; strand=R; shift=0; score=0.790515; CyCCCTGCCTCws ; cor=; Ncor= a 2 3 0 0 0 1 0 1 0 1 0 7 0 c 19 14 26 20 26 0 0 25 26 0 23 6 11 g 3 1 0 0 0 0 25 0 0 0 2 2 13 t 2 8 0 6 0 25 1 0 0 25 1 11 2

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m8 versus oligos_6nt_mkv2_m4_rc (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc); m=5/6; ncol2=10; w=9; offset=2; strand=R; shift=2; score=0.659469; --cyCTGCCTsh- ; cor=; Ncor= a 0 0 8 6 0 0 0 0 0 0 4 16 0 c 0 0 32 23 59 0 0 59 59 0 33 16 0 g 0 0 6 12 0 0 59 0 0 0 15 10 0 t 0 0 13 18 0 59 0 0 0 59 7 17 0

oligos_7nt_mkv2_m11_shift2 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11)
; oligos_7nt_mkv2_m8 versus oligos_7nt_mkv2_m11 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11); m=6/6; ncol2=11; w=9; offset=2; strand=D; shift=2; score=0.613286; --CyCTGCCTChs ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 0 0 10 0 c 0 0 27 18 34 0 0 35 35 0 35 11 15 g 0 0 1 2 1 1 35 0 0 0 0 2 17 t 0 0 4 15 0 34 0 0 0 35 0 12 3

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift6 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=0 (reference); ncol1=11; shift=6; ncol=23; ------AmACTGAAAAw------ ; Alignment reference a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0

oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=1/10; ncol2=11; w=11; offset=0; strand=D; shift=6; score= 1; ------AmACTGAAAAw------ ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0

oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)
; oligos_7nt_mkv2_m5 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=2/10; ncol2=13; w=11; offset=-1; strand=D; shift=5; score=0.838355; -----WAmACTGAAAAwC----- ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0

oligos_7nt_mkv2_m6_shift8 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=3/10; ncol2=11; w=9; offset=2; strand=D; shift=8; score=0.625742; --------msTGAAAAAyr---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 0 0 0 0 c 0 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 0 0 0 0 g 0 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 0 0 0 0 t 0 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4 0 0 0 0

oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)
; oligos_7nt_mkv2_m5 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=4/10; ncol2=12; w=9; offset=2; strand=R; shift=8; score=0.596075; --------MsTGAAAAACrt--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0

dyads_m24_shift1 (dyads_m24dyads_m24)
; oligos_7nt_mkv2_m5 versus dyads_m24 (dyads_m24dyads_m24); m=5/10; ncol2=18; w=11; offset=-5; strand=D; shift=1; score=0.533199; -ygRRAAAmsTGAAAAwyr---- ; cor=; Ncor= a 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 0 0 0 c 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 0 0 0 g 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 0 0 0 t 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0 0 0 0

dyads_m29_shift8 (dyads_m29dyads_m29)
; oligos_7nt_mkv2_m5 versus dyads_m29 (dyads_m29dyads_m29); m=6/10; ncol2=12; w=9; offset=2; strand=D; shift=8; score=0.524527; --------AmTGArAAAyry--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 c 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 g 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 t 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0

dyads_m4_shift0 (dyads_m4dyads_m4)
; oligos_7nt_mkv2_m5 versus dyads_m4 (dyads_m4dyads_m4); m=7/10; ncol2=21; w=11; offset=-6; strand=D; shift=0; score=0.489718; gCkRRAAAACTGAAAATCAyR-- ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0

oligos_8nt_mkv2_m16_shift9 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)
; oligos_7nt_mkv2_m5 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=8/10; ncol2=12; w=8; offset=3; strand=D; shift=9; score=0.467186; ---------YkGAAAATsAyr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 c 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 g 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 t 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0

dyads_m7_shift6 (dyads_m7dyads_m7)
; oligos_7nt_mkv2_m5 versus dyads_m7 (dyads_m7dyads_m7); m=9/10; ncol2=23; w=11; offset=0; strand=D; shift=6; score=0.456224; ------mmACTkrAAAwcdTGrA ; cor=; Ncor= a 0 0 0 0 0 0 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 c 0 0 0 0 0 0 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 g 0 0 0 0 0 0 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 t 0 0 0 0 0 0 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4

oligos_8nt_mkv2_m6_shift1 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; oligos_7nt_mkv2_m5 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=10/10; ncol2=18; w=11; offset=-5; strand=D; shift=1; score=0.427826; -CrTGRAAAATGAGAAAwr---- ; cor=; Ncor= a 0 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 c 0 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 g 0 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 t 0 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m10_shift5 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift5 (dyads_m10dyads_m10)
; dyads_m10 (dyads_m10dyads_m10); m=0 (reference); ncol1=15; shift=5; ncol=26; -----TTCTCATTTTCCaTG------ ; Alignment reference a 0 0 0 0 0 5 4 0 0 0 66 2 3 5 0 0 0 44 5 12 0 0 0 0 0 0 c 0 0 0 0 0 2 9 71 1 72 2 4 9 10 0 72 71 14 9 7 0 0 0 0 0 0 g 0 0 0 0 0 9 4 1 0 0 1 10 4 2 0 0 0 12 8 51 0 0 0 0 0 0 t 0 0 0 0 0 56 55 0 71 0 3 56 56 55 72 0 1 2 50 2 0 0 0 0 0 0

dyads_m10_shift5 (dyads_m10dyads_m10)
; dyads_m10 versus dyads_m10 (dyads_m10dyads_m10); m=1/8; ncol2=15; w=15; offset=0; strand=D; shift=5; score= 1; -----TTCTCATTTTCCaTG------ ; cor=; Ncor= a 0 0 0 0 0 5 4 0 0 0 66 2 3 5 0 0 0 44 5 12 0 0 0 0 0 0 c 0 0 0 0 0 2 9 71 1 72 2 4 9 10 0 72 71 14 9 7 0 0 0 0 0 0 g 0 0 0 0 0 9 4 1 0 0 1 10 4 2 0 0 0 12 8 51 0 0 0 0 0 0 t 0 0 0 0 0 56 55 0 71 0 3 56 56 55 72 0 1 2 50 2 0 0 0 0 0 0

oligos_8nt_mkv2_m6_rc_shift2 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6_rc)
; dyads_m10 versus oligos_8nt_mkv2_m6_rc (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6_rc); m=2/8; ncol2=18; w=15; offset=-3; strand=R; shift=2; score=0.800837; --ywTTTCTCATTTTYCAyG------ ; cor=; Ncor= a 0 0 1 52 2 0 0 15 4 1 99 1 1 0 0 0 0 87 3 7 0 0 0 0 0 0 c 0 0 32 0 0 0 1 85 2 99 0 0 0 0 0 73 96 2 30 2 0 0 0 0 0 0 g 0 0 1 23 0 1 1 1 0 0 1 1 0 0 0 2 2 13 3 89 0 0 0 0 0 0 t 0 0 68 27 100 101 100 1 96 2 2 100 101 102 102 27 4 0 66 4 0 0 0 0 0 0

oligos_7nt_mkv2_m10_rc_shift6 (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10_rc)
; dyads_m10 versus oligos_7nt_mkv2_m10_rc (oligos_7nt_mkv2_m10oligos_7nt_mkv2_m10_rc); m=3/8; ncol2=11; w=11; offset=1; strand=R; shift=6; score=0.703083; ------TCTCATTTTYC--------- ; cor=; Ncor= a 0 0 0 0 0 0 1 18 0 0 112 0 2 0 0 0 2 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 17 77 0 112 0 0 0 0 0 77 105 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 2 16 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 92 1 112 0 0 112 110 112 112 34 3 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m16_rc_shift6 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16_rc)
; dyads_m10 versus oligos_8nt_mkv2_m16_rc (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16_rc); m=4/8; ncol2=12; w=12; offset=1; strand=R; shift=6; score=0.591029; ------yrTsATTTTCmR-------- ; cor=; Ncor= a 0 0 0 0 0 0 5 36 0 0 73 0 1 0 0 0 39 19 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 36 15 0 26 0 0 0 0 0 72 25 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1 19 1 46 0 0 1 0 0 0 2 52 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 31 3 72 1 0 73 71 73 73 1 7 2 0 0 0 0 0 0 0 0

dyads_m27_rc_shift0 (dyads_m27dyads_m27_rc)
; dyads_m10 versus dyads_m27_rc (dyads_m27dyads_m27_rc); m=5/8; ncol2=18; w=13; offset=-5; strand=R; shift=0; score=0.588429; dswTTTThTmATTTTCCr-------- ; cor=; Ncor= a 19 4 23 13 1 0 0 18 11 18 54 2 0 0 1 0 8 39 0 0 0 0 0 0 0 0 c 3 20 1 0 0 0 13 27 8 41 0 0 0 0 0 63 48 7 0 0 0 0 0 0 0 0 g 27 34 5 0 0 0 0 1 2 3 6 0 0 0 0 0 4 17 0 0 0 0 0 0 0 0 t 17 8 37 53 65 66 53 20 45 4 6 64 66 66 65 3 6 3 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m14_rc_shift10 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc)
; dyads_m10 versus oligos_8nt_mkv2_m14_rc (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc); m=6/8; ncol2=12; w=10; offset=5; strand=R; shift=10; score=0.574052; ----------ATTTTCCATGwT---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 79 2 10 0 1 0 0 72 0 3 34 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 83 80 0 9 0 0 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 2 11 0 79 3 1 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 3 78 73 83 81 0 1 0 74 1 46 68 0 0 0 0

dyads_m7_rc_shift8 (dyads_m7dyads_m7_rc)
; dyads_m10 versus dyads_m7_rc (dyads_m7dyads_m7_rc); m=7/8; ncol2=23; w=12; offset=3; strand=R; shift=8; score=0.414247; --------TcATTTTyCAhgwTTTym ; cor=; Ncor= a 0 0 0 0 0 0 0 0 18 14 107 0 0 4 4 3 2 75 31 7 35 6 10 4 4 28 c 0 0 0 0 0 0 0 0 6 71 0 0 0 3 15 51 83 16 31 15 3 16 3 2 29 65 g 0 0 0 0 0 0 0 0 2 15 0 0 0 5 1 16 2 13 5 68 2 3 14 5 4 4 t 0 0 0 0 0 0 0 0 81 7 0 107 107 95 87 37 20 3 40 17 67 82 80 96 70 10

dyads_m29_rc_shift1 (dyads_m29dyads_m29_rc)
; dyads_m10 versus dyads_m29_rc (dyads_m29dyads_m29_rc); m=8/8; ncol2=12; w=8; offset=-4; strand=R; shift=1; score=0.400944; -ryrTTTyTCAkT------------- ; cor=; Ncor= a 0 65 5 46 0 1 0 0 0 1 154 3 6 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 5 48 0 0 0 0 108 0 160 0 19 14 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 87 6 103 0 0 0 0 0 0 9 43 4 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 6 104 14 163 162 163 55 163 2 0 98 139 0 0 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m13_shift1 ; 26 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=0 (reference); ncol1=17; shift=1; ncol=18; -wdgCAGCAGCTGTTCwv ; Alignment reference a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=1/25; ncol2=17; w=17; offset=0; strand=D; shift=1; score= 1; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0

oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=2/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.969646; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1

oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=3/25; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.900447; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=4/25; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.89486; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=5/25; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.871323; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2

oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=6/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.86254; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5

oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m13 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=7/25; ncol2=16; w=16; offset=1; strand=R; shift=2; score=0.836424; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8

dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)
; oligos_8nt_mkv2_m13 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=8/25; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=0.833349; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3

dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)
; oligos_8nt_mkv2_m13 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=9/25; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.829159; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0

oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=10/25; ncol2=18; w=17; offset=0; strand=D; shift=1; score=0.78672; -sygCAGCAGCTGCTGcr ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4

oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)
; oligos_8nt_mkv2_m13 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=11/25; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.767952; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m13 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=12/25; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.737374; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)
; oligos_8nt_mkv2_m13 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=13/25; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.735751; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22

dyads_m3_shift3 (dyads_m3dyads_m3)
; oligos_8nt_mkv2_m13 versus dyads_m3 (dyads_m3dyads_m3); m=14/25; ncol2=15; w=15; offset=2; strand=D; shift=3; score=0.723834; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6

dyads_m21_shift3 (dyads_m21dyads_m21)
; oligos_8nt_mkv2_m13 versus dyads_m21 (dyads_m21dyads_m21); m=15/25; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.71772; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_8nt_mkv2_m13 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=16/25; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.711793; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3

dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)
; oligos_8nt_mkv2_m13 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=17/25; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.669005; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16

oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_8nt_mkv2_m13 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=18/25; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.653771; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0

oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=19/25; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.633314; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11

oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=20/25; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.632354; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11

dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)
; oligos_8nt_mkv2_m13 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=21/25; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.630006; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17

oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_8nt_mkv2_m13 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=22/25; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.625014; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17

oligos_8nt_mkv2_m25_rc_shift5 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25_rc)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m25_rc (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25_rc); m=23/25; ncol2=12; w=12; offset=4; strand=R; shift=5; score=0.546616; -----ygCAACTGTTbc- ; cor=; Ncor= a 0 0 0 0 0 1 1 0 6 5 0 0 0 0 0 0 1 0 c 0 0 0 0 0 2 1 6 0 0 6 0 0 0 0 2 3 0 g 0 0 0 0 0 0 4 0 0 1 0 0 6 0 0 2 1 0 t 0 0 0 0 0 3 0 0 0 0 0 6 0 6 6 2 1 0

oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)
; oligos_8nt_mkv2_m13 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=24/25; ncol2=12; w=12; offset=2; strand=D; shift=3; score=0.54338; ---rmAGCAGGTGst--- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0

oligos_7nt_mkv2_m12_rc_shift5 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12_rc)
; oligos_8nt_mkv2_m13 versus oligos_7nt_mkv2_m12_rc (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12_rc); m=25/25; ncol2=11; w=11; offset=4; strand=R; shift=5; score=0.46688; -----krCAACTGTks-- ; cor=; Ncor= a 0 0 0 0 0 2 5 0 12 12 0 0 0 0 1 1 0 0 c 0 0 0 0 0 2 2 12 0 0 12 0 0 0 0 6 0 0 g 0 0 0 0 0 4 5 0 0 0 0 0 12 0 5 4 0 0 t 0 0 0 0 0 4 0 0 0 0 0 12 0 12 6 1 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m11_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m11_shift2 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11)
; oligos_7nt_mkv2_m11 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11); m=0 (reference); ncol1=11; shift=2; ncol=13; --CyCTGCCTChs ; Alignment reference a 0 0 3 0 0 0 0 0 0 0 0 10 0 c 0 0 27 18 34 0 0 35 35 0 35 11 15 g 0 0 1 2 1 1 35 0 0 0 0 2 17 t 0 0 4 15 0 34 0 0 0 35 0 12 3

oligos_7nt_mkv2_m11_shift2 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11)
; oligos_7nt_mkv2_m11 versus oligos_7nt_mkv2_m11 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11); m=1/7; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 1; --CyCTGCCTChs ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 0 0 10 0 c 0 0 27 18 34 0 0 35 35 0 35 11 15 g 0 0 1 2 1 1 35 0 0 0 0 2 17 t 0 0 4 15 0 34 0 0 0 35 0 12 3

oligos_6nt_mkv2_m4_rc_shift2 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m11 versus oligos_6nt_mkv2_m4_rc (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc); m=2/7; ncol2=10; w=10; offset=0; strand=R; shift=2; score=0.875357; --cyCTGCCTsh- ; cor=; Ncor= a 0 0 8 6 0 0 0 0 0 0 4 16 0 c 0 0 32 23 59 0 0 59 59 0 33 16 0 g 0 0 6 12 0 0 59 0 0 0 15 10 0 t 0 0 13 18 0 59 0 0 0 59 7 17 0

oligos_8nt_mkv2_m20_rc_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc)
; oligos_7nt_mkv2_m11 versus oligos_8nt_mkv2_m20_rc (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc); m=3/7; ncol2=13; w=11; offset=-2; strand=R; shift=0; score=0.830223; CyCCCTGCCTCws ; cor=; Ncor= a 2 3 0 0 0 1 0 1 0 1 0 7 0 c 19 14 26 20 26 0 0 25 26 0 23 6 11 g 3 1 0 0 0 0 25 0 0 0 2 2 13 t 2 8 0 6 0 25 1 0 0 25 1 11 2

dyads_m11_shift0 (dyads_m11dyads_m11)
; oligos_7nt_mkv2_m11 versus dyads_m11 (dyads_m11dyads_m11); m=4/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=0.699274; ccCCCTGCCwct- ; cor=; Ncor= a 2 7 0 0 0 0 0 1 0 9 5 7 0 c 19 15 28 29 29 0 0 28 29 2 16 6 0 g 7 3 1 0 0 0 29 0 0 0 5 3 0 t 1 4 0 0 0 29 0 0 0 18 3 13 0

oligos_8nt_mkv2_m23_shift1 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23)
; oligos_7nt_mkv2_m11 versus oligos_8nt_mkv2_m23 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23); m=5/7; ncol2=12; w=11; offset=-1; strand=D; shift=1; score=0.664623; -hkCCTTCCTCyb ; cor=; Ncor= a 0 3 1 0 0 0 0 0 0 0 0 0 0 c 0 2 1 8 8 0 0 8 8 0 8 3 3 g 0 0 2 0 0 1 0 0 0 0 0 1 2 t 0 3 4 0 0 7 8 0 0 8 0 4 3

oligos_7nt_mkv2_m8_shift0 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8)
; oligos_7nt_mkv2_m11 versus oligos_7nt_mkv2_m8 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8); m=6/7; ncol2=11; w=9; offset=-2; strand=D; shift=0; score=0.613286; smCCCTGCCwc-- ; cor=; Ncor= a 4 10 0 0 0 0 2 0 0 9 6 0 0 c 20 15 34 33 34 3 0 34 34 4 16 0 0 g 9 5 0 1 0 0 32 0 0 5 6 0 0 t 1 4 0 0 0 31 0 0 0 16 6 0 0

oligos_6nt_mkv2_m7_shift5 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7)
; oligos_7nt_mkv2_m11 versus oligos_6nt_mkv2_m7 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7); m=7/7; ncol2=10; w=8; offset=3; strand=D; shift=5; score=0.47595; -----hgCCTCCC ; cor=; Ncor= a 0 0 0 0 0 10 6 0 0 0 0 0 0 c 0 0 0 0 0 10 7 40 40 0 40 40 40 g 0 0 0 0 0 5 19 0 0 0 0 0 0 t 0 0 0 0 0 15 8 0 0 40 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift6 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=0 (reference); ncol1=10; shift=6; ncol=16; ------ssCCCCGCsg ; Alignment reference a 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 1 c 0 0 0 0 0 0 10 7 23 21 23 24 0 25 8 6 g 0 0 0 0 0 0 11 9 2 4 2 1 25 0 9 15 t 0 0 0 0 0 0 4 6 0 0 0 0 0 0 6 3

oligos_6nt_mkv2_m5_shift6 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=1/9; ncol2=10; w=10; offset=0; strand=D; shift=6; score= 1; ------ssCCCCGCsg ; cor=; Ncor= a 0 0 0 0 0 0 0 3 0 0 0 0 0 0 2 1 c 0 0 0 0 0 0 10 7 23 21 23 24 0 25 8 6 g 0 0 0 0 0 0 11 9 2 4 2 1 25 0 9 15 t 0 0 0 0 0 0 4 6 0 0 0 0 0 0 6 3

dyads_m30_shift6 (dyads_m30dyads_m30)
; oligos_6nt_mkv2_m5 versus dyads_m30 (dyads_m30dyads_m30); m=2/9; ncol2=11; w=10; offset=0; strand=D; shift=6; score=0.690755; ------ymCCCMGCCy ; cor=; Ncor= a 0 0 0 0 0 0 2 4 0 0 0 8 0 0 0 2 c 0 0 0 0 0 0 3 3 11 11 11 3 0 11 11 4 g 0 0 0 0 0 0 2 2 0 0 0 0 11 0 0 2 t 0 0 0 0 0 0 4 2 0 0 0 0 0 0 0 3

oligos_7nt_mkv2_m7_shift6 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=3/9; ncol2=11; w=10; offset=0; strand=D; shift=6; score=0.681037; ------ssCCCGGCGs ; cor=; Ncor= a 0 0 0 0 0 0 4 5 1 1 0 0 3 2 0 4 c 0 0 0 0 0 0 17 11 34 29 32 4 5 33 0 11 g 0 0 0 0 0 0 11 14 1 3 4 32 28 1 33 17 t 0 0 0 0 0 0 4 6 0 3 0 0 0 0 3 4

dyads_m12_shift5 (dyads_m12dyads_m12)
; oligos_6nt_mkv2_m5 versus dyads_m12 (dyads_m12dyads_m12); m=4/9; ncol2=14; w=10; offset=-1; strand=D; shift=5; score=0.664288; -----vssCCSCGCSG ; cor=; Ncor= a 0 0 0 0 0 3 0 1 1 0 0 0 0 0 0 0 c 0 0 0 0 0 3 5 6 9 9 8 11 0 10 8 1 g 0 0 0 0 0 3 4 4 1 2 3 0 11 1 3 10 t 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0

oligos_7nt_mkv2_m15_shift7 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)
; oligos_6nt_mkv2_m5 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=5/9; ncol2=11; w=9; offset=1; strand=D; shift=7; score=0.653332; -------ssCCCGCCG ; cor=; Ncor= a 0 0 0 0 0 0 0 4 4 0 1 0 0 3 0 0 c 0 0 0 0 0 0 0 7 11 23 24 26 0 19 23 2 g 0 0 0 0 0 0 0 11 8 3 2 1 27 5 4 25 t 0 0 0 0 0 0 0 5 4 1 0 0 0 0 0 0

oligos_6nt_mkv2_m6_rc_shift7 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6_rc)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m6_rc (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6_rc); m=6/9; ncol2=11; w=9; offset=1; strand=R; shift=7; score=0.565184; -------sCCCGGCGG ; cor=; Ncor= a 0 0 0 0 0 0 0 1 2 1 0 0 0 0 0 1 c 0 0 0 0 0 0 0 11 18 20 23 4 3 25 1 3 g 0 0 0 0 0 0 0 10 4 3 3 22 23 1 25 21 t 0 0 0 0 0 0 0 4 2 2 0 0 0 0 0 1

dyads_m26_shift8 (dyads_m26dyads_m26)
; oligos_6nt_mkv2_m5 versus dyads_m26 (dyads_m26dyads_m26); m=7/9; ncol2=12; w=8; offset=2; strand=D; shift=8; score=0.521724; --------csCCGcsG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 0 1 0 1 4 3 0 c 0 0 0 0 0 0 0 0 19 15 25 27 1 15 13 2 g 0 0 0 0 0 0 0 0 6 10 2 1 26 6 11 24 t 0 0 0 0 0 0 0 0 2 3 0 0 0 3 1 2

oligos_8nt_mkv2_m15_shift8 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)
; oligos_6nt_mkv2_m5 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=8/9; ncol2=12; w=8; offset=2; strand=D; shift=8; score=0.499164; --------vcCCGCCG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4 0 0 1 0 1 0 0 c 0 0 0 0 0 0 0 0 6 9 14 13 0 12 12 1 g 0 0 0 0 0 0 0 0 4 3 0 0 14 1 2 13 t 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0

dyads_m34_shift0 (dyads_m34dyads_m34)
; oligos_6nt_mkv2_m5 versus dyads_m34 (dyads_m34dyads_m34); m=9/9; ncol2=15; w=9; offset=-6; strand=D; shift=0; score=0.407543; ssACGcrsssCCGvs- ; cor=; Ncor= a 1 4 15 0 0 3 8 2 2 2 3 0 0 6 2 0 c 6 7 3 21 1 11 4 7 7 7 15 19 0 6 8 0 g 10 7 2 0 20 5 7 9 11 9 3 2 21 7 8 0 t 4 3 1 0 0 2 2 3 1 3 0 0 0 2 3 0

One-to-n matrix alignment; reference matrix: dyads_m40_shift5 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m40_shift5 (dyads_m40dyads_m40)
; dyads_m40 (dyads_m40dyads_m40); m=0 (reference); ncol1=25; shift=5; ncol=30; -----AAAATGAGAAATrCACAcTkTAGGA ; Alignment reference a 0 0 0 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 14 54 c 0 0 0 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 3 5 g 0 0 0 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 45 2 t 0 0 0 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0 2 3

dyads_m40_shift5 (dyads_m40dyads_m40)
; dyads_m40 versus dyads_m40 (dyads_m40dyads_m40); m=1/10; ncol2=25; w=25; offset=0; strand=D; shift=5; score= 1; -----AAAATGAGAAATrCACAcTkTAGGA ; cor=; Ncor= a 0 0 0 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 14 54 c 0 0 0 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 3 5 g 0 0 0 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 45 2 t 0 0 0 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0 2 3

dyads_m20_rc_shift7 (dyads_m20dyads_m20_rc)
; dyads_m40 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=2/10; ncol2=23; w=23; offset=2; strand=R; shift=7; score=0.902772; -------AATGAGAAAtrCACACTkTAGGA ; cor=; Ncor= a 0 0 0 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 4 0 60 0 10 48 c 0 0 0 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 3 0 0 0 3 4 g 0 0 0 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 35 0 0 60 44 0 t 0 0 0 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46 18 60 0 0 3 8

dyads_m9_shift3 (dyads_m9dyads_m9)
; dyads_m40 versus dyads_m9 (dyads_m9dyads_m9); m=3/10; ncol2=26; w=24; offset=-2; strand=D; shift=3; score=0.819302; ---GrAAAwtrarAAAtgcaCAcTGTAGr- ; cor=; Ncor= a 0 0 0 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 24 0 c 0 0 0 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 6 0 g 0 0 0 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 47 0 t 0 0 0 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13 10 0

dyads_m6_shift16 (dyads_m6dyads_m6)
; dyads_m40 versus dyads_m6 (dyads_m6dyads_m6); m=4/10; ncol2=14; w=14; offset=11; strand=D; shift=16; score=0.548362; ----------------trCACACTgTAGrA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 78 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 5 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1 8

oligos_8nt_mkv2_m11_shift11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11)
; dyads_m40 versus oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=5/10; ncol2=13; w=13; offset=6; strand=D; shift=11; score=0.50842; -----------AGAAATRCACACT------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 59 4 71 72 71 0 18 0 68 0 72 1 3 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 2 2 71 1 72 0 52 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 3 63 0 0 0 1 50 0 1 0 0 9 3 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 10 3 0 0 1 69 2 1 2 0 0 10 66 0 0 0 0 0 0

oligos_8nt_mkv2_m26_rc_shift16 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)
; dyads_m40 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=6/10; ncol2=12; w=12; offset=11; strand=R; shift=16; score=0.452904; ----------------trCACACTGTAG-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 40 0 87 0 87 1 4 5 0 65 8 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 79 0 86 0 85 0 1 0 1 10 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 24 0 0 0 0 0 1 69 0 7 63 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 5 8 0 1 0 1 82 12 87 14 6 0 0

dyads_m23_shift17 (dyads_m23dyads_m23)
; dyads_m40 versus dyads_m23 (dyads_m23dyads_m23); m=7/10; ncol2=12; w=12; offset=12; strand=D; shift=17; score=0.44426; -----------------gMACAcTGTAGr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1 0

dyads_m27_shift2 (dyads_m27dyads_m27)
; dyads_m40 versus dyads_m27 (dyads_m27dyads_m27); m=8/10; ncol2=18; w=15; offset=-3; strand=D; shift=2; score=0.440949; --yGGAAAATkAdAAAAwsh---------- ; cor=; Ncor= a 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 0 0 0 0 0 0 0 0 0 c 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 0 0 0 0 0 0 0 0 0 g 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 0 0 0 0 0 0 0 0 0 t 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0 0 0 0 0 0 0 0 0 0

dyads_m29_shift7 (dyads_m29dyads_m29)
; dyads_m40 versus dyads_m29 (dyads_m29dyads_m29); m=9/10; ncol2=12; w=12; offset=2; strand=D; shift=7; score=0.427977; -------AmTGArAAAyry----------- ; cor=; Ncor= a 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m6_shift0 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6)
; dyads_m40 versus oligos_8nt_mkv2_m6 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6); m=10/10; ncol2=18; w=13; offset=-5; strand=D; shift=0; score=0.422638; CrTGRAAAATGAGAAAwr------------ ; cor=; Ncor= a 4 66 0 4 27 102 102 101 100 2 2 96 1 100 101 100 27 68 0 0 0 0 0 0 0 0 0 0 0 0 c 89 3 13 2 2 0 0 0 1 1 0 0 1 1 1 0 23 1 0 0 0 0 0 0 0 0 0 0 0 0 g 2 30 2 96 73 0 0 0 0 0 99 2 85 1 0 0 0 32 0 0 0 0 0 0 0 0 0 0 0 0 t 7 3 87 0 0 0 0 1 1 99 1 4 15 0 0 2 52 1 0 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m18_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m18_shift0 (dyads_m18dyads_m18)
; dyads_m18 (dyads_m18dyads_m18); m=0 (reference); ncol1=19; shift=0; ncol=25; CCATATTCCAkGTCCTACA------ ; Alignment reference a 9 3 95 1 94 3 16 6 22 74 16 3 2 3 0 1 94 19 80 0 0 0 0 0 0 c 65 72 0 0 0 10 3 65 65 16 18 4 6 69 95 0 0 67 6 0 0 0 0 0 0 g 1 17 0 0 0 6 4 4 3 1 37 78 8 8 0 1 0 3 3 0 0 0 0 0 0 t 20 3 0 94 1 76 72 20 5 4 24 10 79 15 0 93 1 6 6 0 0 0 0 0 0

dyads_m18_shift0 (dyads_m18dyads_m18)
; dyads_m18 versus dyads_m18 (dyads_m18dyads_m18); m=1/5; ncol2=19; w=19; offset=0; strand=D; shift=0; score= 1; CCATATTCCAkGTCCTACA------ ; cor=; Ncor= a 9 3 95 1 94 3 16 6 22 74 16 3 2 3 0 1 94 19 80 0 0 0 0 0 0 c 65 72 0 0 0 10 3 65 65 16 18 4 6 69 95 0 0 67 6 0 0 0 0 0 0 g 1 17 0 0 0 6 4 4 3 1 37 78 8 8 0 1 0 3 3 0 0 0 0 0 0 t 20 3 0 94 1 76 72 20 5 4 24 10 79 15 0 93 1 6 6 0 0 0 0 0 0

dyads_m14_shift0 (dyads_m14dyads_m14)
; dyads_m18 versus dyads_m14 (dyads_m14dyads_m14); m=2/5; ncol2=21; w=19; offset=0; strand=D; shift=0; score=0.872917; cCATAtwCcakGTcCTACAgT---- ; cor=; Ncor= a 19 7 90 0 89 3 28 6 21 58 18 14 15 7 11 8 90 0 90 16 16 0 0 0 0 c 52 64 0 0 1 16 3 67 51 16 9 5 3 58 64 14 0 89 0 7 4 0 0 0 0 g 1 14 0 0 0 11 2 9 5 10 36 67 3 5 9 2 0 0 0 54 2 0 0 0 0 t 18 5 0 90 0 60 57 8 13 6 27 4 69 20 6 66 0 1 0 13 68 0 0 0 0

dyads_m32_rc_shift0 (dyads_m32dyads_m32_rc)
; dyads_m18 versus dyads_m32_rc (dyads_m32dyads_m32_rc); m=3/5; ncol2=25; w=19; offset=0; strand=R; shift=0; score=0.745917; cCATATTyCAgGTCCTACAgTGTGy ; cor=; Ncor= a 14 8 84 0 84 6 10 7 9 66 17 11 9 2 4 3 65 18 70 6 0 0 0 9 6 c 50 68 0 0 0 11 3 49 58 3 17 4 5 60 63 5 6 58 5 14 0 1 1 4 42 g 6 4 0 0 0 7 3 6 3 10 37 65 4 3 9 4 3 3 5 56 0 82 0 64 6 t 14 4 0 84 0 60 68 22 14 5 13 4 66 19 8 72 10 5 4 8 84 1 83 7 30

oligos_8nt_mkv2_m14_rc_shift2 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc)
; dyads_m18 versus oligos_8nt_mkv2_m14_rc (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc); m=4/5; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.452281; --ATTTTCCATGwT----------- ; cor=; Ncor= a 0 0 79 2 10 0 1 0 0 72 0 3 34 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 1 0 0 0 1 83 80 0 9 0 0 14 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 3 0 0 0 0 2 11 0 79 3 1 0 0 0 0 0 0 0 0 0 0 0 t 0 0 3 78 73 83 81 0 1 0 74 1 46 68 0 0 0 0 0 0 0 0 0 0 0

oligos_8nt_mkv2_m21_rc_shift8 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21_rc)
; dyads_m18 versus oligos_8nt_mkv2_m21_rc (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21_rc); m=5/5; ncol2=12; w=11; offset=8; strand=R; shift=8; score=0.419833; --------wmTGTTCTACAr----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 16 20 0 2 0 0 0 0 32 0 31 11 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 10 0 0 0 0 31 0 0 32 1 4 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 0 0 30 0 0 1 0 0 0 0 16 0 0 0 0 0 t 0 0 0 0 0 0 0 0 14 2 32 0 32 32 0 32 0 0 0 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m16_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m16_shift0 (dyads_m16dyads_m16)
; dyads_m16 (dyads_m16dyads_m16); m=0 (reference); ncol1=12; shift=0; ncol=13; ttTTAATTAAaa- ; Alignment reference a 6 6 0 1 24 23 3 1 27 26 14 12 0 c 4 4 0 0 3 1 1 0 0 2 4 6 0 g 6 4 2 0 0 1 1 3 0 0 4 4 0 t 12 14 26 27 1 3 23 24 1 0 6 6 0

dyads_m16_shift0 (dyads_m16dyads_m16)
; dyads_m16 versus dyads_m16 (dyads_m16dyads_m16); m=1/4; ncol2=12; w=12; offset=0; strand=D; shift=0; score= 1; ttTTAATTAAaa- ; cor=; Ncor= a 6 6 0 1 24 23 3 1 27 26 14 12 0 c 4 4 0 0 3 1 1 0 0 2 4 6 0 g 6 4 2 0 0 1 1 3 0 0 4 4 0 t 12 14 26 27 1 3 23 24 1 0 6 6 0

dyads_m38_rc_shift0 (dyads_m38dyads_m38_rc)
; dyads_m16 versus dyads_m38_rc (dyads_m38dyads_m38_rc); m=2/4; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.883152; wwTTATTTAAwa- ; cor=; Ncor= a 9 9 1 2 26 4 0 2 28 23 12 11 0 c 6 5 1 1 0 2 1 0 1 2 3 5 0 g 6 3 0 0 0 1 1 0 0 1 5 7 0 t 8 12 27 26 3 22 27 27 0 3 9 6 0

oligos_8nt_mkv2_m24_shift1 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24)
; dyads_m16 versus oligos_8nt_mkv2_m24 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24); m=3/4; ncol2=12; w=11; offset=1; strand=D; shift=1; score=0.708821; -wwTAAATAAAaw ; cor=; Ncor= a 0 11 13 1 31 31 23 1 29 29 28 16 11 c 0 4 1 1 0 0 1 0 0 2 0 4 6 g 0 3 6 2 0 0 1 1 2 1 2 5 2 t 0 14 12 28 1 1 7 30 1 0 2 7 13

oligos_7nt_mkv2_m9_rc_shift0 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9_rc)
; dyads_m16 versus oligos_7nt_mkv2_m9_rc (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9_rc); m=4/4; ncol2=11; w=11; offset=0; strand=R; shift=0; score= 0.7004; ctTTATTTAaw-- ; cor=; Ncor= a 3 2 0 0 12 0 1 0 13 4 5 0 0 c 6 2 0 0 0 0 0 1 0 3 1 0 0 g 1 3 1 0 0 0 0 0 0 3 3 0 0 t 3 6 12 13 1 13 12 12 0 3 4 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m12_shift1 ; 21 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=0 (reference); ncol1=16; shift=1; ncol=18; -gmyGaCAGCTGtCrkc- ; Alignment reference a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0

oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)
; oligos_8nt_mkv2_m12 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=1/20; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -gmyGaCAGCTGtCrkc- ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0

dyads_m1_shift1 (dyads_m1dyads_m1)
; oligos_8nt_mkv2_m12 versus dyads_m1 (dyads_m1dyads_m1); m=2/20; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.928003; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)
; oligos_8nt_mkv2_m12 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=3/20; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.928003; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)
; oligos_8nt_mkv2_m12 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=4/20; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.822782; --cwGaCAGCTGtCwg-- ; cor=; Ncor= a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0 0

oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)
; oligos_8nt_mkv2_m12 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=5/20; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.78905; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0

oligos_8nt_mkv2_m17_rc_shift2 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)
; oligos_8nt_mkv2_m12 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=6/20; ncol2=15; w=15; offset=1; strand=R; shift=2; score=0.783569; --cmdkCAGCTGTCasy- ; cor=; Ncor= a 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 0 c 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 0 g 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 0 t 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11 0

dyads_m19_shift1 (dyads_m19dyads_m19)
; oligos_8nt_mkv2_m12 versus dyads_m19 (dyads_m19dyads_m19); m=7/20; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.772473; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)
; oligos_8nt_mkv2_m12 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=8/20; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.771647; -srsAACAGCTGTswmm- ; cor=; Ncor= a 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 0 c 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 0 g 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 0 t 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3 0

oligos_8nt_mkv2_m3_rc_shift2 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)
; oligos_8nt_mkv2_m12 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=9/20; ncol2=15; w=15; offset=1; strand=R; shift=2; score=0.769761; --cmsKCAGCTGTCasy- ; cor=; Ncor= a 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 0 c 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 0 g 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 0 t 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10 0

dyads_m36_shift1 (dyads_m36dyads_m36)
; oligos_8nt_mkv2_m12 versus dyads_m36 (dyads_m36dyads_m36); m=10/20; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.763326; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0

oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)
; oligos_8nt_mkv2_m12 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=11/20; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.760802; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0

dyads_m5_rc_shift3 (dyads_m5dyads_m5_rc)
; oligos_8nt_mkv2_m12 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=12/20; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.740617; ---cskCAGCTGTChby- ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 0 c 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 0 g 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 0 t 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17 0

oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)
; oligos_8nt_mkv2_m12 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=13/20; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.740561; ---cskCAGCTGTCwsy- ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 0 c 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 0 g 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 0 t 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17 0

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)
; oligos_8nt_mkv2_m12 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=14/20; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.737378; --hmarCAGCTGTCwb-- ; cor=; Ncor= a 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 0 c 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 0 g 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 0 t 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0 0

dyads_m3_shift2 (dyads_m3dyads_m3)
; oligos_8nt_mkv2_m12 versus dyads_m3 (dyads_m3dyads_m3); m=15/20; ncol2=15; w=15; offset=1; strand=D; shift=2; score=0.727804; --rmArCAGCTGTCwyy- ; cor=; Ncor= a 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 0 c 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 0 g 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 0 t 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6 0

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)
; oligos_8nt_mkv2_m12 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=16/20; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.721423; -akmAGCAGCTGTCysc- ; cor=; Ncor= a 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 0 c 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 0 g 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 0 t 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8 0

dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)
; oligos_8nt_mkv2_m12 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=17/20; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.716809; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m12 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=18/20; ncol2=17; w=16; offset=-1; strand=D; shift=0; score=0.682354; vbdmAGCAGCTGTCmym- ; cor=; Ncor= a 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 0 c 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 0 g 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 0 t 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2 0

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m12 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=19/20; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.657097; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0

dyads_m2_shift1 (dyads_m2dyads_m2)
; oligos_8nt_mkv2_m12 versus dyads_m2 (dyads_m2dyads_m2); m=20/20; ncol2=18; w=16; offset=0; strand=D; shift=1; score=0.63008; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m20_shift0 (dyads_m20dyads_m20)				; dyads_m20 (dyads_m20dyads_m20); m=0 (reference); ncol1=23; shift=0; ncol=27; TCCTAmAGTGTGyaTTTCTCATT---- ; Alignment reference a 8 3 0 0 60 18 46 6 2 2 7 5 7 40 6 1 5 5 0 1 59 3 5 0 0 0 0 c 0 44 60 0 0 35 5 6 9 3 1 3 23 2 4 3 3 47 0 59 0 7 4 0 0 0 0 g 4 3 0 0 0 3 4 44 2 49 4 46 2 11 2 5 3 4 1 0 1 5 4 0 0 0 0 t 48 10 0 60 0 4 5 4 47 6 48 6 28 7 48 51 49 4 59 0 0 45 47 0 0 0 0
dyads_m20_shift0 (dyads_m20dyads_m20)				; dyads_m20 versus dyads_m20 (dyads_m20dyads_m20); m=1/10; ncol2=23; w=23; offset=0; strand=D; shift=0; score= 1; TCCTAmAGTGTGyaTTTCTCATT---- ; cor=; Ncor= a 8 3 0 0 60 18 46 6 2 2 7 5 7 40 6 1 5 5 0 1 59 3 5 0 0 0 0 c 0 44 60 0 0 35 5 6 9 3 1 3 23 2 4 3 3 47 0 59 0 7 4 0 0 0 0 g 4 3 0 0 0 3 4 44 2 49 4 46 2 11 2 5 3 4 1 0 1 5 4 0 0 0 0 t 48 10 0 60 0 4 5 4 47 6 48 6 28 7 48 51 49 4 59 0 0 45 47 0 0 0 0
dyads_m40_rc_shift0 (dyads_m40dyads_m40_rc)				; dyads_m20 versus dyads_m40_rc (dyads_m40dyads_m40_rc); m=2/10; ncol2=25; w=23; offset=0; strand=R; shift=0; score=0.902772; TCCTAmAgTGTGyATTTCTCATTTT-- ; cor=; Ncor= a 3 2 0 0 64 18 51 8 3 1 2 6 1 44 6 1 0 4 3 7 64 0 0 3 4 0 0 c 2 45 63 0 0 35 4 4 5 7 6 1 28 5 1 2 4 47 7 51 0 0 0 3 6 0 0 g 5 3 0 0 0 4 7 42 1 50 3 50 4 11 9 10 7 5 5 3 0 0 1 2 2 0 0 t 54 14 1 64 0 7 2 10 55 6 53 7 31 4 48 51 53 8 49 3 0 64 63 56 52 0 0
dyads_m9_rc_shift1 (dyads_m9dyads_m9_rc)				; dyads_m20 versus dyads_m9_rc (dyads_m9dyads_m9_rc); m=3/10; ncol2=26; w=22; offset=1; strand=R; shift=1; score=0.737463; -yCTACAgTGtgcaTTTytyawTTTyC ; cor=; Ncor= a 0 10 13 0 86 0 67 14 6 6 6 14 7 47 4 3 4 7 17 15 53 33 0 0 0 8 4 c 0 47 64 0 1 82 8 7 5 8 7 6 41 5 7 10 7 51 11 35 19 0 1 0 0 30 64 g 0 6 7 0 0 0 5 58 4 68 17 52 20 15 8 7 5 4 8 15 5 7 1 0 0 7 3 t 0 24 3 87 0 5 7 8 72 5 57 15 19 20 68 67 71 25 51 22 10 47 85 87 87 42 16
dyads_m6_rc_shift0 (dyads_m6dyads_m6_rc)				; dyads_m20 versus dyads_m6_rc (dyads_m6dyads_m6_rc); m=4/10; ncol2=14; w=14; offset=0; strand=R; shift=0; score=0.596039; TyCTAcAGTGTGya------------- ; cor=; Ncor= a 8 1 0 0 91 19 76 7 8 0 0 1 3 51 0 0 0 0 0 0 0 0 0 0 0 0 0 c 1 59 92 0 1 62 5 8 3 0 0 0 36 10 0 0 0 0 0 0 0 0 0 0 0 0 0 g 5 7 0 0 0 6 7 72 1 92 0 91 19 15 0 0 0 0 0 0 0 0 0 0 0 0 0 t 78 25 0 92 0 5 4 5 80 0 92 0 34 16 0 0 0 0 0 0 0 0 0 0 0 0 0
oligos_8nt_mkv2_m11_rc_shift6 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc)				; dyads_m20 versus oligos_8nt_mkv2_m11_rc (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc); m=5/10; ncol2=13; w=13; offset=6; strand=R; shift=6; score=0.547874; ------AGTGTGYATTTCT-------- ; cor=; Ncor= a 0 0 0 0 0 0 66 10 0 0 2 1 2 69 1 0 0 3 10 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 3 9 0 0 1 0 50 1 0 0 0 63 3 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 52 0 72 1 71 2 2 0 0 1 2 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 1 72 0 68 0 18 0 71 72 71 4 59 0 0 0 0 0 0 0 0
oligos_8nt_mkv2_m26_shift2 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26)				; dyads_m20 versus oligos_8nt_mkv2_m26 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26); m=6/10; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.494047; --CTACAGTGTGya------------- ; cor=; Ncor= a 0 0 6 14 87 12 82 1 0 1 0 8 5 56 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 63 7 0 69 1 0 0 0 0 0 24 3 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 10 1 0 1 0 85 0 86 0 79 18 9 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 8 65 0 5 4 1 87 0 87 0 40 19 0 0 0 0 0 0 0 0 0 0 0 0 0
dyads_m29_rc_shift11 (dyads_m29dyads_m29_rc)				; dyads_m20 versus dyads_m29_rc (dyads_m29dyads_m29_rc); m=7/10; ncol2=12; w=12; offset=11; strand=R; shift=11; score=0.483333; -----------ryrTTTyTCAkT---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 65 5 46 0 1 0 0 0 1 154 3 6 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 5 48 0 0 0 0 108 0 160 0 19 14 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 87 6 103 0 0 0 0 0 0 9 43 4 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 6 104 14 163 162 163 55 163 2 0 98 139 0 0 0 0
dyads_m23_rc_shift1 (dyads_m23dyads_m23_rc)				; dyads_m20 versus dyads_m23_rc (dyads_m23dyads_m23_rc); m=8/10; ncol2=12; w=12; offset=1; strand=R; shift=1; score=0.478283; -yCTACAgTGTKc-------------- ; cor=; Ncor= a 0 1 16 0 95 0 84 21 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 44 67 0 0 95 4 14 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 3 2 0 0 0 1 55 0 95 0 67 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 47 10 95 0 0 6 5 95 0 95 26 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dyads_m33_rc_shift1 (dyads_m33dyads_m33_rc)				; dyads_m20 versus dyads_m33_rc (dyads_m33dyads_m33_rc); m=9/10; ncol2=10; w=10; offset=1; strand=R; shift=1; score=0.414113; -yCTACAGTGT---------------- ; cor=; Ncor= a 0 1 2 0 76 0 75 0 0 1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 48 66 0 0 76 1 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 6 3 0 0 0 0 76 0 68 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 21 5 76 0 0 0 0 76 1 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
oligos_6nt_mkv2_m8_rc_shift12 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc)				; dyads_m20 versus oligos_6nt_mkv2_m8_rc (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc); m=10/10; ncol2=10; w=10; offset=12; strand=R; shift=12; score=0.407724; ------------tdTTTCTCay----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 5 54 0 0 0 0 0 0 98 6 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 34 5 0 0 0 154 0 154 11 44 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 30 52 0 0 0 0 0 0 32 3 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 85 43 154 154 154 0 154 0 13 101 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4dyads_m4)				; dyads_m4 (dyads_m4dyads_m4); m=0 (reference); ncol1=21; shift=0; ncol=29; gCkRRAAAACTGAAAATCAyR-------- ; Alignment reference a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 0 0 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 0 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 0 0 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0 0 0 0 0 0
dyads_m4_shift0 (dyads_m4dyads_m4)				; dyads_m4 versus dyads_m4 (dyads_m4dyads_m4); m=1/8; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 1; gCkRRAAAACTGAAAATCAyR-------- ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 0 0 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 0 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 0 0 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0 0 0 0 0 0
dyads_m24_shift1 (dyads_m24dyads_m24)				; dyads_m4 versus dyads_m24 (dyads_m24dyads_m24); m=2/8; ncol2=18; w=18; offset=1; strand=D; shift=1; score=0.700623; -ygRRAAAmsTGAAAAwyr---------- ; cor=; Ncor= a 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 0 0 0 0 0 0 0 0 0 c 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 g 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 0 0 0 0 0 0 0 0 0 t 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0 0 0 0 0 0 0 0 0 0
oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)				; dyads_m4 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=3/8; ncol2=13; w=13; offset=5; strand=D; shift=5; score=0.563196; -----WAmACTGAAAAwC----------- ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0 0 0 0 0 0
oligos_8nt_mkv2_m16_shift9 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)				; dyads_m4 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=4/8; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.542879; ---------YkGAAAATsAyr-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0 0 0 0 0 0 0
oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)				; dyads_m4 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=5/8; ncol2=11; w=11; offset=6; strand=D; shift=6; score=0.489718; ------AmACTGAAAAw------------ ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0 0 0 0 0 0 0
oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)				; dyads_m4 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=6/8; ncol2=12; w=12; offset=8; strand=R; shift=8; score=0.445154; --------MsTGAAAAACrt--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0 0 0 0 0 0
dyads_m7_shift6 (dyads_m7dyads_m7)				; dyads_m4 versus dyads_m7 (dyads_m7dyads_m7); m=7/8; ncol2=23; w=15; offset=6; strand=D; shift=6; score=0.432109; ------mmACTkrAAAwcdTGrAAAATgA ; cor=; Ncor= a 0 0 0 0 0 0 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 107 107 0 7 81 c 0 0 0 0 0 0 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 0 0 0 15 2 g 0 0 0 0 0 0 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 0 0 0 71 6 t 0 0 0 0 0 0 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4 0 0 107 14 18
dyads_m29_shift8 (dyads_m29dyads_m29)				; dyads_m4 versus dyads_m29 (dyads_m29dyads_m29); m=8/8; ncol2=12; w=12; offset=8; strand=D; shift=8; score=0.409592; --------AmTGArAAAyry--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift3 (dyads_m3dyads_m3)				; dyads_m3 (dyads_m3dyads_m3); m=0 (reference); ncol1=15; shift=3; ncol=18; ---rmArCAGCTGTCwyy ; Alignment reference a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6
dyads_m3_shift3 (dyads_m3dyads_m3)				; dyads_m3 versus dyads_m3 (dyads_m3dyads_m3); m=1/29; ncol2=15; w=15; offset=0; strand=D; shift=3; score= 1; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6
oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)				; dyads_m3 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=2/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.936315; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5
dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)				; dyads_m3 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=3/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.914462; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)				; dyads_m3 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=4/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.91171; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)				; dyads_m3 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=5/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.911546; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0
dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)				; dyads_m3 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=6/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.911042; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)				; dyads_m3 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=7/29; ncol2=16; w=15; offset=-1; strand=R; shift=2; score=0.878388; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8
oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)				; dyads_m3 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=8/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.87481; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11
oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)				; dyads_m3 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=9/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.872422; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11
dyads_m8_shift3 (dyads_m8dyads_m8)				; dyads_m3 versus dyads_m8 (dyads_m8dyads_m8); m=10/29; ncol2=15; w=15; offset=0; strand=D; shift=3; score=0.868842; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)				; dyads_m3 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=11/29; ncol2=14; w=14; offset=0; strand=R; shift=3; score=0.867342; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0
oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)				; dyads_m3 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=12/29; ncol2=15; w=15; offset=0; strand=R; shift=3; score=0.85086; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10
oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)				; dyads_m3 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=13/29; ncol2=17; w=15; offset=-2; strand=R; shift=1; score=0.836515; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)				; dyads_m3 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=14/29; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.829785; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2
dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)				; dyads_m3 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=15/29; ncol2=14; w=14; offset=1; strand=R; shift=4; score=0.828376; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17
oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)				; dyads_m3 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=16/29; ncol2=14; w=14; offset=1; strand=R; shift=4; score=0.828216; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17
oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)				; dyads_m3 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=17/29; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.82507; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6
dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)				; dyads_m3 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=18/29; ncol2=18; w=15; offset=-3; strand=R; shift=0; score=0.771503; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)				; dyads_m3 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=19/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.764256; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0
oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)				; dyads_m3 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=20/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.727804; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1
oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)				; dyads_m3 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=21/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.726765; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10
dyads_m1_shift2 (dyads_m1dyads_m1)				; dyads_m3 versus dyads_m1 (dyads_m1dyads_m1); m=22/29; ncol2=16; w=15; offset=-1; strand=D; shift=2; score=0.726765; --vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10
oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)				; dyads_m3 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=23/29; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=0.723834; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0
oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)				; dyads_m3 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=24/29; ncol2=16; w=14; offset=-2; strand=R; shift=1; score=0.716962; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0
oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)				; dyads_m3 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=25/29; ncol2=17; w=15; offset=-2; strand=R; shift=1; score=0.71002; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1
dyads_m21_shift3 (dyads_m21dyads_m21)				; dyads_m3 versus dyads_m21 (dyads_m21dyads_m21); m=26/29; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.69303; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0
dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)				; dyads_m3 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=27/29; ncol2=17; w=14; offset=-3; strand=R; shift=0; score=0.662588; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0
oligos_8nt_mkv2_m25_shift3 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)				; dyads_m3 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=28/29; ncol2=12; w=12; offset=0; strand=D; shift=3; score=0.574341; ---gvAACAGTTGcr--- ; cor=; Ncor= a 0 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 c 0 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 g 0 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 t 0 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0
oligos_7nt_mkv2_m12_shift4 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)				; dyads_m3 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=29/29; ncol2=11; w=11; offset=1; strand=D; shift=4; score=0.532562; ----smACAGTTGym--- ; cor=; Ncor= a 0 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 c 0 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 g 0 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 t 0 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m23_shift14 (dyads_m23dyads_m23)				; dyads_m23 (dyads_m23dyads_m23); m=0 (reference); ncol1=12; shift=14; ncol=26; --------------gMACAcTGTAGr ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1
dyads_m23_shift14 (dyads_m23dyads_m23)				; dyads_m23 versus dyads_m23 (dyads_m23dyads_m23); m=1/8; ncol2=12; w=12; offset=0; strand=D; shift=14; score= 1; --------------gMACAcTGTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 26 95 0 95 5 6 0 0 95 10 47 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 67 0 95 0 55 1 0 0 0 2 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 0 0 0 0 14 4 95 0 0 67 44 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 21 84 0 95 0 16 1
dyads_m6_shift13 (dyads_m6dyads_m6)				; dyads_m23 versus dyads_m6 (dyads_m6dyads_m6); m=2/8; ncol2=14; w=12; offset=-1; strand=D; shift=13; score=0.811881; -------------trCACACTgTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 16 34 0 92 0 80 5 4 5 0 92 0 25 c 0 0 0 0 0 0 0 0 0 0 0 0 0 15 19 91 0 92 1 72 7 6 0 0 0 7 g 0 0 0 0 0 0 0 0 0 0 0 0 0 10 36 0 0 0 3 8 5 62 1 0 92 59 t 0 0 0 0 0 0 0 0 0 0 0 0 0 51 3 1 0 0 8 7 76 19 91 0 0 1
oligos_8nt_mkv2_m26_rc_shift13 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc)				; dyads_m23 versus oligos_8nt_mkv2_m26_rc (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26_rc); m=3/8; ncol2=12; w=11; offset=-1; strand=R; shift=13; score=0.799973; -------------trCACACTGTAG- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 19 40 0 87 0 87 1 4 5 0 65 8 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 9 18 79 0 86 0 85 0 1 0 1 10 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 3 24 0 0 0 0 0 1 69 0 7 63 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 56 5 8 0 1 0 1 82 12 87 14 6 0
dyads_m33_shift16 (dyads_m33dyads_m33)				; dyads_m23 versus dyads_m33 (dyads_m33dyads_m33); m=4/8; ncol2=10; w=10; offset=2; strand=D; shift=16; score=0.794922; ----------------ACACTGTAGr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 54 1 76 0 0 0 0 76 5 21 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 68 0 76 0 0 0 0 3 6 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1 76 0 0 66 48 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 75 0 76 0 2 1
dyads_m20_rc_shift4 (dyads_m20dyads_m20_rc)				; dyads_m23 versus dyads_m20_rc (dyads_m20dyads_m20_rc); m=5/8; ncol2=23; w=12; offset=-10; strand=R; shift=4; score=0.478283; ----AATGAGAAAtrCACACTkTAGG ; cor=; Ncor= a 0 0 0 0 47 45 0 0 59 4 49 51 48 7 28 6 48 6 47 4 5 4 0 60 0 10 c 0 0 0 0 4 5 1 0 1 4 3 5 2 11 2 46 4 49 2 44 4 3 0 0 0 3 g 0 0 0 0 4 7 0 59 0 47 3 3 4 2 23 3 1 3 9 6 5 35 0 0 60 44 t 0 0 0 0 5 3 59 1 0 5 5 1 6 40 7 5 7 2 2 6 46 18 60 0 0 3
dyads_m32_shift14 (dyads_m32dyads_m32)				; dyads_m23 versus dyads_m32 (dyads_m32dyads_m32); m=6/8; ncol2=25; w=12; offset=0; strand=D; shift=14; score=0.45898; --------------rCACAcTGTAGG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 30 7 83 1 84 8 4 5 10 72 8 19 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 64 0 82 0 56 5 3 3 4 9 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 4 1 1 0 14 5 58 6 5 63 60 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 9 0 0 0 6 70 18 65 3 4 2
dyads_m9_shift0 (dyads_m9dyads_m9)				; dyads_m23 versus dyads_m9 (dyads_m9dyads_m9); m=7/8; ncol2=26; w=12; offset=-14; strand=D; shift=0; score=0.447898; GrAAAwtrarAAAtgcaCAcTGTAGr ; cor=; Ncor= a 16 42 87 87 85 47 10 22 51 25 71 67 68 20 19 15 57 5 72 8 7 5 0 87 3 24 c 3 7 0 0 1 7 5 15 8 4 5 7 8 15 20 52 17 68 4 58 5 0 0 0 7 6 g 64 30 0 0 1 0 19 35 11 51 7 10 7 5 41 6 7 8 5 7 8 82 1 0 64 47 t 4 8 0 0 0 33 53 15 17 7 4 3 4 47 7 14 6 6 6 14 67 0 86 0 13 10
dyads_m40_shift2 (dyads_m40dyads_m40)				; dyads_m23 versus dyads_m40 (dyads_m40dyads_m40); m=8/8; ncol2=25; w=12; offset=-12; strand=D; shift=2; score=0.44426; --AAAATGAGAAATrCACAcTkTAGG ; cor=; Ncor= a 0 0 52 56 63 64 0 3 49 8 53 51 48 4 31 7 53 6 55 10 2 7 0 64 1 14 c 0 0 2 2 1 0 0 3 5 5 7 10 9 11 4 50 3 50 1 42 7 4 0 0 0 3 g 0 0 6 3 0 0 0 51 7 47 4 2 1 5 28 1 6 7 5 4 4 35 0 0 63 45 t 0 0 4 3 0 0 64 7 3 4 0 1 6 44 1 6 2 1 3 8 51 18 64 0 0 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m26_shift2 (dyads_m26dyads_m26)				; dyads_m26 (dyads_m26dyads_m26); m=0 (reference); ncol1=12; shift=2; ncol=14; --csCCGcsGCGss ; Alignment reference a 0 0 1 0 1 0 1 4 3 0 1 0 3 2 c 0 0 19 15 25 27 1 15 13 2 24 3 10 8 g 0 0 6 10 2 1 26 6 11 24 2 25 12 16 t 0 0 2 3 0 0 0 3 1 2 1 0 3 2
dyads_m26_shift2 (dyads_m26dyads_m26)				; dyads_m26 versus dyads_m26 (dyads_m26dyads_m26); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=2; score= 1; --csCCGcsGCGss ; cor=; Ncor= a 0 0 1 0 1 0 1 4 3 0 1 0 3 2 c 0 0 19 15 25 27 1 15 13 2 24 3 10 8 g 0 0 6 10 2 1 26 6 11 24 2 25 12 16 t 0 0 2 3 0 0 0 3 1 2 1 0 3 2
oligos_8nt_mkv2_m15_shift2 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)				; dyads_m26 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=2/7; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.931423; --vcCCGCCGcGss ; cor=; Ncor= a 0 0 4 0 0 1 0 1 0 0 2 0 1 1 c 0 0 6 9 14 13 0 12 12 1 9 0 5 4 g 0 0 4 3 0 0 14 1 2 13 2 14 8 7 t 0 0 0 2 0 0 0 0 0 0 1 0 0 2
oligos_6nt_mkv2_m6_shift2 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)				; dyads_m26 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=3/7; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.742676; --ssCCGCCGGGs- ; cor=; Ncor= a 0 0 3 2 1 0 0 0 0 0 2 2 4 0 c 0 0 11 13 21 25 1 23 22 3 3 4 10 0 g 0 0 10 9 3 1 25 3 4 23 20 18 11 0 t 0 0 2 2 1 0 0 0 0 0 1 2 1 0
oligos_7nt_mkv2_m7_rc_shift3 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc)				; dyads_m26 versus oligos_7nt_mkv2_m7_rc (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc); m=4/7; ncol2=11; w=11; offset=1; strand=R; shift=3; score=0.71108; ---ssCGCCGGGss ; cor=; Ncor= a 0 0 0 2 4 3 0 0 0 0 3 0 6 4 c 0 0 0 16 17 33 1 28 32 4 3 1 14 11 g 0 0 0 14 11 0 33 5 4 32 29 34 11 17 t 0 0 0 4 4 0 2 3 0 0 1 1 5 4
oligos_7nt_mkv2_m15_shift1 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)				; dyads_m26 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=5/7; ncol2=11; w=10; offset=-1; strand=D; shift=1; score=0.678867; -ssCCCGCCGsg-- ; cor=; Ncor= a 0 4 4 0 1 0 0 3 0 0 3 3 0 0 c 0 7 11 23 24 26 0 19 23 2 10 5 0 0 g 0 11 8 3 2 1 27 5 4 25 11 18 0 0 t 0 5 4 1 0 0 0 0 0 0 3 1 0 0
dyads_m12_rc_shift2 (dyads_m12dyads_m12_rc)				; dyads_m26 versus dyads_m12_rc (dyads_m12dyads_m12_rc); m=6/7; ncol2=14; w=12; offset=0; strand=R; shift=2; score=0.62499; --ssCCSGCGSGGs ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 4 7 8 10 3 1 11 0 3 2 1 4 g 0 0 6 3 2 1 8 10 0 11 8 9 9 6 t 0 0 1 1 1 0 0 0 0 0 0 0 1 1
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)				; dyads_m26 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=7/7; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=0.521724; ssCCCCGCsg---- ; cor=; Ncor= a 0 3 0 0 0 0 0 0 2 1 0 0 0 0 c 10 7 23 21 23 24 0 25 8 6 0 0 0 0 g 11 9 2 4 2 1 25 0 9 15 0 0 0 0 t 4 6 0 0 0 0 0 0 6 3 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m36_shift1 (dyads_m36dyads_m36)				; dyads_m36 (dyads_m36dyads_m36); m=0 (reference); ncol1=15; shift=1; ncol=18; -rvkGACAGCTGctks-- ; Alignment reference a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0
dyads_m36_shift1 (dyads_m36dyads_m36)				; dyads_m36 versus dyads_m36 (dyads_m36dyads_m36); m=1/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score= 1; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0
dyads_m19_shift1 (dyads_m19dyads_m19)				; dyads_m36 versus dyads_m19 (dyads_m19dyads_m19); m=2/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score= 0.9759; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0
oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)				; dyads_m36 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=3/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.970708; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0
oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)				; dyads_m36 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=4/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.969149; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0
oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)				; dyads_m36 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=5/30; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.934337; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)				; dyads_m36 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=6/30; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.912193; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0
dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)				; dyads_m36 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=7/30; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.911042; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)				; dyads_m36 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=8/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.908563; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0
dyads_m5_shift1 (dyads_m5dyads_m5)				; dyads_m36 versus dyads_m5 (dyads_m5dyads_m5); m=9/30; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.906945; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)				; dyads_m36 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=10/30; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.905622; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0
dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)				; dyads_m36 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=11/30; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.886652; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)				; dyads_m36 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=12/30; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.872768; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0
oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)				; dyads_m36 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=13/30; ncol2=16; w=15; offset=0; strand=R; shift=1; score=0.840281; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0
oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)				; dyads_m36 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=14/30; ncol2=17; w=15; offset=0; strand=R; shift=1; score=0.830296; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7
oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)				; dyads_m36 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=15/30; ncol2=17; w=15; offset=0; strand=D; shift=1; score=0.827072; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6
oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)				; dyads_m36 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=16/30; ncol2=17; w=15; offset=0; strand=R; shift=1; score=0.818534; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)				; dyads_m36 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=17/30; ncol2=16; w=15; offset=0; strand=R; shift=1; score=0.802625; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0
oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)				; dyads_m36 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=18/30; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.795203; --cwGaCAGCTGtCwg-- ; cor=; Ncor= a 0 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 c 0 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 t 0 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0
dyads_m1_shift1 (dyads_m1dyads_m1)				; dyads_m36 versus dyads_m1 (dyads_m1dyads_m1); m=19/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.774901; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)				; dyads_m36 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=20/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.774901; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0
oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)				; dyads_m36 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=21/30; ncol2=16; w=15; offset=0; strand=D; shift=1; score=0.763326; -gmyGaCAGCTGtCrkc- ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0
dyads_m2_shift1 (dyads_m2dyads_m2)				; dyads_m36 versus dyads_m2 (dyads_m2dyads_m2); m=22/30; ncol2=18; w=15; offset=0; strand=D; shift=1; score=0.742126; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7
oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)				; dyads_m36 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=23/30; ncol2=17; w=15; offset=0; strand=R; shift=1; score=0.735751; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6
oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)				; dyads_m36 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=24/30; ncol2=17; w=15; offset=0; strand=D; shift=1; score=0.729473; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4
oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)				; dyads_m36 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=25/30; ncol2=16; w=14; offset=1; strand=D; shift=2; score=0.713013; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4
dyads_m21_shift2 (dyads_m21dyads_m21)				; dyads_m36 versus dyads_m21 (dyads_m21dyads_m21); m=26/30; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.706576; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0
dyads_m25_shift2 (dyads_m25dyads_m25)				; dyads_m36 versus dyads_m25 (dyads_m25dyads_m25); m=27/30; ncol2=17; w=14; offset=1; strand=D; shift=2; score=0.652863; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8
oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)				; dyads_m36 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=28/30; ncol2=12; w=12; offset=1; strand=D; shift=2; score=0.596803; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; dyads_m36 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=29/30; ncol2=18; w=15; offset=-1; strand=D; shift=0; score=0.583601; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2
oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)				; dyads_m36 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=30/30; ncol2=11; w=11; offset=2; strand=D; shift=3; score=0.525172; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m9_shift1 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9)				; oligos_7nt_mkv2_m9 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9); m=0 (reference); ncol1=11; shift=1; ncol=12; -wtTAAATAAag ; Alignment reference a 0 4 3 0 12 12 13 1 13 12 6 3 c 0 3 3 0 0 0 0 0 0 1 3 1 g 0 1 3 0 1 0 0 0 0 0 2 6 t 0 5 4 13 0 1 0 12 0 0 2 3
oligos_7nt_mkv2_m9_shift1 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9)				; oligos_7nt_mkv2_m9 versus oligos_7nt_mkv2_m9 (oligos_7nt_mkv2_m9oligos_7nt_mkv2_m9); m=1/4; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 1; -wtTAAATAAag ; cor=; Ncor= a 0 4 3 0 12 12 13 1 13 12 6 3 c 0 3 3 0 0 0 0 0 0 1 3 1 g 0 1 3 0 1 0 0 0 0 0 2 6 t 0 5 4 13 0 1 0 12 0 0 2 3
dyads_m38_shift0 (dyads_m38dyads_m38)				; oligos_7nt_mkv2_m9 versus dyads_m38 (dyads_m38dyads_m38); m=2/4; ncol2=12; w=11; offset=-1; strand=D; shift=0; score=0.860166; twTTAAATAAww ; cor=; Ncor= a 6 9 3 0 27 27 22 3 26 27 12 8 c 7 5 1 0 0 1 1 0 0 0 3 6 g 5 3 2 1 0 1 2 0 1 1 5 6 t 11 12 23 28 2 0 4 26 2 1 9 9
oligos_8nt_mkv2_m24_shift1 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24)				; oligos_7nt_mkv2_m9 versus oligos_8nt_mkv2_m24 (oligos_8nt_mkv2_m24oligos_8nt_mkv2_m24); m=3/4; ncol2=12; w=11; offset=0; strand=D; shift=1; score=0.851868; -wwTAAATAAAa ; cor=; Ncor= a 0 11 13 1 31 31 23 1 29 29 28 16 c 0 4 1 1 0 0 1 0 0 2 0 4 g 0 3 6 2 0 0 1 1 2 1 2 5 t 0 14 12 28 1 1 7 30 1 0 2 7
dyads_m16_shift0 (dyads_m16dyads_m16)				; oligos_7nt_mkv2_m9 versus dyads_m16 (dyads_m16dyads_m16); m=4/4; ncol2=12; w=11; offset=-1; strand=D; shift=0; score= 0.7004; ttTTAATTAAaa ; cor=; Ncor= a 6 6 0 1 24 23 3 1 27 26 14 12 c 4 4 0 0 3 1 1 0 0 2 4 6 g 6 4 2 0 0 1 1 3 0 0 4 4 t 12 14 26 27 1 3 23 24 1 0 6 6

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)				; oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=0 (reference); ncol1=16; shift=2; ncol=18; --rgmACAGCTGCTGcws ; Alignment reference a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4
oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=1/27; ncol2=16; w=16; offset=0; strand=D; shift=2; score= 1; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4
oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=2/27; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.89486; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6
oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=3/27; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.88696; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4
oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=4/27; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.883572; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7
oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=5/27; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.869366; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3
oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=6/27; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.866139; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6
dyads_m25_shift2 (dyads_m25dyads_m25)				; oligos_8nt_mkv2_m8 versus dyads_m25 (dyads_m25dyads_m25); m=7/27; ncol2=17; w=16; offset=0; strand=D; shift=2; score=0.828996; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)				; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=8/27; ncol2=16; w=15; offset=-1; strand=D; shift=1; score=0.814765; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)				; oligos_8nt_mkv2_m8 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=9/27; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.802692; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0
dyads_m2_shift1 (dyads_m2dyads_m2)				; oligos_8nt_mkv2_m8 versus dyads_m2 (dyads_m2dyads_m2); m=10/27; ncol2=18; w=16; offset=-1; strand=D; shift=1; score=0.800214; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7
oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)				; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=11/27; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.760891; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)				; oligos_8nt_mkv2_m8 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=12/27; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.725047; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)				; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=13/27; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.722913; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0
dyads_m21_shift2 (dyads_m21dyads_m21)				; oligos_8nt_mkv2_m8 versus dyads_m21 (dyads_m21dyads_m21); m=14/27; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.719563; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0
dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)				; oligos_8nt_mkv2_m8 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=15/27; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.716962; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=16/27; ncol2=18; w=16; offset=-2; strand=D; shift=0; score=0.716124; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2
dyads_m36_shift1 (dyads_m36dyads_m36)				; oligos_8nt_mkv2_m8 versus dyads_m36 (dyads_m36dyads_m36); m=17/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.713013; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0
dyads_m19_shift1 (dyads_m19dyads_m19)				; oligos_8nt_mkv2_m8 versus dyads_m19 (dyads_m19dyads_m19); m=18/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.662736; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0
oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=19/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.646746; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0
oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=20/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.645441; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0
dyads_m5_shift1 (dyads_m5dyads_m5)				; oligos_8nt_mkv2_m8 versus dyads_m5 (dyads_m5dyads_m5); m=21/27; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.620177; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)				; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=22/27; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.618683; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0
oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=23/27; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.594322; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0
dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)				; oligos_8nt_mkv2_m8 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=24/27; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.587616; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0
oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=25/27; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.547171; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0
oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)				; oligos_8nt_mkv2_m8 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=26/27; ncol2=12; w=12; offset=2; strand=R; shift=4; score=0.541527; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0
oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)				; oligos_8nt_mkv2_m8 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=27/27; ncol2=11; w=11; offset=1; strand=D; shift=3; score=0.491725; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)				; oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=0 (reference); ncol1=17; shift=1; ncol=18; -vbdmAGCAGCTGTCmym ; Alignment reference a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=1/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score= 1; -vbdmAGCAGCTGTCmym ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2
oligos_8nt_mkv2_m27_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=2/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.969442; -vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 0 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 0 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 0 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 0 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6
oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=3/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.969232; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)				; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=4/27; ncol2=16; w=16; offset=1; strand=R; shift=2; score=0.899735; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8
oligos_7nt_mkv2_m13_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)				; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=5/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.882741; --grmArCAGCTGTCwyc ; cor=; Ncor= a 0 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5
dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)				; oligos_8nt_mkv2_m1 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=6/27; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=0.88046; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3
oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=7/27; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.871323; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0
oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=8/27; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.869366; -swgCAGCAGCTGTkcy- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0
oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=9/27; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.846661; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)				; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=10/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.840343; --srsAACAGCTGTswmm ; cor=; Ncor= a 0 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3
dyads_m3_shift3 (dyads_m3dyads_m3)				; oligos_8nt_mkv2_m1 versus dyads_m3 (dyads_m3dyads_m3); m=11/27; ncol2=15; w=15; offset=2; strand=D; shift=3; score=0.829785; ---rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6
dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)				; oligos_8nt_mkv2_m1 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=12/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.818534; ---smagCAGCTGTCmby ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22
dyads_m19_rc_shift3 (dyads_m19dyads_m19_rc)				; oligos_8nt_mkv2_m1 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=13/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.798678; ---smrbCAGCTGTChby ; cor=; Ncor= a 0 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16
oligos_8nt_mkv2_m17_rc_shift3 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=14/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.792927; ---cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11
oligos_8nt_mkv2_m22_rc_shift3 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=15/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.791251; ---cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)				; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=16/27; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.783988; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0
dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)				; oligos_8nt_mkv2_m1 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=17/27; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.759677; arGrCAGCAGCTGTTmh- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0
oligos_8nt_mkv2_m3_rc_shift3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=18/27; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.753963; ---cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)				; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=19/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.742298; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0
oligos_7nt_mkv2_m4_rc_shift4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)				; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=20/27; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.732546; ----cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17
dyads_m5_rc_shift4 (dyads_m5dyads_m5_rc)				; oligos_8nt_mkv2_m1 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=21/27; ncol2=14; w=14; offset=3; strand=R; shift=4; score=0.732454; ----cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17
dyads_m8_shift3 (dyads_m8dyads_m8)				; oligos_8nt_mkv2_m1 versus dyads_m8 (dyads_m8dyads_m8); m=22/27; ncol2=15; w=15; offset=2; strand=D; shift=3; score=0.695913; ---bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10
oligos_8nt_mkv2_m12_shift2 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=23/27; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.682354; --gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1
oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=24/27; ncol2=18; w=17; offset=0; strand=D; shift=1; score=0.675737; -sygCAGCAGCTGCTGcr ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4
dyads_m21_shift3 (dyads_m21dyads_m21)				; oligos_8nt_mkv2_m1 versus dyads_m21 (dyads_m21dyads_m21); m=25/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.622768; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)				; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=26/27; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.600967; ---cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0
oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=27/27; ncol2=12; w=12; offset=2; strand=D; shift=3; score=0.511066; ---rmAGCAGGTGst--- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m24_shift4 (dyads_m24dyads_m24)				; dyads_m24 (dyads_m24dyads_m24); m=0 (reference); ncol1=18; shift=4; ncol=23; ----ygRRAAAmsTGAAAAwyr- ; Alignment reference a 0 0 0 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 c 0 0 0 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 g 0 0 0 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 t 0 0 0 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0
dyads_m24_shift4 (dyads_m24dyads_m24)				; dyads_m24 versus dyads_m24 (dyads_m24dyads_m24); m=1/9; ncol2=18; w=18; offset=0; strand=D; shift=4; score= 1; ----ygRRAAAmsTGAAAAwyr- ; cor=; Ncor= a 0 0 0 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 c 0 0 0 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 g 0 0 0 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 t 0 0 0 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0
dyads_m27_shift4 (dyads_m27dyads_m27)				; dyads_m24 versus dyads_m27 (dyads_m27dyads_m27); m=2/9; ncol2=18; w=18; offset=0; strand=D; shift=4; score=0.701163; ----yGGAAAATkAdAAAAwsh- ; cor=; Ncor= a 0 0 0 0 3 6 3 65 66 66 64 6 4 45 20 53 66 65 53 37 8 17 0 c 0 0 0 0 17 4 0 0 0 0 0 6 3 2 1 0 0 0 0 5 34 27 0 g 0 0 0 0 7 48 63 0 0 0 0 0 41 8 27 13 0 0 0 1 20 3 0 t 0 0 0 0 39 8 0 1 0 0 2 54 18 11 18 0 0 1 13 23 4 19 0
dyads_m4_shift3 (dyads_m4dyads_m4)				; dyads_m24 versus dyads_m4 (dyads_m4dyads_m4); m=3/9; ncol2=21; w=18; offset=-1; strand=D; shift=3; score=0.700623; ---gCkRRAAAACTGAAAATCAy ; cor=; Ncor= a 0 0 0 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 c 0 0 0 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 g 0 0 0 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 t 0 0 0 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4
dyads_m7_shift0 (dyads_m7dyads_m7)				; dyads_m24 versus dyads_m7 (dyads_m7dyads_m7); m=4/9; ncol2=23; w=18; offset=-4; strand=D; shift=0; score=0.638194; mmACTkrAAAwcdTGrAAAATgA ; cor=; Ncor= a 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 107 107 0 7 81 c 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 0 0 0 15 2 g 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 0 0 0 71 6 t 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4 0 0 107 14 18
oligos_8nt_mkv2_m4_shift8 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)				; dyads_m24 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=5/9; ncol2=13; w=13; offset=4; strand=D; shift=8; score=0.594764; --------WAmACTGAAAAwC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 c 0 0 0 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 g 0 0 0 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 t 0 0 0 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0
oligos_7nt_mkv2_m6_shift11 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)				; dyads_m24 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=6/9; ncol2=11; w=11; offset=7; strand=D; shift=11; score=0.583076; -----------msTGAAAAAyr- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 0 c 0 0 0 0 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 0 g 0 0 0 0 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 0 t 0 0 0 0 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4 0
oligos_7nt_mkv2_m5_shift9 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)				; dyads_m24 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=7/9; ncol2=11; w=11; offset=5; strand=D; shift=9; score=0.533199; ---------AmACTGAAAAw--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 c 0 0 0 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 g 0 0 0 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 t 0 0 0 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0
oligos_8nt_mkv2_m9_rc_shift11 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)				; dyads_m24 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=8/9; ncol2=12; w=11; offset=7; strand=R; shift=11; score=0.531012; -----------MsTGAAAAACrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 c 0 0 0 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 g 0 0 0 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 t 0 0 0 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51
dyads_m29_shift11 (dyads_m29dyads_m29)				; dyads_m24 versus dyads_m29 (dyads_m29dyads_m29); m=9/9; ncol2=12; w=11; offset=7; strand=D; shift=11; score=0.449941; -----------AmTGArAAAyry ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 c 0 0 0 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 g 0 0 0 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 t 0 0 0 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)				; oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=0 (reference); ncol1=17; shift=1; ncol=18; -swsAACAGCTGCTGchm ; Alignment reference a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4
oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=1/25; ncol2=17; w=17; offset=0; strand=D; shift=1; score= 1; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4
oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=2/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.969646; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6
oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=3/25; ncol2=16; w=16; offset=1; strand=D; shift=2; score=0.88696; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4
oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=4/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.86851; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7
oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=5/25; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.848932; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6
oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=6/25; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.846661; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=7/25; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.828917; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=8/25; ncol2=18; w=17; offset=-1; strand=D; shift=0; score=0.827759; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2
dyads_m25_shift2 (dyads_m25dyads_m25)				; oligos_8nt_mkv2_m2 versus dyads_m25 (dyads_m25dyads_m25); m=9/25; ncol2=17; w=16; offset=1; strand=D; shift=2; score=0.805868; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8
dyads_m2_shift1 (dyads_m2dyads_m2)				; oligos_8nt_mkv2_m2 versus dyads_m2 (dyads_m2dyads_m2); m=10/25; ncol2=18; w=17; offset=0; strand=D; shift=1; score=0.804693; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7
oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=11/25; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.751148; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0
dyads_m21_shift2 (dyads_m21dyads_m21)				; oligos_8nt_mkv2_m2 versus dyads_m21 (dyads_m21dyads_m21); m=12/25; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.745037; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)				; oligos_8nt_mkv2_m2 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=13/25; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.733631; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0
dyads_m36_shift1 (dyads_m36dyads_m36)				; oligos_8nt_mkv2_m2 versus dyads_m36 (dyads_m36dyads_m36); m=14/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.729473; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0
dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)				; oligos_8nt_mkv2_m2 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=15/25; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.71002; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=16/25; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.703385; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0
dyads_m19_shift1 (dyads_m19dyads_m19)				; oligos_8nt_mkv2_m2 versus dyads_m19 (dyads_m19dyads_m19); m=17/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.653747; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)				; oligos_8nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=18/25; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.652231; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0
oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=19/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.629598; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0
oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=20/25; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.627706; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0
dyads_m5_shift1 (dyads_m5dyads_m5)				; oligos_8nt_mkv2_m2 versus dyads_m5 (dyads_m5dyads_m5); m=21/25; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.624237; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=22/25; ncol2=14; w=14; offset=0; strand=D; shift=1; score=0.621102; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0
oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=23/25; ncol2=12; w=12; offset=1; strand=D; shift=2; score=0.553124; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0
oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=24/25; ncol2=12; w=12; offset=3; strand=R; shift=4; score=0.535045; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0
oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=25/25; ncol2=11; w=11; offset=2; strand=D; shift=3; score=0.468748; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=0 (reference); ncol1=14; shift=2; ncol=17; --cwGaCAGCTGtCwg- ; Alignment reference a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=1/21; ncol2=14; w=14; offset=0; strand=D; shift=2; score= 1; --cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=2/21; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.894525; --hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=3/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.868996; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10
dyads_m1_shift1 (dyads_m1dyads_m1)				; oligos_6nt_mkv2_m1 versus dyads_m1 (dyads_m1dyads_m1); m=4/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.868996; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10
dyads_m19_rc_shift2 (dyads_m19dyads_m19_rc)				; oligos_6nt_mkv2_m1 versus dyads_m19_rc (dyads_m19dyads_m19_rc); m=5/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.824628; --smrbCAGCTGTChby ; cor=; Ncor= a 0 0 9 15 18 4 0 49 0 2 0 1 0 1 16 4 10 c 0 0 17 17 10 14 50 0 0 48 0 0 2 47 14 14 16 g 0 0 15 8 13 16 0 0 49 0 0 49 0 0 3 18 8 t 0 0 9 10 9 16 0 1 1 0 50 0 48 2 17 14 16
oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=6/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.822782; -gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1
oligos_8nt_mkv2_m22_rc_shift2 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m22_rc (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22_rc); m=7/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.816836; --cmdkCAGCTGTCaby ; cor=; Ncor= a 0 0 6 10 7 1 0 28 0 0 0 0 0 0 17 1 5 c 0 0 13 9 3 0 28 0 0 27 0 0 0 27 4 9 10 g 0 0 5 4 9 17 0 0 28 0 0 28 0 1 3 11 2 t 0 0 4 5 9 10 0 0 0 1 28 0 28 0 4 7 11
oligos_8nt_mkv2_m17_rc_shift2 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m17_rc (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17_rc); m=8/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.814029; --cmdkCAGCTGTCasy ; cor=; Ncor= a 0 0 6 10 7 1 0 27 0 0 0 0 0 0 17 1 4 c 0 0 12 9 3 0 27 0 0 27 0 0 0 26 4 9 10 g 0 0 5 4 8 16 0 0 27 0 0 27 0 1 2 11 2 t 0 0 4 4 9 10 0 0 0 0 27 0 27 0 4 6 11
oligos_8nt_mkv2_m3_rc_shift2 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=9/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.808925; --cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10
dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)				; oligos_6nt_mkv2_m1 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=10/21; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.79691; -mvrGACAGCTGwGsv- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0
dyads_m36_rc_shift2 (dyads_m36dyads_m36_rc)				; oligos_6nt_mkv2_m1 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=11/21; ncol2=15; w=14; offset=0; strand=R; shift=2; score=0.795203; --smagCAGCTGTCmby ; cor=; Ncor= a 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 c 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 g 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 t 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22
oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=12/21; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.785906; --kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=13/21; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.771906; -rswGACAGCTGmsg-- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0
dyads_m5_shift1 (dyads_m5dyads_m5)				; oligos_6nt_mkv2_m1 versus dyads_m5 (dyads_m5dyads_m5); m=14/21; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.771828; -rvdGACAGCTGmsg-- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0
dyads_m3_shift2 (dyads_m3dyads_m3)				; oligos_6nt_mkv2_m1 versus dyads_m3 (dyads_m3dyads_m3); m=15/21; ncol2=15; w=14; offset=0; strand=D; shift=2; score=0.764256; --rmArCAGCTGTCwyy ; cor=; Ncor= a 0 0 8 6 20 13 0 22 0 1 0 0 0 0 7 3 5 c 0 0 3 10 2 1 22 0 1 20 0 0 2 17 5 9 7 g 0 0 6 4 0 7 0 0 21 1 0 22 0 3 2 4 4 t 0 0 5 2 0 1 0 0 0 0 22 0 20 2 8 6 6
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=16/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.716528; -srsAACAGCTGTswmm ; cor=; Ncor= a 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3
oligos_7nt_mkv2_m13_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m13 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13); m=17/21; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.70475; -grmArCAGCTGTCwyc ; cor=; Ncor= a 0 4 8 6 20 13 0 21 0 1 0 0 0 0 7 3 5 c 0 4 2 10 1 1 21 0 1 19 0 0 2 16 4 9 7 g 0 8 6 4 0 6 0 0 20 1 0 21 0 3 2 3 4 t 0 5 5 1 0 1 0 0 0 0 21 0 19 2 8 6 5
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=18/21; ncol2=16; w=14; offset=-1; strand=R; shift=1; score=0.680013; -akmAGCAGCTGTCysc ; cor=; Ncor= a 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8
oligos_8nt_mkv2_m10_rc_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=19/21; ncol2=17; w=14; offset=-2; strand=R; shift=0; score=0.609995; rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=20/21; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=0.600967; vbdmAGCAGCTGTCmym ; cor=; Ncor= a 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 c 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 g 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 t 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2
oligos_8nt_mkv2_m27_shift0 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m27 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27); m=21/21; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=0.587165; vvdCAGCAGCTGTCyyh ; cor=; Ncor= a 7 5 6 3 17 1 0 20 0 0 0 0 0 0 4 3 5 c 5 6 2 14 1 0 20 0 1 20 0 0 1 14 9 8 7 g 5 6 6 2 0 18 0 0 19 0 0 19 0 3 1 3 2 t 3 3 6 1 2 1 0 0 0 0 20 1 19 3 6 6 6

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m9_shift9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9)				; oligos_8nt_mkv2_m9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9); m=0 (reference); ncol1=12; shift=9; ncol=23; ---------ayGTTTTTCAsK-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 51 4 20 1 2 1 0 3 0 95 8 1 0 0 c 0 0 0 0 0 0 0 0 0 7 52 1 0 0 1 2 0 94 1 29 3 0 0 g 0 0 0 0 0 0 0 0 0 19 5 77 0 1 0 0 0 0 0 47 27 0 0 t 0 0 0 0 0 0 0 0 0 23 39 2 99 97 98 98 97 6 4 16 69 0 0
oligos_8nt_mkv2_m9_shift9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9)				; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m9 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9); m=1/12; ncol2=12; w=12; offset=0; strand=D; shift=9; score= 1; ---------ayGTTTTTCAsK-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 51 4 20 1 2 1 0 3 0 95 8 1 0 0 c 0 0 0 0 0 0 0 0 0 7 52 1 0 0 1 2 0 94 1 29 3 0 0 g 0 0 0 0 0 0 0 0 0 19 5 77 0 1 0 0 0 0 0 47 27 0 0 t 0 0 0 0 0 0 0 0 0 23 39 2 99 97 98 98 97 6 4 16 69 0 0
oligos_7nt_mkv2_m6_rc_shift10 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6_rc)				; oligos_8nt_mkv2_m9 versus oligos_7nt_mkv2_m6_rc (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6_rc); m=2/12; ncol2=11; w=11; offset=1; strand=R; shift=10; score=0.894083; ----------yrTTTTTCAsk-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 4 58 0 15 1 0 0 0 139 16 2 0 0 c 0 0 0 0 0 0 0 0 0 0 93 16 0 0 0 1 1 138 0 41 1 0 0 g 0 0 0 0 0 0 0 0 0 0 4 59 0 0 0 0 0 0 0 59 58 0 0 t 0 0 0 0 0 0 0 0 0 0 38 6 139 124 138 138 138 1 0 23 78 0 0
dyads_m29_rc_shift9 (dyads_m29dyads_m29_rc)				; oligos_8nt_mkv2_m9 versus dyads_m29_rc (dyads_m29dyads_m29_rc); m=3/12; ncol2=12; w=12; offset=0; strand=R; shift=9; score=0.872856; ---------ryrTTTyTCAkT-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 65 5 46 0 1 0 0 0 1 154 3 6 0 0 c 0 0 0 0 0 0 0 0 0 5 48 0 0 0 0 108 0 160 0 19 14 0 0 g 0 0 0 0 0 0 0 0 0 87 6 103 0 0 0 0 0 0 9 43 4 0 0 t 0 0 0 0 0 0 0 0 0 6 104 14 163 162 163 55 163 2 0 98 139 0 0
oligos_8nt_mkv2_m4_rc_shift11 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4_rc)				; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m4_rc (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4_rc); m=4/12; ncol2=13; w=10; offset=2; strand=R; shift=11; score=0.623539; -----------GwTTTTCAGTkT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 4 44 1 1 0 0 2 118 0 0 3 24 c 0 0 0 0 0 0 0 0 0 0 0 30 1 1 2 0 1 126 11 2 0 0 11 g 0 0 0 0 0 0 0 0 0 0 0 92 3 3 1 1 0 0 0 115 0 77 1 t 0 0 0 0 0 0 0 0 0 0 0 5 83 126 127 130 130 3 2 14 131 51 95
dyads_m39_rc_shift10 (dyads_m39dyads_m39_rc)				; oligos_8nt_mkv2_m9 versus dyads_m39_rc (dyads_m39dyads_m39_rc); m=5/12; ncol2=10; w=10; offset=1; strand=R; shift=10; score=0.608481; ----------yrTATTTCwC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 6 26 0 56 0 0 0 0 27 4 0 0 0 c 0 0 0 0 0 0 0 0 0 0 23 5 0 0 0 0 0 56 3 40 0 0 0 g 0 0 0 0 0 0 0 0 0 0 6 20 0 0 0 0 0 0 1 7 0 0 0 t 0 0 0 0 0 0 0 0 0 0 21 5 56 0 56 56 56 0 25 5 0 0 0
oligos_8nt_mkv2_m16_rc_shift8 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16_rc)				; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m16_rc (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16_rc); m=6/12; ncol2=12; w=11; offset=-1; strand=R; shift=8; score=0.604377; --------yrTsATTTTCmR--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 5 36 0 0 73 0 1 0 0 0 39 19 0 0 0 c 0 0 0 0 0 0 0 0 36 15 0 26 0 0 0 0 0 72 25 0 0 0 0 g 0 0 0 0 0 0 0 0 1 19 1 46 0 0 1 0 0 0 2 52 0 0 0 t 0 0 0 0 0 0 0 0 31 3 72 1 0 73 71 73 73 1 7 2 0 0 0
oligos_6nt_mkv2_m8_rc_shift10 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc)				; oligos_8nt_mkv2_m9 versus oligos_6nt_mkv2_m8_rc (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8_rc); m=7/12; ncol2=10; w=10; offset=1; strand=R; shift=10; score=0.603326; ----------tdTTTCTCay--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 5 54 0 0 0 0 0 0 98 6 0 0 0 c 0 0 0 0 0 0 0 0 0 0 34 5 0 0 0 154 0 154 11 44 0 0 0 g 0 0 0 0 0 0 0 0 0 0 30 52 0 0 0 0 0 0 32 3 0 0 0 t 0 0 0 0 0 0 0 0 0 0 85 43 154 154 154 0 154 0 13 101 0 0 0
oligos_7nt_mkv2_m5_rc_shift12 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5_rc)				; oligos_8nt_mkv2_m9 versus oligos_7nt_mkv2_m5_rc (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5_rc); m=8/12; ncol2=11; w=9; offset=3; strand=R; shift=12; score=0.596075; ------------wTTTTCAGTkT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 36 2 0 0 0 0 98 0 0 3 8 c 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 98 0 0 0 0 10 g 0 0 0 0 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 98 0 40 0 t 0 0 0 0 0 0 0 0 0 0 0 0 60 90 98 98 98 0 0 0 98 55 80
dyads_m24_rc_shift10 (dyads_m24dyads_m24_rc)				; oligos_8nt_mkv2_m9 versus dyads_m24_rc (dyads_m24dyads_m24_rc); m=9/12; ncol2=18; w=11; offset=1; strand=R; shift=10; score=0.531012; ----------yrwTTTTCAskTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1 17 14 0 0 0 0 0 31 2 0 0 0 c 0 0 0 0 0 0 0 0 0 0 21 6 0 0 0 1 1 34 0 15 1 0 0 g 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 0 0 0 14 20 1 0 t 0 0 0 0 0 0 0 0 0 0 12 1 20 34 34 33 33 0 3 3 13 33 34
dyads_m7_rc_shift0 (dyads_m7dyads_m7_rc)				; oligos_8nt_mkv2_m9 versus dyads_m7_rc (dyads_m7dyads_m7_rc); m=10/12; ncol2=23; w=12; offset=-9; strand=R; shift=0; score= 0.4461; TcATTTTyCAhgwTTTymAGTkk ; cor=; Ncor= a 18 14 107 0 0 4 4 3 2 75 31 7 35 6 10 4 4 28 106 0 0 7 16 c 6 71 0 0 0 3 15 51 83 16 31 15 3 16 3 2 29 65 1 0 0 13 6 g 2 15 0 0 0 5 1 16 2 13 5 68 2 3 14 5 4 4 0 107 0 38 27 t 81 7 0 107 107 95 87 37 20 3 40 17 67 82 80 96 70 10 0 0 107 49 58
dyads_m4_rc_shift8 (dyads_m4dyads_m4_rc)				; oligos_8nt_mkv2_m9 versus dyads_m4_rc (dyads_m4dyads_m4_rc); m=11/12; ncol2=21; w=12; offset=-1; strand=R; shift=8; score=0.445154; --------YrTGATTTTCAGTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4 0 0 15 0 0 0 0 0 13 0 0 0 0 c 0 0 0 0 0 0 0 0 12 3 2 3 0 0 0 0 0 16 0 1 0 0 0 g 0 0 0 0 0 0 0 0 0 9 0 13 0 0 0 0 0 0 0 15 0 2 0 t 0 0 0 0 0 0 0 0 4 0 14 0 1 16 16 16 16 0 3 0 16 14 16
oligos_8nt_mkv2_m6_rc_shift10 (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6_rc)				; oligos_8nt_mkv2_m9 versus oligos_8nt_mkv2_m6_rc (oligos_8nt_mkv2_m6oligos_8nt_mkv2_m6_rc); m=12/12; ncol2=18; w=11; offset=1; strand=R; shift=10; score=0.422138; ----------ywTTTCTCATTTT ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 1 52 2 0 0 15 4 1 99 1 1 0 0 c 0 0 0 0 0 0 0 0 0 0 32 0 0 0 1 85 2 99 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 1 23 0 1 1 1 0 0 1 1 0 0 0 t 0 0 0 0 0 0 0 0 0 0 68 27 100 101 100 1 96 2 2 100 101 102 102

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m20_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)				; oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=0 (reference); ncol1=13; shift=0; ncol=13; swGAGGCAGGGrG ; Alignment reference a 2 11 1 25 0 0 1 25 0 6 0 8 2 c 13 2 2 0 0 0 25 0 0 0 0 1 3 g 11 6 23 0 26 25 0 0 26 20 26 14 19 t 0 7 0 1 0 1 0 1 0 0 0 3 2
oligos_8nt_mkv2_m20_shift0 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)				; oligos_8nt_mkv2_m20 versus oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=1/7; ncol2=13; w=13; offset=0; strand=D; shift=0; score= 1; swGAGGCAGGGrG ; cor=; Ncor= a 2 11 1 25 0 0 1 25 0 6 0 8 2 c 13 2 2 0 0 0 25 0 0 0 0 1 3 g 11 6 23 0 26 25 0 0 26 20 26 14 19 t 0 7 0 1 0 1 0 1 0 0 0 3 2
dyads_m11_rc_shift1 (dyads_m11dyads_m11_rc)				; oligos_8nt_mkv2_m20 versus dyads_m11_rc (dyads_m11dyads_m11_rc); m=2/7; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 0.8834; -agwGGCAGGGgg ; cor=; Ncor= a 0 13 3 18 0 0 0 29 0 0 0 4 1 c 0 3 5 0 0 0 29 0 0 0 1 3 7 g 0 6 16 2 29 28 0 0 29 29 28 15 19 t 0 7 5 9 0 1 0 0 0 0 0 7 2
oligos_7nt_mkv2_m11_rc_shift0 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc)				; oligos_8nt_mkv2_m20 versus oligos_7nt_mkv2_m11_rc (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc); m=3/7; ncol2=11; w=11; offset=0; strand=R; shift=0; score=0.830223; sdGAGGCAGrG-- ; cor=; Ncor= a 3 12 0 35 0 0 0 34 0 15 4 0 0 c 17 2 0 0 0 0 35 1 1 2 1 0 0 g 15 11 35 0 35 35 0 0 34 18 27 0 0 t 0 10 0 0 0 0 0 0 0 0 3 0 0
oligos_7nt_mkv2_m8_rc_shift2 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc)				; oligos_8nt_mkv2_m20 versus oligos_7nt_mkv2_m8_rc (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc); m=4/7; ncol2=11; w=11; offset=2; strand=R; shift=2; score=0.790515; --gwGGCAGGGks ; cor=; Ncor= a 0 0 6 16 0 0 0 31 0 0 0 4 1 c 0 0 6 5 0 0 32 0 0 1 0 5 9 g 0 0 16 4 34 34 0 3 34 33 34 15 20 t 0 0 6 9 0 0 2 0 0 0 0 10 4
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4)				; oligos_8nt_mkv2_m20 versus oligos_6nt_mkv2_m4 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4); m=5/7; ncol2=10; w=10; offset=1; strand=D; shift=1; score=0.724907; -dsAGGCAGrg-- ; cor=; Ncor= a 0 17 7 59 0 0 0 59 0 18 13 0 0 c 0 10 15 0 0 0 59 0 0 12 6 0 0 g 0 16 33 0 59 59 0 0 59 23 32 0 0 t 0 16 4 0 0 0 0 0 0 6 8 0 0
oligos_8nt_mkv2_m23_rc_shift0 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc)				; oligos_8nt_mkv2_m20 versus oligos_8nt_mkv2_m23_rc (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc); m=6/7; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.663767; vrGAGGAAGGmd- ; cor=; Ncor= a 3 4 0 8 0 0 8 7 0 0 4 3 0 c 2 1 0 0 0 0 0 1 0 0 2 0 0 g 3 3 8 0 8 8 0 0 8 8 1 2 0 t 0 0 0 0 0 0 0 0 0 0 1 3 0
dyads_m30_rc_shift2 (dyads_m30dyads_m30_rc)				; oligos_8nt_mkv2_m20 versus dyads_m30_rc (dyads_m30dyads_m30_rc); m=7/7; ncol2=11; w=11; offset=2; strand=R; shift=2; score=0.596506; --yrGGCKGGGkr ; cor=; Ncor= a 0 0 2 3 0 0 0 0 0 0 0 2 4 c 0 0 4 2 0 0 11 0 0 0 0 2 2 g 0 0 2 4 11 11 0 3 11 11 11 3 3 t 0 0 3 2 0 0 0 8 0 0 0 4 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m7_shift4 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7)				; oligos_6nt_mkv2_m7 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7); m=0 (reference); ncol1=10; shift=4; ncol=14; ----hgCCTCCCwa ; Alignment reference a 0 0 0 0 10 6 0 0 0 0 0 0 17 16 c 0 0 0 0 10 7 40 40 0 40 40 40 6 9 g 0 0 0 0 5 19 0 0 0 0 0 0 5 8 t 0 0 0 0 15 8 0 0 40 0 0 0 12 7
oligos_6nt_mkv2_m7_shift4 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7)				; oligos_6nt_mkv2_m7 versus oligos_6nt_mkv2_m7 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7); m=1/4; ncol2=10; w=10; offset=0; strand=D; shift=4; score= 1; ----hgCCTCCCwa ; cor=; Ncor= a 0 0 0 0 10 6 0 0 0 0 0 0 17 16 c 0 0 0 0 10 7 40 40 0 40 40 40 6 9 g 0 0 0 0 5 19 0 0 0 0 0 0 5 8 t 0 0 0 0 15 8 0 0 40 0 0 0 12 7
oligos_7nt_mkv2_m11_shift1 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11)				; oligos_6nt_mkv2_m7 versus oligos_7nt_mkv2_m11 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11); m=2/4; ncol2=11; w=8; offset=-3; strand=D; shift=1; score=0.47595; -CyCTGCCTChs-- ; cor=; Ncor= a 0 3 0 0 0 0 0 0 0 0 10 0 0 0 c 0 27 18 34 0 0 35 35 0 35 11 15 0 0 g 0 1 2 1 1 35 0 0 0 0 2 17 0 0 t 0 4 15 0 34 0 0 0 35 0 12 3 0 0
oligos_8nt_mkv2_m23_shift0 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23)				; oligos_6nt_mkv2_m7 versus oligos_8nt_mkv2_m23 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23); m=3/4; ncol2=12; w=8; offset=-4; strand=D; shift=0; score=0.412254; hkCCTTCCTCyb-- ; cor=; Ncor= a 3 1 0 0 0 0 0 0 0 0 0 0 0 0 c 2 1 8 8 0 0 8 8 0 8 3 3 0 0 g 0 2 0 0 1 0 0 0 0 0 1 2 0 0 t 3 4 0 0 7 8 0 0 8 0 4 3 0 0
oligos_6nt_mkv2_m4_rc_shift1 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc)				; oligos_6nt_mkv2_m7 versus oligos_6nt_mkv2_m4_rc (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4_rc); m=4/4; ncol2=10; w=7; offset=-3; strand=R; shift=1; score=0.406966; -cyCTGCCTsh--- ; cor=; Ncor= a 0 8 6 0 0 0 0 0 0 4 16 0 0 0 c 0 32 23 59 0 0 59 59 0 33 16 0 0 0 g 0 6 12 0 0 59 0 0 0 15 10 0 0 0 t 0 13 18 0 59 0 0 0 59 7 17 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m7_shift2 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)				; oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=0 (reference); ncol1=11; shift=2; ncol=14; --ssCCCGGCGss- ; Alignment reference a 0 0 4 5 1 1 0 0 3 2 0 4 4 0 c 0 0 17 11 34 29 32 4 5 33 0 11 14 0 g 0 0 11 14 1 3 4 32 28 1 33 17 16 0 t 0 0 4 6 0 3 0 0 0 0 3 4 2 0
oligos_7nt_mkv2_m7_shift2 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)				; oligos_7nt_mkv2_m7 versus oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=1/7; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 1; --ssCCCGGCGss- ; cor=; Ncor= a 0 0 4 5 1 1 0 0 3 2 0 4 4 0 c 0 0 17 11 34 29 32 4 5 33 0 11 14 0 g 0 0 11 14 1 3 4 32 28 1 33 17 16 0 t 0 0 4 6 0 3 0 0 0 0 3 4 2 0
oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)				; oligos_7nt_mkv2_m7 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=2/7; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.885944; --ssCCCGCCGsg- ; cor=; Ncor= a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0
oligos_6nt_mkv2_m6_rc_shift3 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6_rc)				; oligos_7nt_mkv2_m7 versus oligos_6nt_mkv2_m6_rc (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6_rc); m=3/7; ncol2=11; w=10; offset=1; strand=R; shift=3; score=0.801271; ---sCCCGGCGGss ; cor=; Ncor= a 0 0 0 1 2 1 0 0 0 0 0 1 2 2 c 0 0 0 11 18 20 23 4 3 25 1 3 9 10 g 0 0 0 10 4 3 3 22 23 1 25 21 13 11 t 0 0 0 4 2 2 0 0 0 0 0 1 2 3
oligos_8nt_mkv2_m15_rc_shift2 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15_rc)				; oligos_7nt_mkv2_m7 versus oligos_8nt_mkv2_m15_rc (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15_rc); m=4/7; ncol2=12; w=11; offset=0; strand=R; shift=2; score=0.787447; --ssCgCGGCGGgb ; cor=; Ncor= a 0 0 2 0 0 1 0 0 0 0 0 0 2 0 c 0 0 7 8 14 2 13 2 1 14 0 0 3 4 g 0 0 4 5 0 9 1 12 12 0 13 14 9 6 t 0 0 1 1 0 2 0 0 1 0 1 0 0 4
dyads_m26_rc_shift2 (dyads_m26dyads_m26_rc)				; oligos_7nt_mkv2_m7 versus dyads_m26_rc (dyads_m26dyads_m26_rc); m=5/7; ncol2=12; w=11; offset=0; strand=R; shift=2; score=0.71108; --ssCGCsgCGGsg ; cor=; Ncor= a 0 0 2 3 0 1 2 1 3 0 0 0 3 2 c 0 0 16 12 25 2 24 11 6 26 1 2 10 6 g 0 0 8 10 3 24 2 13 15 1 27 25 15 19 t 0 0 2 3 0 1 0 3 4 1 0 1 0 1
oligos_6nt_mkv2_m5_shift2 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m7 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=6/7; ncol2=10; w=10; offset=0; strand=D; shift=2; score=0.681037; --ssCCCCGCsg-- ; cor=; Ncor= a 0 0 0 3 0 0 0 0 0 0 2 1 0 0 c 0 0 10 7 23 21 23 24 0 25 8 6 0 0 g 0 0 11 9 2 4 2 1 25 0 9 15 0 0 t 0 0 4 6 0 0 0 0 0 0 6 3 0 0
dyads_m12_shift0 (dyads_m12dyads_m12)				; oligos_7nt_mkv2_m7 versus dyads_m12 (dyads_m12dyads_m12); m=7/7; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=0.626799; vssCCSCGCSGGss ; cor=; Ncor= a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m39_shift3 (dyads_m39dyads_m39)				; dyads_m39 (dyads_m39dyads_m39); m=0 (reference); ncol1=10; shift=3; ncol=14; ---GwGAAATAyr- ; Alignment reference a 0 0 0 5 25 0 56 56 56 0 56 5 21 0 c 0 0 0 7 1 0 0 0 0 0 0 20 6 0 g 0 0 0 40 3 56 0 0 0 0 0 5 23 0 t 0 0 0 4 27 0 0 0 0 56 0 26 6 0
dyads_m39_shift3 (dyads_m39dyads_m39)				; dyads_m39 versus dyads_m39 (dyads_m39dyads_m39); m=1/6; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 1; ---GwGAAATAyr- ; cor=; Ncor= a 0 0 0 5 25 0 56 56 56 0 56 5 21 0 c 0 0 0 7 1 0 0 0 0 0 0 20 6 0 g 0 0 0 40 3 56 0 0 0 0 0 5 23 0 t 0 0 0 4 27 0 0 0 0 56 0 26 6 0
oligos_7nt_mkv2_m6_shift2 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)				; dyads_m39 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=2/6; ncol2=11; w=10; offset=-1; strand=D; shift=2; score=0.700857; --msTGAAAAAyr- ; cor=; Ncor= a 0 0 78 23 0 1 138 138 138 124 139 6 38 0 c 0 0 58 59 0 0 0 0 0 0 0 59 4 0 g 0 0 1 41 0 138 1 1 0 0 0 16 93 0 t 0 0 2 16 139 0 0 0 1 15 0 58 4 0
oligos_8nt_mkv2_m9_rc_shift2 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)				; dyads_m39 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=3/6; ncol2=12; w=10; offset=-1; strand=R; shift=2; score=0.608481; --MsTGAAAAACrt ; cor=; Ncor= a 0 0 69 16 4 6 97 98 98 97 99 2 39 23 c 0 0 27 47 0 0 0 0 0 1 0 77 5 19 g 0 0 3 29 1 94 0 2 1 0 0 1 52 7 t 0 0 1 8 95 0 3 0 1 2 1 20 4 51
oligos_6nt_mkv2_m8_shift1 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8)				; dyads_m39 versus oligos_6nt_mkv2_m8 (oligos_6nt_mkv2_m8oligos_6nt_mkv2_m8); m=4/6; ncol2=10; w=8; offset=-2; strand=D; shift=1; score=0.559766; -rtGAGAAAha--- ; cor=; Ncor= a 0 101 13 0 154 0 154 154 154 43 85 0 0 0 c 0 3 32 0 0 0 0 0 0 52 30 0 0 0 g 0 44 11 154 0 154 0 0 0 5 34 0 0 0 t 0 6 98 0 0 0 0 0 0 54 5 0 0 0
dyads_m29_shift0 (dyads_m29dyads_m29)				; dyads_m39 versus dyads_m29 (dyads_m29dyads_m29); m=5/6; ncol2=12; w=9; offset=-3; strand=D; shift=0; score=0.547389; AmTGArAAAyry-- ; cor=; Ncor= a 139 98 0 2 163 55 163 162 163 14 104 6 0 0 c 4 43 9 0 0 0 0 0 0 103 6 87 0 0 g 14 19 0 160 0 108 0 0 0 0 48 5 0 0 t 6 3 154 1 0 0 0 1 0 46 5 65 0 0
oligos_8nt_mkv2_m11_shift4 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11)				; dyads_m39 versus oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=6/6; ncol2=13; w=9; offset=1; strand=D; shift=4; score=0.49244; ----AGAAATRCAC ; cor=; Ncor= a 0 0 0 0 59 4 71 72 71 0 18 0 68 0 c 0 0 0 0 0 2 1 0 0 2 2 71 1 72 g 0 0 0 0 3 63 0 0 0 1 50 0 1 0 t 0 0 0 0 10 3 0 0 1 69 2 1 2 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)				; oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=0 (reference); ncol1=13; shift=5; ncol=24; -----WAmACTGAAAAwC------ ; Alignment reference a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0
oligos_8nt_mkv2_m4_shift5 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4)				; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m4 (oligos_8nt_mkv2_m4oligos_8nt_mkv2_m4); m=1/9; ncol2=13; w=13; offset=0; strand=D; shift=5; score= 1; -----WAmACTGAAAAwC------ ; cor=; Ncor= a 0 0 0 0 0 90 95 51 131 14 2 3 130 130 127 126 83 5 0 0 0 0 0 0 c 0 0 0 0 0 6 1 77 0 115 0 0 0 1 1 3 3 92 0 0 0 0 0 0 g 0 0 0 0 0 2 11 0 0 2 11 126 1 0 2 1 1 30 0 0 0 0 0 0 t 0 0 0 0 0 33 24 3 0 0 118 2 0 0 1 1 44 4 0 0 0 0 0 0
oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5)				; oligos_8nt_mkv2_m4 versus oligos_7nt_mkv2_m5 (oligos_7nt_mkv2_m5oligos_7nt_mkv2_m5); m=2/9; ncol2=11; w=11; offset=1; strand=D; shift=6; score=0.838355; ------AmACTGAAAAw------- ; cor=; Ncor= a 0 0 0 0 0 0 80 55 98 0 0 0 98 98 98 90 60 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 40 0 98 0 0 0 0 0 4 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 10 0 0 0 0 98 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 3 0 0 98 0 0 0 0 2 36 0 0 0 0 0 0 0
oligos_7nt_mkv2_m6_shift8 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6)				; oligos_8nt_mkv2_m4 versus oligos_7nt_mkv2_m6 (oligos_7nt_mkv2_m6oligos_7nt_mkv2_m6); m=3/9; ncol2=11; w=10; offset=3; strand=D; shift=8; score=0.639996; --------msTGAAAAAyr----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 78 23 0 1 138 138 138 124 139 6 38 0 0 0 0 0 c 0 0 0 0 0 0 0 0 58 59 0 0 0 0 0 0 0 59 4 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 41 0 138 1 1 0 0 0 16 93 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 16 139 0 0 0 1 15 0 58 4 0 0 0 0 0
oligos_8nt_mkv2_m9_rc_shift8 (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc)				; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m9_rc (oligos_8nt_mkv2_m9oligos_8nt_mkv2_m9_rc); m=4/9; ncol2=12; w=10; offset=3; strand=R; shift=8; score=0.623539; --------MsTGAAAAACrt---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 69 16 4 6 97 98 98 97 99 2 39 23 0 0 0 0 c 0 0 0 0 0 0 0 0 27 47 0 0 0 0 0 1 0 77 5 19 0 0 0 0 g 0 0 0 0 0 0 0 0 3 29 1 94 0 2 1 0 0 1 52 7 0 0 0 0 t 0 0 0 0 0 0 0 0 1 8 95 0 3 0 1 2 1 20 4 51 0 0 0 0
dyads_m24_shift1 (dyads_m24dyads_m24)				; oligos_8nt_mkv2_m4 versus dyads_m24 (dyads_m24dyads_m24); m=5/9; ncol2=18; w=13; offset=-4; strand=D; shift=1; score=0.594764; -ygRRAAAmsTGAAAAwyr----- ; cor=; Ncor= a 0 3 8 25 24 32 34 33 13 3 3 0 33 33 34 34 20 1 12 0 0 0 0 0 c 0 12 0 0 0 2 0 1 20 14 0 0 0 0 0 0 0 10 0 0 0 0 0 0 g 0 2 20 9 9 0 0 0 1 15 0 34 1 1 0 0 0 6 21 0 0 0 0 0 t 0 17 6 0 1 0 0 0 0 2 31 0 0 0 0 0 14 17 1 0 0 0 0 0
dyads_m4_shift0 (dyads_m4dyads_m4)				; oligos_8nt_mkv2_m4 versus dyads_m4 (dyads_m4dyads_m4); m=6/9; ncol2=21; w=13; offset=-5; strand=D; shift=0; score=0.563196; gCkRRAAAACTGAAAATCAyR--- ; cor=; Ncor= a 3 1 2 11 5 16 16 14 16 0 3 0 16 16 16 16 1 0 14 0 4 0 0 0 c 1 11 0 0 0 0 0 2 0 15 0 0 0 0 0 0 0 13 0 9 0 0 0 0 g 9 3 9 5 11 0 0 0 0 1 0 16 0 0 0 0 0 3 2 3 12 0 0 0 t 3 1 5 0 0 0 0 0 0 0 13 0 0 0 0 0 15 0 0 4 0 0 0 0
dyads_m29_shift8 (dyads_m29dyads_m29)				; oligos_8nt_mkv2_m4 versus dyads_m29 (dyads_m29dyads_m29); m=7/9; ncol2=12; w=10; offset=3; strand=D; shift=8; score=0.555704; --------AmTGArAAAyry---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 139 98 0 2 163 55 163 162 163 14 104 6 0 0 0 0 c 0 0 0 0 0 0 0 0 4 43 9 0 0 0 0 0 0 103 6 87 0 0 0 0 g 0 0 0 0 0 0 0 0 14 19 0 160 0 108 0 0 0 0 48 5 0 0 0 0 t 0 0 0 0 0 0 0 0 6 3 154 1 0 0 0 1 0 46 5 65 0 0 0 0
oligos_8nt_mkv2_m16_shift9 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16)				; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m16 (oligos_8nt_mkv2_m16oligos_8nt_mkv2_m16); m=8/9; ncol2=12; w=9; offset=4; strand=D; shift=9; score=0.498435; ---------YkGAAAATsAyr--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2 7 1 73 73 71 73 0 1 72 3 31 0 0 0 c 0 0 0 0 0 0 0 0 0 52 2 0 0 0 1 0 0 46 1 19 1 0 0 0 g 0 0 0 0 0 0 0 0 0 0 25 72 0 0 0 0 0 26 0 15 36 0 0 0 t 0 0 0 0 0 0 0 0 0 19 39 0 0 0 1 0 73 0 0 36 5 0 0 0
dyads_m7_shift6 (dyads_m7dyads_m7)				; oligos_8nt_mkv2_m4 versus dyads_m7 (dyads_m7dyads_m7); m=9/9; ncol2=23; w=12; offset=1; strand=D; shift=6; score=0.472281; ------mmACTkrAAAwcdTGrAA ; cor=; Ncor= a 0 0 0 0 0 0 58 49 107 0 0 10 70 96 80 82 67 17 40 3 20 37 87 95 c 0 0 0 0 0 0 27 38 0 107 0 4 4 5 14 3 2 68 5 13 2 16 1 5 g 0 0 0 0 0 0 6 13 0 0 1 65 29 2 3 16 3 15 31 16 83 51 15 3 t 0 0 0 0 0 0 16 7 0 0 106 28 4 4 10 6 35 7 31 75 2 3 4 4

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=0 (reference); ncol1=16; shift=1; ncol=17; -vmwGaCAGCTGtCwkb ; Alignment reference a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=1/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10
dyads_m1_shift1 (dyads_m1dyads_m1)				; oligos_7nt_mkv2_m1 versus dyads_m1 (dyads_m1dyads_m1); m=2/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score= 1; -vmwGaCAGCTGtCwkb ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10
oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=3/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.928003; -gmyGaCAGCTGtCrkc ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1); m=4/19; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.868996; --cwGaCAGCTGtCwg- ; cor=; Ncor= a 0 0 8 14 5 23 0 35 0 0 0 0 6 0 16 4 0 c 0 0 21 3 4 3 35 0 0 35 0 0 3 26 3 2 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 5 3 21 0 t 0 0 4 15 0 6 0 0 0 0 35 0 23 4 13 8 0
dyads_m19_shift1 (dyads_m19dyads_m19)				; oligos_7nt_mkv2_m1 versus dyads_m19 (dyads_m19dyads_m19); m=5/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.812212; -rvdGACAGCTGvyks- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0
oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=6/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.808909; -rvtGACAGCTGmhkg- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0
oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=7/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.805464; -rstGACAGCTGmhkg- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0
oligos_8nt_mkv2_m3_rc_shift2 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m3_rc (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3_rc); m=8/19; ncol2=15; w=15; offset=1; strand=R; shift=2; score=0.801669; --cmsKCAGCTGTCasy ; cor=; Ncor= a 0 0 5 7 5 1 0 24 0 0 0 0 0 0 16 1 4 c 0 0 10 9 8 0 24 0 0 24 0 0 1 24 3 8 8 g 0 0 4 5 6 6 0 0 24 0 0 24 0 0 1 11 2 t 0 0 5 3 5 17 0 0 0 0 24 0 23 0 4 4 10
dyads_m36_shift1 (dyads_m36dyads_m36)				; oligos_7nt_mkv2_m1 versus dyads_m36 (dyads_m36dyads_m36); m=9/19; ncol2=15; w=15; offset=0; strand=D; shift=1; score=0.774901; -rvkGACAGCTGctks- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3); m=10/19; ncol2=16; w=16; offset=0; strand=D; shift=1; score=0.764901; -srsAACAGCTGTswmm ; cor=; Ncor= a 0 3 7 4 15 14 0 18 0 1 0 1 0 0 10 5 5 c 0 5 2 6 1 1 18 0 2 16 0 0 1 12 1 7 7 g 0 6 6 7 1 3 0 0 16 1 0 17 0 5 2 3 3 t 0 4 3 1 1 0 0 0 0 0 18 0 17 1 5 3 3
dyads_m8_shift2 (dyads_m8dyads_m8)				; oligos_7nt_mkv2_m1 versus dyads_m8 (dyads_m8dyads_m8); m=11/19; ncol2=15; w=15; offset=1; strand=D; shift=2; score=0.763334; --bsCwCAGCTGTCybk ; cor=; Ncor= a 0 0 3 4 3 11 0 20 0 1 0 0 3 0 4 0 2 c 0 0 6 7 17 2 20 0 0 18 0 0 0 17 7 6 3 g 0 0 5 5 0 2 0 0 20 0 0 20 0 0 2 7 5 t 0 0 6 4 0 5 0 0 0 1 20 0 17 3 7 7 10
dyads_m5_rc_shift3 (dyads_m5dyads_m5_rc)				; oligos_7nt_mkv2_m1 versus dyads_m5_rc (dyads_m5dyads_m5_rc); m=12/19; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.760426; ---cskCAGCTGTChby ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 1 0 0 1 17 4 13 c 0 0 0 20 17 6 57 0 0 57 0 0 1 43 16 16 21 g 0 0 0 9 16 15 0 0 57 0 0 57 0 5 9 21 6 t 0 0 0 14 12 32 0 0 0 0 56 0 56 8 15 16 17
oligos_7nt_mkv2_m4_rc_shift3 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4_rc (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4_rc); m=13/19; ncol2=14; w=14; offset=2; strand=R; shift=3; score=0.759761; ---cskCAGCTGTCwsy ; cor=; Ncor= a 0 0 0 14 12 4 0 57 0 0 0 0 0 1 19 4 13 c 0 0 0 20 18 6 56 0 0 57 0 0 1 43 14 17 22 g 0 0 0 9 15 15 1 0 57 0 0 57 0 5 9 22 5 t 0 0 0 14 12 32 0 0 0 0 57 0 56 8 15 14 17
oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/19; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.756774; -grwGACAGCTGyTkyc ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=15/19; ncol2=14; w=14; offset=1; strand=D; shift=2; score=0.748158; --hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=16/19; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.737151; -akmAGCAGCTGTCysc ; cor=; Ncor= a 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8
dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)				; oligos_7nt_mkv2_m1 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=17/19; ncol2=15; w=15; offset=0; strand=R; shift=1; score=0.726765; -rrwGACAGCTGyTky- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0
oligos_8nt_mkv2_m10_rc_shift0 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=18/19; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.662618; rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5
oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=19/19; ncol2=14; w=14; offset=1; strand=R; shift=2; score=0.655261; --kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m26_shift14 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26)				; oligos_8nt_mkv2_m26 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26); m=0 (reference); ncol1=12; shift=14; ncol=26; --------------CTACAGTGTGya ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 14 87 12 82 1 0 1 0 8 5 56 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 7 0 69 1 0 0 0 0 0 24 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 0 1 0 85 0 86 0 79 18 9 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 65 0 5 4 1 87 0 87 0 40 19
oligos_8nt_mkv2_m26_shift14 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26)				; oligos_8nt_mkv2_m26 versus oligos_8nt_mkv2_m26 (oligos_8nt_mkv2_m26oligos_8nt_mkv2_m26); m=1/9; ncol2=12; w=12; offset=0; strand=D; shift=14; score= 1; --------------CTACAGTGTGya ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 14 87 12 82 1 0 1 0 8 5 56 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 7 0 69 1 0 0 0 0 0 24 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 0 1 0 85 0 86 0 79 18 9 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 65 0 5 4 1 87 0 87 0 40 19
dyads_m6_rc_shift12 (dyads_m6dyads_m6_rc)				; oligos_8nt_mkv2_m26 versus dyads_m6_rc (dyads_m6dyads_m6_rc); m=2/9; ncol2=14; w=12; offset=-2; strand=R; shift=12; score=0.831536; ------------TyCTAcAGTGTGya ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 8 1 0 0 91 19 76 7 8 0 0 1 3 51 c 0 0 0 0 0 0 0 0 0 0 0 0 1 59 92 0 1 62 5 8 3 0 0 0 36 10 g 0 0 0 0 0 0 0 0 0 0 0 0 5 7 0 0 0 6 7 72 1 92 0 91 19 15 t 0 0 0 0 0 0 0 0 0 0 0 0 78 25 0 92 0 5 4 5 80 0 92 0 34 16
dyads_m23_rc_shift13 (dyads_m23dyads_m23_rc)				; oligos_8nt_mkv2_m26 versus dyads_m23_rc (dyads_m23dyads_m23_rc); m=3/9; ncol2=12; w=11; offset=-1; strand=R; shift=13; score=0.799973; -------------yCTACAgTGTKc- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 1 16 0 95 0 84 21 0 0 0 2 3 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 44 67 0 0 95 4 14 0 0 0 0 50 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 0 1 55 0 95 0 67 21 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 47 10 95 0 0 6 5 95 0 95 26 21 0
dyads_m33_rc_shift13 (dyads_m33dyads_m33_rc)				; oligos_8nt_mkv2_m26 versus dyads_m33_rc (dyads_m33dyads_m33_rc); m=4/9; ncol2=10; w=9; offset=-1; strand=R; shift=13; score=0.671399; -------------yCTACAGTGT--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 76 0 75 0 0 1 5 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 48 66 0 0 76 1 0 0 6 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 6 3 0 0 0 0 76 0 68 17 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 21 5 76 0 0 0 0 76 1 54 0 0 0
dyads_m20_shift12 (dyads_m20dyads_m20)				; oligos_8nt_mkv2_m26 versus dyads_m20 (dyads_m20dyads_m20); m=5/9; ncol2=23; w=12; offset=-2; strand=D; shift=12; score=0.494047; ------------TCCTAmAGTGTGya ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 8 3 0 0 60 18 46 6 2 2 7 5 7 40 c 0 0 0 0 0 0 0 0 0 0 0 0 0 44 60 0 0 35 5 6 9 3 1 3 23 2 g 0 0 0 0 0 0 0 0 0 0 0 0 4 3 0 0 0 3 4 44 2 49 4 46 2 11 t 0 0 0 0 0 0 0 0 0 0 0 0 48 10 0 60 0 4 5 4 47 6 48 6 28 7
dyads_m40_rc_shift12 (dyads_m40dyads_m40_rc)				; oligos_8nt_mkv2_m26 versus dyads_m40_rc (dyads_m40dyads_m40_rc); m=6/9; ncol2=25; w=12; offset=-2; strand=R; shift=12; score=0.452904; ------------TCCTAmAgTGTGyA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 3 2 0 0 64 18 51 8 3 1 2 6 1 44 c 0 0 0 0 0 0 0 0 0 0 0 0 2 45 63 0 0 35 4 4 5 7 6 1 28 5 g 0 0 0 0 0 0 0 0 0 0 0 0 5 3 0 0 0 4 7 42 1 50 3 50 4 11 t 0 0 0 0 0 0 0 0 0 0 0 0 54 14 1 64 0 7 2 10 55 6 53 7 31 4
oligos_8nt_mkv2_m11_rc_shift18 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc)				; oligos_8nt_mkv2_m26 versus oligos_8nt_mkv2_m11_rc (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11_rc); m=7/9; ncol2=13; w=8; offset=4; strand=R; shift=18; score=0.44416; ------------------AGTGTGYA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 10 0 0 2 1 2 69 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 9 0 0 1 0 50 1 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 0 72 1 71 2 2 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 72 0 68 0 18 0
dyads_m9_rc_shift13 (dyads_m9dyads_m9_rc)				; oligos_8nt_mkv2_m26 versus dyads_m9_rc (dyads_m9dyads_m9_rc); m=8/9; ncol2=26; w=12; offset=-1; strand=R; shift=13; score=0.431592; -------------yCTACAgTGtgca ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 10 13 0 86 0 67 14 6 6 6 14 7 47 c 0 0 0 0 0 0 0 0 0 0 0 0 0 47 64 0 1 82 8 7 5 8 7 6 41 5 g 0 0 0 0 0 0 0 0 0 0 0 0 0 6 7 0 0 0 5 58 4 68 17 52 20 15 t 0 0 0 0 0 0 0 0 0 0 0 0 0 24 3 87 0 5 7 8 72 5 57 15 19 20
dyads_m32_rc_shift0 (dyads_m32dyads_m32_rc)				; oligos_8nt_mkv2_m26 versus dyads_m32_rc (dyads_m32dyads_m32_rc); m=9/9; ncol2=25; w=11; offset=-14; strand=R; shift=0; score=0.41068; cCATATTyCAgGTCCTACAgTGTGy- ; cor=; Ncor= a 14 8 84 0 84 6 10 7 9 66 17 11 9 2 4 3 65 18 70 6 0 0 0 9 6 0 c 50 68 0 0 0 11 3 49 58 3 17 4 5 60 63 5 6 58 5 14 0 1 1 4 42 0 g 6 4 0 0 0 7 3 6 3 10 37 65 4 3 9 4 3 3 5 56 0 82 0 64 6 0 t 14 4 0 84 0 60 68 22 14 5 13 4 66 19 8 72 10 5 4 8 84 1 83 7 30 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4); m=0 (reference); ncol1=10; shift=3; ncol=13; ---dsAGGCAGrg ; Alignment reference a 0 0 0 17 7 59 0 0 0 59 0 18 13 c 0 0 0 10 15 0 0 0 59 0 0 12 6 g 0 0 0 16 33 0 59 59 0 0 59 23 32 t 0 0 0 16 4 0 0 0 0 0 0 6 8
oligos_6nt_mkv2_m4_shift3 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4 (oligos_6nt_mkv2_m4oligos_6nt_mkv2_m4); m=1/7; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 1; ---dsAGGCAGrg ; cor=; Ncor= a 0 0 0 17 7 59 0 0 0 59 0 18 13 c 0 0 0 10 15 0 0 0 59 0 0 12 6 g 0 0 0 16 33 0 59 59 0 0 59 23 32 t 0 0 0 16 4 0 0 0 0 0 0 6 8
oligos_7nt_mkv2_m11_rc_shift2 (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m11_rc (oligos_7nt_mkv2_m11oligos_7nt_mkv2_m11_rc); m=2/7; ncol2=11; w=10; offset=-1; strand=R; shift=2; score=0.875357; --sdGAGGCAGrG ; cor=; Ncor= a 0 0 3 12 0 35 0 0 0 34 0 15 4 c 0 0 17 2 0 0 0 0 35 1 1 2 1 g 0 0 15 11 35 0 35 35 0 0 34 18 27 t 0 0 0 10 0 0 0 0 0 0 0 0 3
dyads_m11_rc_shift3 (dyads_m11dyads_m11_rc)				; oligos_6nt_mkv2_m4 versus dyads_m11_rc (dyads_m11dyads_m11_rc); m=3/7; ncol2=12; w=10; offset=0; strand=R; shift=3; score=0.749262; ---agwGGCAGGG ; cor=; Ncor= a 0 0 0 13 3 18 0 0 0 29 0 0 0 c 0 0 0 3 5 0 0 0 29 0 0 0 1 g 0 0 0 6 16 2 29 28 0 0 29 29 28 t 0 0 0 7 5 9 0 1 0 0 0 0 0
oligos_8nt_mkv2_m20_shift2 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)				; oligos_6nt_mkv2_m4 versus oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=4/7; ncol2=13; w=10; offset=-1; strand=D; shift=2; score=0.724907; --swGAGGCAGGG ; cor=; Ncor= a 0 0 2 11 1 25 0 0 1 25 0 6 0 c 0 0 13 2 2 0 0 0 25 0 0 0 0 g 0 0 11 6 23 0 26 25 0 0 26 20 26 t 0 0 0 7 0 1 0 1 0 1 0 0 0
oligos_7nt_mkv2_m8_rc_shift4 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc)				; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m8_rc (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8_rc); m=5/7; ncol2=11; w=9; offset=1; strand=R; shift=4; score=0.659469; ----gwGGCAGGG ; cor=; Ncor= a 0 0 0 0 6 16 0 0 0 31 0 0 0 c 0 0 0 0 6 5 0 0 32 0 0 1 0 g 0 0 0 0 16 4 34 34 0 3 34 33 34 t 0 0 0 0 6 9 0 0 2 0 0 0 0
oligos_8nt_mkv2_m23_rc_shift2 (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc)				; oligos_6nt_mkv2_m4 versus oligos_8nt_mkv2_m23_rc (oligos_8nt_mkv2_m23oligos_8nt_mkv2_m23_rc); m=6/7; ncol2=12; w=10; offset=-1; strand=R; shift=2; score=0.588894; --vrGAGGAAGGm ; cor=; Ncor= a 0 0 3 4 0 8 0 0 8 7 0 0 4 c 0 0 2 1 0 0 0 0 0 1 0 0 2 g 0 0 3 3 8 0 8 8 0 0 8 8 1 t 0 0 0 0 0 0 0 0 0 0 0 0 1
oligos_6nt_mkv2_m7_rc_shift0 (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7_rc)				; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m7_rc (oligos_6nt_mkv2_m7oligos_6nt_mkv2_m7_rc); m=7/7; ncol2=10; w=7; offset=-3; strand=R; shift=0; score=0.406966; twGGGAGGcd--- ; cor=; Ncor= a 7 12 0 0 0 40 0 0 8 15 0 0 0 c 8 5 0 0 0 0 0 0 19 5 0 0 0 g 9 6 40 40 40 0 40 40 7 10 0 0 0 t 16 17 0 0 0 0 0 0 6 10 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m21_shift3 (dyads_m21dyads_m21)				; dyads_m21 (dyads_m21dyads_m21); m=0 (reference); ncol1=14; shift=3; ncol=18; ---ssAGCAGCTGCTss- ; Alignment reference a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0
dyads_m21_shift3 (dyads_m21dyads_m21)				; dyads_m21 versus dyads_m21 (dyads_m21dyads_m21); m=1/17; ncol2=14; w=14; offset=0; strand=D; shift=3; score= 1; ---ssAGCAGCTGCTss- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc)				; dyads_m21 versus oligos_6nt_mkv2_m2_rc (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2_rc); m=2/17; ncol2=14; w=14; offset=0; strand=R; shift=3; score=0.81204; ---kmaGCAGCTGTcyc- ; cor=; Ncor= a 0 0 0 9 11 26 2 0 42 0 1 0 0 0 1 7 7 0 c 0 0 0 8 15 5 1 42 0 1 41 0 0 3 27 12 15 0 g 0 0 0 12 9 4 36 0 0 41 0 0 41 0 5 10 10 0 t 0 0 0 13 7 7 3 0 0 0 0 42 1 39 9 13 10 0
oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; dyads_m21 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=3/17; ncol2=18; w=14; offset=-2; strand=D; shift=1; score=0.762862; -sygCAGCAGCTGCTGcr ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4
oligos_6nt_mkv2_m3_shift3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3)				; dyads_m21 versus oligos_6nt_mkv2_m3 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3); m=4/17; ncol2=14; w=14; offset=0; strand=D; shift=3; score=0.745137; ---hmarCAGCTGTCwb- ; cor=; Ncor= a 0 0 0 10 12 20 23 0 36 0 1 0 0 2 0 10 4 0 c 0 0 0 9 11 8 1 36 0 1 34 0 0 3 25 5 14 0 g 0 0 0 7 7 5 10 0 0 35 1 0 36 1 4 7 9 0 t 0 0 0 10 6 3 2 0 0 0 0 36 0 30 7 14 9 0
oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)				; dyads_m21 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=5/17; ncol2=17; w=14; offset=-2; strand=R; shift=1; score=0.745037; -kdgCAGCAGCTGTTsws ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1
oligos_8nt_mkv2_m8_shift3 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)				; dyads_m21 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=6/17; ncol2=16; w=14; offset=0; strand=D; shift=3; score=0.719563; ---rgmACAGCTGCTGcw ; cor=; Ncor= a 0 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 c 0 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 g 0 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 t 0 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6
oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)				; dyads_m21 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=7/17; ncol2=17; w=14; offset=-2; strand=D; shift=1; score=0.71772; -wdgCAGCAGCTGTTCwv ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0
dyads_m25_shift3 (dyads_m25dyads_m25)				; dyads_m21 versus dyads_m25 (dyads_m25dyads_m25); m=8/17; ncol2=17; w=14; offset=0; strand=D; shift=3; score=0.714677; ---dkAACAGCTGCTGyC ; cor=; Ncor= a 0 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 c 0 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 g 0 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 t 0 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2
dyads_m36_shift2 (dyads_m36dyads_m36)				; dyads_m21 versus dyads_m36 (dyads_m36dyads_m36); m=9/17; ncol2=15; w=14; offset=-1; strand=D; shift=2; score=0.706576; --rvkGACAGCTGctks- ; cor=; Ncor= a 0 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 c 0 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 g 0 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 t 0 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)				; dyads_m21 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=10/17; ncol2=16; w=14; offset=-1; strand=R; shift=2; score=0.704539; --akmAGCAGCTGTCysc ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8
dyads_m3_rc_shift2 (dyads_m3dyads_m3_rc)				; dyads_m21 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=11/17; ncol2=15; w=14; offset=-1; strand=R; shift=2; score=0.69303; --rrwGACAGCTGyTky- ; cor=; Ncor= a 0 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 c 0 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 g 0 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 t 0 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0
oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)				; dyads_m21 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=12/17; ncol2=12; w=12; offset=0; strand=D; shift=3; score=0.684465; ---rmAGCAGGTGst--- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0
oligos_8nt_mkv2_m27_rc_shift2 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)				; dyads_m21 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=13/17; ncol2=17; w=14; offset=-1; strand=R; shift=2; score=0.651207; --drrGACAGCTGCTGhb ; cor=; Ncor= a 0 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 c 0 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 g 0 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 t 0 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5
oligos_7nt_mkv2_m13_rc_shift2 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)				; dyads_m21 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=14/17; ncol2=16; w=14; offset=-1; strand=R; shift=2; score=0.645862; --grwGACAGCTGyTkyc ; cor=; Ncor= a 0 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 c 0 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 g 0 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 t 0 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4
oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)				; dyads_m21 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=15/17; ncol2=17; w=14; offset=-2; strand=R; shift=1; score=0.627824; -rrrcAGCAGCTGTCtyy ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5
dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)				; dyads_m21 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=16/17; ncol2=18; w=14; offset=-3; strand=R; shift=0; score=0.624225; tagaCAGCAGCTGTyyym ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3
oligos_8nt_mkv2_m1_rc_shift2 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)				; dyads_m21 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=17/17; ncol2=17; w=14; offset=-1; strand=R; shift=2; score=0.622768; --krkGACAGCTGCTkhv ; cor=; Ncor= a 0 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 c 0 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 g 0 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 t 0 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=0 (reference); ncol1=14; shift=2; ncol=18; --grgACAGCTGCtkm-- ; Alignment reference a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=1/31; ncol2=14; w=14; offset=0; strand=D; shift=2; score= 1; --grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=2/31; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.930869; --vwGACAGCTGytkd-- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0
dyads_m36_shift1 (dyads_m36dyads_m36)				; oligos_6nt_mkv2_m2 versus dyads_m36 (dyads_m36dyads_m36); m=3/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.912193; -rvkGACAGCTGctks-- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=4/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.872015; -gsrGACAGCTGCTkmt- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0
dyads_m19_shift1 (dyads_m19dyads_m19)				; oligos_6nt_mkv2_m2 versus dyads_m19 (dyads_m19dyads_m19); m=5/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.870723; -rvdGACAGCTGvyks-- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0
dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)				; oligos_6nt_mkv2_m2 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=6/31; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.867342; -rrwGACAGCTGyTky-- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0
oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=7/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.862061; -rvtGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0
oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=8/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.861474; -rstGACAGCTGmhkg-- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0
dyads_m21_shift2 (dyads_m21dyads_m21)				; oligos_6nt_mkv2_m2 versus dyads_m21 (dyads_m21dyads_m21); m=9/31; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.81204; --ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0
oligos_8nt_mkv2_m3_shift1 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m3 (oligos_8nt_mkv2_m3oligos_8nt_mkv2_m3); m=10/31; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.80933; -rstGACAGCTGMskg-- ; cor=; Ncor= a 0 10 4 4 0 23 0 24 0 0 0 0 17 5 3 5 0 0 c 0 2 11 1 0 0 24 0 0 24 0 0 6 6 5 4 0 0 g 0 8 8 3 24 1 0 0 24 0 0 24 0 8 9 10 0 0 t 0 4 1 16 0 0 0 0 0 0 24 0 1 5 7 5 0 0
oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=11/31; ncol2=16; w=14; offset=-1; strand=R; shift=1; score=0.803906; -grwGACAGCTGyTkyc- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0
oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=12/31; ncol2=17; w=14; offset=-1; strand=R; shift=1; score=0.803149; -drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7
oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=13/31; ncol2=16; w=14; offset=0; strand=D; shift=2; score=0.802692; --rgmACAGCTGCTGcws ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4
oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=14/31; ncol2=17; w=14; offset=-1; strand=D; shift=1; score=0.799103; -rraGACAGCTGCTgyyy ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6
dyads_m5_shift1 (dyads_m5dyads_m5)				; oligos_6nt_mkv2_m2 versus dyads_m5 (dyads_m5dyads_m5); m=15/31; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.79754; -rvdGACAGCTGmsg--- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=16/31; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.796612; -rswGACAGCTGmsg--- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0
dyads_m8_rc_shift1 (dyads_m8dyads_m8_rc)				; oligos_6nt_mkv2_m2 versus dyads_m8_rc (dyads_m8dyads_m8_rc); m=17/31; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.788588; -mvrGACAGCTGwGsv-- ; cor=; Ncor= a 0 10 7 7 3 17 0 20 1 0 0 0 5 0 4 6 0 0 c 0 5 7 2 0 0 20 0 0 20 0 0 2 0 5 5 0 0 g 0 3 6 7 17 0 0 0 18 0 0 20 2 17 7 6 0 0 t 0 2 0 4 0 3 0 0 1 0 20 0 11 3 4 3 0 0
oligos_6nt_mkv2_m1_rc_shift2 (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc (oligos_6nt_mkv2_m1oligos_6nt_mkv2_m1_rc); m=18/31; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.785906; --cwGaCAGCTGtCwg-- ; cor=; Ncor= a 0 0 8 13 4 23 0 35 0 0 0 0 6 0 15 4 0 0 c 0 0 21 3 5 3 35 0 0 35 0 0 3 26 3 2 0 0 g 0 0 2 3 26 3 0 0 35 0 0 35 3 4 3 21 0 0 t 0 0 4 16 0 6 0 0 0 0 35 0 23 5 14 8 0 0
oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=19/31; ncol2=17; w=14; offset=-1; strand=R; shift=1; score=0.783988; -krkGACAGCTGCTkhvb ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=20/31; ncol2=16; w=14; offset=-1; strand=R; shift=1; score=0.764672; -kkwsACAGCTGTTsys- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0
oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=21/31; ncol2=17; w=14; offset=-1; strand=R; shift=1; score=0.737374; -bwGAACAGCTGCTGchw ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6
oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=22/31; ncol2=17; w=14; offset=-1; strand=D; shift=1; score=0.733631; -swsAACAGCTGCTGchm ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4
dyads_m25_shift2 (dyads_m25dyads_m25)				; oligos_6nt_mkv2_m2 versus dyads_m25 (dyads_m25dyads_m25); m=23/31; ncol2=17; w=14; offset=0; strand=D; shift=2; score=0.72895; --dkAACAGCTGCTGyCy ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8
dyads_m2_shift1 (dyads_m2dyads_m2)				; oligos_6nt_mkv2_m2 versus dyads_m2 (dyads_m2dyads_m2); m=24/31; ncol2=18; w=14; offset=-1; strand=D; shift=1; score=0.720512; -krrrACAGCTGCTGtct ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7
oligos_8nt_mkv2_m12_shift1 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m12 (oligos_8nt_mkv2_m12oligos_8nt_mkv2_m12); m=25/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.657097; -gmyGaCAGCTGtCrkc- ; cor=; Ncor= a 0 1 3 0 1 4 0 6 0 0 0 0 1 0 4 0 0 0 c 0 1 3 2 0 0 6 0 0 6 0 0 1 5 0 0 4 0 g 0 4 0 0 5 1 0 0 6 0 0 6 0 0 2 3 1 0 t 0 0 0 4 0 1 0 0 0 0 6 0 4 1 0 3 1 0
dyads_m1_shift1 (dyads_m1dyads_m1)				; oligos_6nt_mkv2_m2 versus dyads_m1 (dyads_m1dyads_m1); m=26/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.655261; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1 (oligos_7nt_mkv2_m1oligos_7nt_mkv2_m1); m=27/31; ncol2=16; w=14; offset=-1; strand=D; shift=1; score=0.655261; -vmwGaCAGCTGtCwkb- ; cor=; Ncor= a 0 10 7 10 2 17 0 28 0 0 0 0 6 0 14 2 2 0 c 0 7 18 2 1 3 28 0 0 28 0 0 2 25 2 1 9 0 g 0 9 1 2 25 2 0 0 28 0 0 28 3 1 2 18 7 0 t 0 2 2 14 0 6 0 0 0 0 28 0 17 2 10 7 10 0
oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=28/31; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.651707; --gvAACAGTTGcr---- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0
oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=29/31; ncol2=12; w=12; offset=2; strand=R; shift=4; score=0.60547; ----asCACCTGCTky-- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=30/31; ncol2=18; w=14; offset=-2; strand=D; shift=0; score=0.593376; sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2
oligos_7nt_mkv2_m12_shift3 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m12 (oligos_7nt_mkv2_m12oligos_7nt_mkv2_m12); m=31/31; ncol2=11; w=11; offset=1; strand=D; shift=3; score=0.561346; ---smACAGTTGym---- ; cor=; Ncor= a 0 0 0 1 6 12 0 12 0 0 0 0 0 4 0 0 0 0 c 0 0 0 4 5 0 12 0 0 0 0 0 5 4 0 0 0 0 g 0 0 0 6 0 0 0 0 12 0 0 12 2 2 0 0 0 0 t 0 0 0 1 1 0 0 0 0 12 12 0 5 2 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m30_shift1 (dyads_m30dyads_m30)				; dyads_m30 (dyads_m30dyads_m30); m=0 (reference); ncol1=11; shift=1; ncol=14; -ymCCCMGCCyr-- ; Alignment reference a 0 2 4 0 0 0 8 0 0 0 2 3 0 0 c 0 3 3 11 11 11 3 0 11 11 4 2 0 0 g 0 2 2 0 0 0 0 11 0 0 2 4 0 0 t 0 4 2 0 0 0 0 0 0 0 3 2 0 0
dyads_m30_shift1 (dyads_m30dyads_m30)				; dyads_m30 versus dyads_m30 (dyads_m30dyads_m30); m=1/8; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 1; -ymCCCMGCCyr-- ; cor=; Ncor= a 0 2 4 0 0 0 8 0 0 0 2 3 0 0 c 0 3 3 11 11 11 3 0 11 11 4 2 0 0 g 0 2 2 0 0 0 0 11 0 0 2 4 0 0 t 0 4 2 0 0 0 0 0 0 0 3 2 0 0
oligos_7nt_mkv2_m8_shift1 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8)				; dyads_m30 versus oligos_7nt_mkv2_m8 (oligos_7nt_mkv2_m8oligos_7nt_mkv2_m8); m=2/8; ncol2=11; w=11; offset=0; strand=D; shift=1; score=0.815323; -smCCCTGCCwc-- ; cor=; Ncor= a 0 4 10 0 0 0 0 2 0 0 9 6 0 0 c 0 20 15 34 33 34 3 0 34 34 4 16 0 0 g 0 9 5 0 1 0 0 32 0 0 5 6 0 0 t 0 1 4 0 0 0 31 0 0 0 16 6 0 0
dyads_m11_shift1 (dyads_m11dyads_m11)				; dyads_m30 versus dyads_m11 (dyads_m11dyads_m11); m=3/8; ncol2=12; w=11; offset=0; strand=D; shift=1; score=0.714061; -ccCCCTGCCwct- ; cor=; Ncor= a 0 2 7 0 0 0 0 0 1 0 9 5 7 0 c 0 19 15 28 29 29 0 0 28 29 2 16 6 0 g 0 7 3 1 0 0 0 29 0 0 0 5 3 0 t 0 1 4 0 0 0 29 0 0 0 18 3 13 0
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)				; dyads_m30 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=4/8; ncol2=10; w=10; offset=0; strand=D; shift=1; score=0.690755; -ssCCCCGCsg--- ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 2 1 0 0 0 c 0 10 7 23 21 23 24 0 25 8 6 0 0 0 g 0 11 9 2 4 2 1 25 0 9 15 0 0 0 t 0 4 6 0 0 0 0 0 0 6 3 0 0 0
oligos_8nt_mkv2_m20_rc_shift1 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc)				; dyads_m30 versus oligos_8nt_mkv2_m20_rc (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20_rc); m=5/8; ncol2=13; w=11; offset=0; strand=R; shift=1; score=0.596506; -CyCCCTGCCTCws ; cor=; Ncor= a 0 2 3 0 0 0 1 0 1 0 1 0 7 0 c 0 19 14 26 20 26 0 0 25 26 0 23 6 11 g 0 3 1 0 0 0 0 25 0 0 0 2 2 13 t 0 2 8 0 6 0 25 1 0 0 25 1 11 2
oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)				; dyads_m30 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=6/8; ncol2=11; w=10; offset=1; strand=D; shift=2; score=0.59112; --ssCCCGCCGsg- ; cor=; Ncor= a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0
dyads_m12_shift0 (dyads_m12dyads_m12)				; dyads_m30 versus dyads_m12 (dyads_m12dyads_m12); m=7/8; ncol2=14; w=11; offset=-1; strand=D; shift=0; score=0.566606; vssCCSCGCSGGss ; cor=; Ncor= a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0
oligos_8nt_mkv2_m15_shift3 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)				; dyads_m30 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=8/8; ncol2=12; w=9; offset=2; strand=D; shift=3; score=0.457706; ---vcCCGCCGcGs ; cor=; Ncor= a 0 0 0 4 0 0 1 0 1 0 0 2 0 1 c 0 0 0 6 9 14 13 0 12 12 1 9 0 5 g 0 0 0 4 3 0 0 14 1 2 13 2 14 8 t 0 0 0 0 2 0 0 0 0 0 0 1 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=0 (reference); ncol1=18; shift=1; ncol=19; -sygCAGCAGCTGCTGcrs ; Alignment reference a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2
oligos_8nt_mkv2_m5_shift1 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=1/14; ncol2=18; w=18; offset=0; strand=D; shift=1; score= 1; -sygCAGCAGCTGCTGcrs ; cor=; Ncor= a 0 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 c 0 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 g 0 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 t 0 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2
oligos_8nt_mkv2_m2_rc_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m2_rc (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2_rc); m=2/14; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.827759; -kdgCAGCAGCTGTTsws- ; cor=; Ncor= a 0 4 8 2 2 19 1 0 21 0 0 0 0 1 0 1 7 4 0 c 0 2 1 2 15 0 1 21 0 1 21 1 0 4 1 7 4 9 0 g 0 9 6 13 1 1 19 0 0 20 0 0 21 0 4 12 3 7 0 t 0 6 6 4 3 1 0 0 0 0 0 20 0 16 16 1 7 1 0
oligos_8nt_mkv2_m13_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m13 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13); m=3/14; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.78672; -wdgCAGCAGCTGTTCwv- ; cor=; Ncor= a 0 6 5 2 2 18 1 0 18 0 0 0 0 1 0 1 6 6 0 c 0 4 2 2 14 0 1 19 0 0 18 0 0 2 2 13 4 6 0 g 0 4 7 12 1 0 17 0 0 19 1 0 19 0 3 4 2 7 0 t 0 5 5 3 2 1 0 0 1 0 0 19 0 16 14 1 7 0 0
dyads_m21_shift3 (dyads_m21dyads_m21)				; oligos_8nt_mkv2_m5 versus dyads_m21 (dyads_m21dyads_m21); m=4/14; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.762862; ---ssAGCAGCTGCTss-- ; cor=; Ncor= a 0 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 c 0 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 g 0 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 t 0 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0
oligos_8nt_mkv2_m8_rc_shift1 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m8_rc (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8_rc); m=5/14; ncol2=16; w=16; offset=0; strand=R; shift=1; score=0.716124; -swgCAGCAGCTGTkcy-- ; cor=; Ncor= a 0 4 6 3 1 17 1 0 17 0 0 0 0 1 1 4 3 0 0 c 0 6 4 1 15 0 1 18 0 0 18 1 0 1 3 6 5 0 0 g 0 5 3 12 1 0 16 0 0 18 0 0 18 0 9 4 4 0 0 t 0 3 5 2 1 1 0 0 1 0 0 17 0 16 5 4 6 0 0
oligos_8nt_mkv2_m27_rc_shift2 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=6/14; ncol2=17; w=17; offset=1; strand=R; shift=2; score=0.701806; --drrGACAGCTGCTGhbb ; cor=; Ncor= a 0 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 c 0 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 g 0 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 t 0 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1); m=7/14; ncol2=17; w=17; offset=0; strand=D; shift=1; score=0.675737; -vbdmAGCAGCTGTCmym- ; cor=; Ncor= a 0 3 2 3 3 11 1 0 12 0 0 0 0 1 0 6 1 3 0 c 0 4 3 0 8 0 0 12 0 0 11 0 0 0 10 3 4 6 0 g 0 3 4 6 1 0 9 0 0 12 1 0 12 0 1 1 2 1 0 t 0 2 3 3 0 1 2 0 0 0 0 12 0 11 1 2 5 2 0
oligos_8nt_mkv2_m10_rc_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m10_rc (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10_rc); m=8/14; ncol2=17; w=17; offset=0; strand=R; shift=1; score=0.670588; -rrrcAGCAGCTGTCtyy- ; cor=; Ncor= a 0 6 5 5 4 15 1 0 17 0 1 0 0 0 0 4 3 3 0 c 0 3 3 1 10 1 1 17 0 0 16 0 0 1 14 3 5 6 0 g 0 6 5 7 2 0 14 0 0 17 0 0 16 0 2 1 3 3 0 t 0 2 4 4 1 1 1 0 0 0 0 17 1 16 1 9 6 5 0
oligos_7nt_mkv2_m2_rc_shift2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc)				; oligos_8nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2_rc); m=9/14; ncol2=16; w=16; offset=1; strand=R; shift=2; score=0.66825; --akmAGCAGCTGTCysc- ; cor=; Ncor= a 0 0 11 7 9 25 2 0 34 0 1 0 0 0 0 6 6 7 0 c 0 0 8 8 14 2 1 34 0 1 33 0 0 2 24 11 12 13 0 g 0 0 7 10 6 2 30 0 0 33 0 0 33 0 4 6 9 6 0 t 0 0 8 9 5 5 1 0 0 0 0 34 1 32 6 11 7 8 0
dyads_m25_rc_shift0 (dyads_m25dyads_m25_rc)				; oligos_8nt_mkv2_m5 versus dyads_m25_rc (dyads_m25dyads_m25_rc); m=10/14; ncol2=17; w=16; offset=-1; strand=R; shift=0; score=0.666952; arGrCAGCAGCTGTTmh-- ; cor=; Ncor= a 6 8 2 8 1 14 2 0 12 0 1 0 0 0 0 4 5 0 0 c 3 0 1 1 13 0 0 15 0 0 13 0 0 2 2 6 4 0 0 g 3 4 12 4 1 0 12 0 0 15 1 0 15 0 1 3 2 0 0 t 3 3 0 2 0 1 1 0 3 0 0 15 0 13 12 2 4 0 0
dyads_m2_rc_shift0 (dyads_m2dyads_m2_rc)				; oligos_8nt_mkv2_m5 versus dyads_m2_rc (dyads_m2dyads_m2_rc); m=11/14; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=0.663081; tagaCAGCAGCTGTyyym- ; cor=; Ncor= a 3 7 3 8 0 12 2 0 13 0 0 0 0 0 0 3 2 4 0 c 3 0 2 0 12 0 0 13 0 0 12 0 0 2 8 4 4 5 0 g 2 3 7 3 1 0 10 0 0 13 1 0 13 0 1 0 1 1 0 t 5 3 1 2 0 1 1 0 0 0 0 13 0 11 4 6 6 3 0
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)				; oligos_8nt_mkv2_m5 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=12/14; ncol2=14; w=14; offset=2; strand=D; shift=3; score=0.593376; ---grgACAGCTGCtkm-- ; cor=; Ncor= a 0 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 c 0 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 g 0 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 t 0 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0
dyads_m36_rc_shift3 (dyads_m36dyads_m36_rc)				; oligos_8nt_mkv2_m5 versus dyads_m36_rc (dyads_m36dyads_m36_rc); m=13/14; ncol2=15; w=15; offset=2; strand=R; shift=3; score=0.583601; ---smagCAGCTGTCmby- ; cor=; Ncor= a 0 0 0 13 18 23 3 0 66 0 1 0 0 0 1 17 9 11 0 c 0 0 0 23 25 13 5 67 0 0 63 0 0 4 50 22 21 25 0 g 0 0 0 17 10 15 43 0 0 66 1 0 67 1 4 12 18 9 0 t 0 0 0 14 14 16 16 0 1 1 2 67 0 62 12 16 19 22 0
oligos_8nt_mkv2_m7_shift3 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)				; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=14/14; ncol2=12; w=12; offset=2; strand=D; shift=3; score=0.532923; ---rmAGCAGGTGst---- ; cor=; Ncor= a 0 0 0 8 5 16 0 0 15 0 0 0 0 2 2 0 0 0 0 c 0 0 0 3 8 1 0 16 1 0 0 1 1 7 4 0 0 0 0 g 0 0 0 5 3 0 17 0 1 17 17 0 16 5 1 0 0 0 0 t 0 0 0 1 1 0 0 1 0 0 0 16 0 3 10 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m9_shift3 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9)				; oligos_6nt_mkv2_m9 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9); m=0 (reference); ncol1=10; shift=3; ncol=13; ---rrAGGTGGaa ; Alignment reference a 0 0 0 24 16 41 0 0 0 0 0 17 25 c 0 0 0 4 10 0 0 0 0 0 0 10 5 g 0 0 0 12 11 0 41 41 0 41 41 7 5 t 0 0 0 1 4 0 0 0 41 0 0 7 6
oligos_6nt_mkv2_m9_shift3 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9)				; oligos_6nt_mkv2_m9 versus oligos_6nt_mkv2_m9 (oligos_6nt_mkv2_m9oligos_6nt_mkv2_m9); m=1/3; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 1; ---rrAGGTGGaa ; cor=; Ncor= a 0 0 0 24 16 41 0 0 0 0 0 17 25 c 0 0 0 4 10 0 0 0 0 0 0 10 5 g 0 0 0 12 11 0 41 41 0 41 41 7 5 t 0 0 0 1 4 0 0 0 41 0 0 7 6
dyads_m17_rc_shift4 (dyads_m17dyads_m17_rc)				; oligos_6nt_mkv2_m9 versus dyads_m17_rc (dyads_m17dyads_m17_rc); m=2/3; ncol2=10; w=9; offset=1; strand=R; shift=4; score=0.679742; ----kwGGTGGCh ; cor=; Ncor= a 0 0 0 0 4 11 0 0 0 0 0 0 9 c 0 0 0 0 5 1 0 0 1 0 0 27 9 g 0 0 0 0 11 5 27 27 0 27 27 0 1 t 0 0 0 0 7 10 0 0 26 0 0 0 8
oligos_8nt_mkv2_m7_shift0 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7)				; oligos_6nt_mkv2_m9 versus oligos_8nt_mkv2_m7 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7); m=3/3; ncol2=12; w=9; offset=-3; strand=D; shift=0; score=0.507586; rmAGCAGGTGst- ; cor=; Ncor= a 8 5 16 0 0 15 0 0 0 0 2 2 0 c 3 8 1 0 16 1 0 0 1 1 7 4 0 g 5 3 0 17 0 1 17 17 0 16 5 1 0 t 1 1 0 0 1 0 0 0 16 0 3 10 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m14_shift0 (dyads_m14dyads_m14)				; dyads_m14 (dyads_m14dyads_m14); m=0 (reference); ncol1=21; shift=0; ncol=25; cCATAtwCcakGTcCTACAgT---- ; Alignment reference a 19 7 90 0 89 3 28 6 21 58 18 14 15 7 11 8 90 0 90 16 16 0 0 0 0 c 52 64 0 0 1 16 3 67 51 16 9 5 3 58 64 14 0 89 0 7 4 0 0 0 0 g 1 14 0 0 0 11 2 9 5 10 36 67 3 5 9 2 0 0 0 54 2 0 0 0 0 t 18 5 0 90 0 60 57 8 13 6 27 4 69 20 6 66 0 1 0 13 68 0 0 0 0
dyads_m14_shift0 (dyads_m14dyads_m14)				; dyads_m14 versus dyads_m14 (dyads_m14dyads_m14); m=1/5; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 1; cCATAtwCcakGTcCTACAgT---- ; cor=; Ncor= a 19 7 90 0 89 3 28 6 21 58 18 14 15 7 11 8 90 0 90 16 16 0 0 0 0 c 52 64 0 0 1 16 3 67 51 16 9 5 3 58 64 14 0 89 0 7 4 0 0 0 0 g 1 14 0 0 0 11 2 9 5 10 36 67 3 5 9 2 0 0 0 54 2 0 0 0 0 t 18 5 0 90 0 60 57 8 13 6 27 4 69 20 6 66 0 1 0 13 68 0 0 0 0
dyads_m18_shift0 (dyads_m18dyads_m18)				; dyads_m14 versus dyads_m18 (dyads_m18dyads_m18); m=2/5; ncol2=19; w=19; offset=0; strand=D; shift=0; score=0.872917; CCATATTCCAkGTCCTACA------ ; cor=; Ncor= a 9 3 95 1 94 3 16 6 22 74 16 3 2 3 0 1 94 19 80 0 0 0 0 0 0 c 65 72 0 0 0 10 3 65 65 16 18 4 6 69 95 0 0 67 6 0 0 0 0 0 0 g 1 17 0 0 0 6 4 4 3 1 37 78 8 8 0 1 0 3 3 0 0 0 0 0 0 t 20 3 0 94 1 76 72 20 5 4 24 10 79 15 0 93 1 6 6 0 0 0 0 0 0
dyads_m32_rc_shift0 (dyads_m32dyads_m32_rc)				; dyads_m14 versus dyads_m32_rc (dyads_m32dyads_m32_rc); m=3/5; ncol2=25; w=21; offset=0; strand=R; shift=0; score=0.805402; cCATATTyCAgGTCCTACAgTGTGy ; cor=; Ncor= a 14 8 84 0 84 6 10 7 9 66 17 11 9 2 4 3 65 18 70 6 0 0 0 9 6 c 50 68 0 0 0 11 3 49 58 3 17 4 5 60 63 5 6 58 5 14 0 1 1 4 42 g 6 4 0 0 0 7 3 6 3 10 37 65 4 3 9 4 3 3 5 56 0 82 0 64 6 t 14 4 0 84 0 60 68 22 14 5 13 4 66 19 8 72 10 5 4 8 84 1 83 7 30
oligos_8nt_mkv2_m21_rc_shift8 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21_rc)				; dyads_m14 versus oligos_8nt_mkv2_m21_rc (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21_rc); m=4/5; ncol2=12; w=12; offset=8; strand=R; shift=8; score=0.455219; --------wmTGTTCTACAr----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 16 20 0 2 0 0 0 0 32 0 31 11 0 0 0 0 0 c 0 0 0 0 0 0 0 0 1 10 0 0 0 0 31 0 0 32 1 4 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 0 0 30 0 0 1 0 0 0 0 16 0 0 0 0 0 t 0 0 0 0 0 0 0 0 14 2 32 0 32 32 0 32 0 0 0 1 0 0 0 0 0
oligos_8nt_mkv2_m14_rc_shift2 (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc)				; dyads_m14 versus oligos_8nt_mkv2_m14_rc (oligos_8nt_mkv2_m14oligos_8nt_mkv2_m14_rc); m=5/5; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.403477; --ATTTTCCATGwT----------- ; cor=; Ncor= a 0 0 79 2 10 0 1 0 0 72 0 3 34 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 1 0 0 0 1 83 80 0 9 0 0 14 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 3 0 0 0 0 2 11 0 79 3 1 0 0 0 0 0 0 0 0 0 0 0 t 0 0 3 78 73 83 81 0 1 0 74 1 46 68 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m6_shift5 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)				; oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=0 (reference); ncol1=11; shift=5; ncol=16; -----ssCCGCCGGGs ; Alignment reference a 0 0 0 0 0 3 2 1 0 0 0 0 0 2 2 4 c 0 0 0 0 0 11 13 21 25 1 23 22 3 3 4 10 g 0 0 0 0 0 10 9 3 1 25 3 4 23 20 18 11 t 0 0 0 0 0 2 2 1 0 0 0 0 0 1 2 1
oligos_6nt_mkv2_m6_shift5 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)				; oligos_6nt_mkv2_m6 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=1/8; ncol2=11; w=11; offset=0; strand=D; shift=5; score= 1; -----ssCCGCCGGGs ; cor=; Ncor= a 0 0 0 0 0 3 2 1 0 0 0 0 0 2 2 4 c 0 0 0 0 0 11 13 21 25 1 23 22 3 3 4 10 g 0 0 0 0 0 10 9 3 1 25 3 4 23 20 18 11 t 0 0 0 0 0 2 2 1 0 0 0 0 0 1 2 1
oligos_8nt_mkv2_m15_shift5 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)				; oligos_6nt_mkv2_m6 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=2/8; ncol2=12; w=11; offset=0; strand=D; shift=5; score=0.823855; -----vcCCGCCGcGs ; cor=; Ncor= a 0 0 0 0 0 4 0 0 1 0 1 0 0 2 0 1 c 0 0 0 0 0 6 9 14 13 0 12 12 1 9 0 5 g 0 0 0 0 0 4 3 0 0 14 1 2 13 2 14 8 t 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 0
oligos_7nt_mkv2_m7_rc_shift6 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc)				; oligos_6nt_mkv2_m6 versus oligos_7nt_mkv2_m7_rc (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7_rc); m=3/8; ncol2=11; w=10; offset=1; strand=R; shift=6; score=0.801271; ------ssCGCCGGGs ; cor=; Ncor= a 0 0 0 0 0 0 2 4 3 0 0 0 0 3 0 6 c 0 0 0 0 0 0 16 17 33 1 28 32 4 3 1 14 g 0 0 0 0 0 0 14 11 0 33 5 4 32 29 34 11 t 0 0 0 0 0 0 4 4 0 2 3 0 0 1 1 5
oligos_7nt_mkv2_m15_shift4 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)				; oligos_6nt_mkv2_m6 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=4/8; ncol2=11; w=10; offset=-1; strand=D; shift=4; score=0.78658; ----ssCCCGCCGsg- ; cor=; Ncor= a 0 0 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 0 0 5 4 1 0 0 0 0 0 0 3 1 0
dyads_m12_shift2 (dyads_m12dyads_m12)				; oligos_6nt_mkv2_m6 versus dyads_m12 (dyads_m12dyads_m12); m=5/8; ncol2=14; w=11; offset=-3; strand=D; shift=2; score=0.743492; --vssCCSCGCSGGss ; cor=; Ncor= a 0 0 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 0 0 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 0 0 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0
dyads_m26_shift5 (dyads_m26dyads_m26)				; oligos_6nt_mkv2_m6 versus dyads_m26 (dyads_m26dyads_m26); m=6/8; ncol2=12; w=11; offset=0; strand=D; shift=5; score=0.742676; -----csCCGcsGCGs ; cor=; Ncor= a 0 0 0 0 0 1 0 1 0 1 4 3 0 1 0 3 c 0 0 0 0 0 19 15 25 27 1 15 13 2 24 3 10 g 0 0 0 0 0 6 10 2 1 26 6 11 24 2 25 12 t 0 0 0 0 0 2 3 0 0 0 3 1 2 1 0 3
oligos_6nt_mkv2_m5_rc_shift7 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m6 versus oligos_6nt_mkv2_m5_rc (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5_rc); m=7/8; ncol2=10; w=9; offset=2; strand=R; shift=7; score=0.565184; -------csGCGGGGs ; cor=; Ncor= a 0 0 0 0 0 0 0 3 6 0 0 0 0 0 0 6 c 0 0 0 0 0 0 0 15 9 0 25 1 2 4 2 9 g 0 0 0 0 0 0 0 6 8 25 0 24 23 21 23 7 t 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 3
dyads_m34_shift0 (dyads_m34dyads_m34)				; oligos_6nt_mkv2_m6 versus dyads_m34 (dyads_m34dyads_m34); m=8/8; ncol2=15; w=10; offset=-5; strand=D; shift=0; score=0.442045; ssACGcrsssCCGvs- ; cor=; Ncor= a 1 4 15 0 0 3 8 2 2 2 3 0 0 6 2 0 c 6 7 3 21 1 11 4 7 7 7 15 19 0 6 8 0 g 10 7 2 0 20 5 7 9 11 9 3 2 21 7 8 0 t 4 3 1 0 0 2 2 3 1 3 0 0 0 2 3 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)				; oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=0 (reference); ncol1=11; shift=2; ncol=14; --ssCCCGCCGsg- ; Alignment reference a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0
oligos_7nt_mkv2_m15_shift2 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15)				; oligos_7nt_mkv2_m15 versus oligos_7nt_mkv2_m15 (oligos_7nt_mkv2_m15oligos_7nt_mkv2_m15); m=1/8; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 1; --ssCCCGCCGsg- ; cor=; Ncor= a 0 0 4 4 0 1 0 0 3 0 0 3 3 0 c 0 0 7 11 23 24 26 0 19 23 2 10 5 0 g 0 0 11 8 3 2 1 27 5 4 25 11 18 0 t 0 0 5 4 1 0 0 0 0 0 0 3 1 0
oligos_7nt_mkv2_m7_shift2 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7)				; oligos_7nt_mkv2_m15 versus oligos_7nt_mkv2_m7 (oligos_7nt_mkv2_m7oligos_7nt_mkv2_m7); m=2/8; ncol2=11; w=11; offset=0; strand=D; shift=2; score=0.885944; --ssCCCGGCGss- ; cor=; Ncor= a 0 0 4 5 1 1 0 0 3 2 0 4 4 0 c 0 0 17 11 34 29 32 4 5 33 0 11 14 0 g 0 0 11 14 1 3 4 32 28 1 33 17 16 0 t 0 0 4 6 0 3 0 0 0 0 3 4 2 0
oligos_6nt_mkv2_m6_shift3 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6)				; oligos_7nt_mkv2_m15 versus oligos_6nt_mkv2_m6 (oligos_6nt_mkv2_m6oligos_6nt_mkv2_m6); m=3/8; ncol2=11; w=10; offset=1; strand=D; shift=3; score=0.78658; ---ssCCGCCGGGs ; cor=; Ncor= a 0 0 0 3 2 1 0 0 0 0 0 2 2 4 c 0 0 0 11 13 21 25 1 23 22 3 3 4 10 g 0 0 0 10 9 3 1 25 3 4 23 20 18 11 t 0 0 0 2 2 1 0 0 0 0 0 1 2 1
oligos_8nt_mkv2_m15_shift3 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15)				; oligos_7nt_mkv2_m15 versus oligos_8nt_mkv2_m15 (oligos_8nt_mkv2_m15oligos_8nt_mkv2_m15); m=4/8; ncol2=12; w=10; offset=1; strand=D; shift=3; score=0.732153; ---vcCCGCCGcGs ; cor=; Ncor= a 0 0 0 4 0 0 1 0 1 0 0 2 0 1 c 0 0 0 6 9 14 13 0 12 12 1 9 0 5 g 0 0 0 4 3 0 0 14 1 2 13 2 14 8 t 0 0 0 0 2 0 0 0 0 0 0 1 0 0
dyads_m12_shift0 (dyads_m12dyads_m12)				; oligos_7nt_mkv2_m15 versus dyads_m12 (dyads_m12dyads_m12); m=5/8; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=0.729556; vssCCSCGCSGGss ; cor=; Ncor= a 3 0 1 1 0 0 0 0 0 0 0 1 1 1 c 3 5 6 9 9 8 11 0 10 8 1 2 3 6 g 3 4 4 1 2 3 0 11 1 3 10 8 7 4 t 2 2 0 0 0 0 0 0 0 0 0 0 0 0
dyads_m26_shift3 (dyads_m26dyads_m26)				; oligos_7nt_mkv2_m15 versus dyads_m26 (dyads_m26dyads_m26); m=6/8; ncol2=12; w=10; offset=1; strand=D; shift=3; score=0.678867; ---csCCGcsGCGs ; cor=; Ncor= a 0 0 0 1 0 1 0 1 4 3 0 1 0 3 c 0 0 0 19 15 25 27 1 15 13 2 24 3 10 g 0 0 0 6 10 2 1 26 6 11 24 2 25 12 t 0 0 0 2 3 0 0 0 3 1 2 1 0 3
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5)				; oligos_7nt_mkv2_m15 versus oligos_6nt_mkv2_m5 (oligos_6nt_mkv2_m5oligos_6nt_mkv2_m5); m=7/8; ncol2=10; w=9; offset=-1; strand=D; shift=1; score=0.653332; -ssCCCCGCsg--- ; cor=; Ncor= a 0 0 3 0 0 0 0 0 0 2 1 0 0 0 c 0 10 7 23 21 23 24 0 25 8 6 0 0 0 g 0 11 9 2 4 2 1 25 0 9 15 0 0 0 t 0 4 6 0 0 0 0 0 0 6 3 0 0 0
dyads_m30_shift1 (dyads_m30dyads_m30)				; oligos_7nt_mkv2_m15 versus dyads_m30 (dyads_m30dyads_m30); m=8/8; ncol2=11; w=10; offset=-1; strand=D; shift=1; score=0.59112; -ymCCCMGCCyr-- ; cor=; Ncor= a 0 2 4 0 0 0 8 0 0 0 2 3 0 0 c 0 3 3 11 11 11 3 0 11 11 4 2 0 0 g 0 2 2 0 0 0 0 11 0 0 2 4 0 0 t 0 4 2 0 0 0 0 0 0 0 3 2 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m25_shift2 (dyads_m25dyads_m25)				; dyads_m25 (dyads_m25dyads_m25); m=0 (reference); ncol1=17; shift=2; ncol=19; --dkAACAGCTGCTGyCyt ; Alignment reference a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6
dyads_m25_shift2 (dyads_m25dyads_m25)				; dyads_m25 versus dyads_m25 (dyads_m25dyads_m25); m=1/24; ncol2=17; w=17; offset=0; strand=D; shift=2; score= 1; --dkAACAGCTGCTGyCyt ; cor=; Ncor= a 0 0 4 2 12 13 0 15 0 0 3 0 1 1 0 2 0 3 3 c 0 0 2 3 1 0 15 0 1 15 0 0 12 0 1 4 12 4 3 g 0 0 4 6 2 2 0 0 13 0 0 15 0 0 13 1 1 0 3 t 0 0 5 4 0 0 0 0 1 0 12 0 2 14 1 8 2 8 6
dyads_m2_shift1 (dyads_m2dyads_m2)				; dyads_m25 versus dyads_m2 (dyads_m2dyads_m2); m=2/24; ncol2=18; w=17; offset=-1; strand=D; shift=1; score=0.88108; -krrrACAGCTGCTGtcta ; cor=; Ncor= a 0 3 6 6 4 11 0 13 0 0 0 0 1 1 0 2 1 3 5 c 0 1 1 0 1 0 13 0 1 13 0 0 10 0 1 3 7 3 2 g 0 5 4 4 8 2 0 0 12 0 0 13 0 0 12 0 2 0 3 t 0 4 2 3 0 0 0 0 0 0 13 0 2 12 0 8 3 7 3
oligos_8nt_mkv2_m13_rc_shift1 (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc)				; dyads_m25 versus oligos_8nt_mkv2_m13_rc (oligos_8nt_mkv2_m13oligos_8nt_mkv2_m13_rc); m=3/24; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.829159; -bwGAACAGCTGCTGchw- ; cor=; Ncor= a 0 0 7 1 14 16 0 19 0 0 1 0 0 1 2 3 5 5 0 c 0 7 2 4 3 0 19 0 1 19 0 0 17 0 1 12 7 4 0 g 0 6 4 13 2 2 0 0 18 0 0 19 1 0 14 2 2 4 0 t 0 6 6 1 0 1 0 0 0 0 18 0 1 18 2 2 5 6 0
oligos_8nt_mkv2_m8_shift2 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8)				; dyads_m25 versus oligos_8nt_mkv2_m8 (oligos_8nt_mkv2_m8oligos_8nt_mkv2_m8); m=4/24; ncol2=16; w=16; offset=0; strand=D; shift=2; score=0.828996; --rgmACAGCTGCTGcws- ; cor=; Ncor= a 0 0 6 4 5 16 0 17 0 0 1 0 0 1 1 2 5 3 0 c 0 0 4 4 9 0 18 0 0 18 0 0 16 0 1 12 3 5 0 g 0 0 5 6 3 1 0 1 18 0 0 18 1 0 15 1 4 6 0 t 0 0 3 4 1 1 0 0 0 0 17 0 1 17 1 3 6 4 0
oligos_8nt_mkv2_m2_shift1 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2)				; dyads_m25 versus oligos_8nt_mkv2_m2 (oligos_8nt_mkv2_m2oligos_8nt_mkv2_m2); m=5/24; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.805868; -swsAACAGCTGCTGchm- ; cor=; Ncor= a 0 1 7 1 16 16 0 20 0 0 0 0 0 1 3 4 6 6 0 c 0 7 3 12 4 0 21 0 0 20 0 0 19 1 1 13 6 9 0 g 0 9 4 7 1 4 0 1 21 1 0 21 1 0 15 2 1 2 0 t 0 4 7 1 0 1 0 0 0 0 21 0 1 19 2 2 8 4 0
oligos_8nt_mkv2_m27_rc_shift1 (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc)				; dyads_m25 versus oligos_8nt_mkv2_m27_rc (oligos_8nt_mkv2_m27oligos_8nt_mkv2_m27_rc); m=6/24; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.788345; -drrGACAGCTGCTGhbb- ; cor=; Ncor= a 0 6 6 6 3 19 1 20 0 0 0 0 1 2 1 6 3 3 0 c 0 2 3 1 3 0 19 0 0 19 0 0 18 0 2 6 6 5 0 g 0 7 8 9 14 1 0 0 20 1 0 20 0 1 14 2 6 5 0 t 0 5 3 4 0 0 0 0 0 0 20 0 1 17 3 6 5 7 0
oligos_8nt_mkv2_m1_rc_shift1 (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc)				; dyads_m25 versus oligos_8nt_mkv2_m1_rc (oligos_8nt_mkv2_m1oligos_8nt_mkv2_m1_rc); m=7/24; ncol2=17; w=16; offset=-1; strand=R; shift=1; score=0.759677; -krkGACAGCTGCTkhvb- ; cor=; Ncor= a 0 2 5 2 1 11 0 12 0 0 0 0 2 1 0 3 3 2 0 c 0 1 2 1 1 0 12 0 1 12 0 0 9 0 1 6 4 3 0 g 0 6 4 3 10 0 0 0 11 0 0 12 0 0 8 0 3 4 0 t 0 3 1 6 0 1 0 0 0 0 12 0 1 11 3 3 2 3 0
oligos_8nt_mkv2_m10_shift1 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10)				; dyads_m25 versus oligos_8nt_mkv2_m10 (oligos_8nt_mkv2_m10oligos_8nt_mkv2_m10); m=8/24; ncol2=17; w=16; offset=-1; strand=D; shift=1; score=0.758892; -rraGACAGCTGCTgyyy- ; cor=; Ncor= a 0 5 6 9 1 16 1 17 0 0 0 0 1 1 1 4 4 2 0 c 0 3 3 1 2 0 16 0 0 17 0 0 14 0 2 7 5 6 0 g 0 6 5 3 14 1 0 0 16 0 0 17 1 1 10 1 3 3 0 t 0 3 3 4 0 0 0 0 1 0 17 0 1 15 4 5 5 6 0
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2)				; dyads_m25 versus oligos_6nt_mkv2_m2 (oligos_6nt_mkv2_m2oligos_6nt_mkv2_m2); m=9/24; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.72895; --grgACAGCTGCtkm--- ; cor=; Ncor= a 0 0 10 13 9 39 1 42 0 0 0 0 3 7 7 13 0 0 0 c 0 0 10 10 5 0 41 0 0 41 0 0 36 4 9 12 0 0 0 g 0 0 15 12 27 3 0 0 41 1 0 42 1 5 15 8 0 0 0 t 0 0 7 7 1 0 0 0 1 0 42 0 2 26 11 9 0 0 0
dyads_m21_shift2 (dyads_m21dyads_m21)				; dyads_m25 versus dyads_m21 (dyads_m21dyads_m21); m=10/24; ncol2=14; w=14; offset=0; strand=D; shift=2; score=0.714677; --ssAGCAGCTGCTss--- ; cor=; Ncor= a 0 0 11 7 45 6 0 50 0 0 2 1 1 3 7 11 0 0 0 c 0 0 14 24 1 1 51 0 3 49 0 0 44 3 14 16 0 0 0 g 0 0 16 14 3 44 0 0 49 3 0 51 1 1 24 14 0 0 0 t 0 0 11 7 3 1 1 2 0 0 50 0 6 45 7 11 0 0 0
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2)				; dyads_m25 versus oligos_7nt_mkv2_m2 (oligos_7nt_mkv2_m2oligos_7nt_mkv2_m2); m=11/24; ncol2=16; w=15; offset=-1; strand=D; shift=1; score=0.714485; -gsrGACAGCTGCTkmt-- ; cor=; Ncor= a 0 8 7 11 6 32 1 34 0 0 0 0 1 5 5 9 8 0 0 c 0 6 9 6 4 0 33 0 0 33 0 0 30 2 6 10 7 0 0 g 0 13 12 11 24 2 0 0 33 1 0 34 1 2 14 8 8 0 0 t 0 7 6 6 0 0 0 0 1 0 34 0 2 25 9 7 11 0 0
oligos_7nt_mkv2_m13_rc_shift1 (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc)				; dyads_m25 versus oligos_7nt_mkv2_m13_rc (oligos_7nt_mkv2_m13oligos_7nt_mkv2_m13_rc); m=12/24; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.697775; -grwGACAGCTGyTkyc-- ; cor=; Ncor= a 0 5 6 8 2 19 0 21 0 0 0 0 1 0 1 5 5 0 0 c 0 4 3 2 3 0 21 0 1 20 0 0 6 0 4 6 8 0 0 g 0 7 9 4 16 2 0 0 19 1 0 21 1 1 10 2 4 0 0 t 0 5 3 7 0 0 0 0 1 0 21 0 13 20 6 8 4 0 0
oligos_6nt_mkv2_m3_rc_shift2 (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc)				; dyads_m25 versus oligos_6nt_mkv2_m3_rc (oligos_6nt_mkv2_m3oligos_6nt_mkv2_m3_rc); m=13/24; ncol2=14; w=14; offset=0; strand=R; shift=2; score=0.670975; --vwGACAGCTGytkd--- ; cor=; Ncor= a 0 0 9 14 7 30 0 36 0 0 0 0 2 3 6 10 0 0 0 c 0 0 9 7 4 1 36 0 1 35 0 0 10 5 7 7 0 0 0 g 0 0 14 5 25 3 0 0 34 1 0 36 1 8 11 9 0 0 0 t 0 0 4 10 0 2 0 0 1 0 36 0 23 20 12 10 0 0 0
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5)				; dyads_m25 versus oligos_8nt_mkv2_m5 (oligos_8nt_mkv2_m5oligos_8nt_mkv2_m5); m=14/24; ncol2=18; w=16; offset=-2; strand=D; shift=0; score=0.666952; sygCAGCAGCTGCTGcrs- ; cor=; Ncor= a 2 4 4 1 16 0 0 18 0 0 0 0 1 2 1 2 5 4 0 c 7 5 4 13 0 0 18 0 1 17 0 0 17 0 3 8 4 5 0 g 5 4 8 3 0 17 0 0 17 1 0 18 0 0 13 4 5 7 0 t 4 5 2 1 2 1 0 0 0 0 18 0 0 16 1 4 4 2 0
dyads_m3_rc_shift1 (dyads_m3dyads_m3_rc)				; dyads_m25 versus dyads_m3_rc (dyads_m3dyads_m3_rc); m=15/24; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=0.662588; -rrwGACAGCTGyTky--- ; cor=; Ncor= a 0 6 6 8 2 20 0 22 0 0 0 0 1 0 2 5 0 0 0 c 0 4 4 2 3 0 22 0 1 21 0 0 7 0 4 6 0 0 0 g 0 7 9 5 17 2 0 0 20 1 0 22 1 2 10 3 0 0 0 t 0 5 3 7 0 0 0 0 1 0 22 0 13 20 6 8 0 0 0
dyads_m36_shift1 (dyads_m36dyads_m36)				; dyads_m25 versus dyads_m36 (dyads_m36dyads_m36); m=16/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.652863; -rvkGACAGCTGctks--- ; cor=; Ncor= a 0 22 19 16 12 62 0 67 2 1 1 0 16 16 14 14 0 0 0 c 0 9 18 12 4 1 67 0 1 66 0 0 43 15 10 17 0 0 0 g 0 25 21 22 50 4 0 0 63 0 0 67 5 13 25 23 0 0 0 t 0 11 9 17 1 0 0 0 1 0 66 0 3 23 18 13 0 0 0
oligos_7nt_mkv2_m3_rc_shift1 (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc)				; dyads_m25 versus oligos_7nt_mkv2_m3_rc (oligos_7nt_mkv2_m3oligos_7nt_mkv2_m3_rc); m=17/24; ncol2=16; w=15; offset=-1; strand=R; shift=1; score=0.652721; -kkwsACAGCTGTTsys-- ; cor=; Ncor= a 0 3 3 5 1 17 0 18 0 0 0 0 0 1 1 3 4 0 0 c 0 3 3 2 5 0 17 0 1 16 0 0 3 1 7 6 6 0 0 g 0 7 7 1 12 1 0 0 16 2 0 18 1 1 6 2 5 0 0 t 0 5 5 10 0 0 1 0 1 0 18 0 14 15 4 7 3 0 0
dyads_m19_shift1 (dyads_m19dyads_m19)				; dyads_m25 versus dyads_m19 (dyads_m19dyads_m19); m=18/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.595154; -rvdGACAGCTGvyks--- ; cor=; Ncor= a 0 16 14 17 2 48 0 50 0 1 1 0 16 9 10 9 0 0 0 c 0 8 18 3 0 0 49 0 0 49 0 0 16 13 8 15 0 0 0 g 0 16 14 14 47 2 0 0 48 0 0 50 14 10 17 17 0 0 0 t 0 10 4 16 1 0 1 0 2 0 49 0 4 18 15 9 0 0 0
oligos_8nt_mkv2_m17_shift1 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17)				; dyads_m25 versus oligos_8nt_mkv2_m17 (oligos_8nt_mkv2_m17oligos_8nt_mkv2_m17); m=19/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.584481; -rstGACAGCTGmhkg--- ; cor=; Ncor= a 0 11 6 4 0 27 0 27 0 0 0 0 10 9 4 4 0 0 0 c 0 2 11 2 1 0 27 0 0 27 0 0 16 8 4 5 0 0 0 g 0 10 9 4 26 0 0 0 27 0 0 27 0 3 9 12 0 0 0 t 0 4 1 17 0 0 0 0 0 0 27 0 1 7 10 6 0 0 0
oligos_8nt_mkv2_m22_shift1 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22)				; dyads_m25 versus oligos_8nt_mkv2_m22 (oligos_8nt_mkv2_m22oligos_8nt_mkv2_m22); m=20/24; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=0.582771; -rvtGACAGCTGmhkg--- ; cor=; Ncor= a 0 11 7 4 0 28 0 28 1 0 0 0 10 9 5 4 0 0 0 c 0 2 11 3 1 0 28 0 0 28 0 0 17 9 4 5 0 0 0 g 0 10 9 4 27 0 0 0 27 0 0 28 0 3 9 13 0 0 0 t 0 5 1 17 0 0 0 0 0 0 28 0 1 7 10 6 0 0 0
dyads_m5_shift1 (dyads_m5dyads_m5)				; dyads_m25 versus dyads_m5 (dyads_m5dyads_m5); m=21/24; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.561534; -rvdGACAGCTGmsg---- ; cor=; Ncor= a 0 17 16 15 8 56 0 56 0 0 0 0 32 12 14 0 0 0 0 c 0 6 21 9 5 0 57 0 0 57 0 0 15 16 9 0 0 0 0 g 0 21 16 16 43 1 0 0 57 0 0 57 6 17 20 0 0 0 0 t 0 13 4 17 1 0 0 1 0 0 57 0 4 12 14 0 0 0 0
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4)				; dyads_m25 versus oligos_7nt_mkv2_m4 (oligos_7nt_mkv2_m4oligos_7nt_mkv2_m4); m=22/24; ncol2=14; w=13; offset=-1; strand=D; shift=1; score=0.560227; -rswGACAGCTGmsg---- ; cor=; Ncor= a 0 17 14 15 8 56 0 57 0 0 0 0 32 12 14 0 0 0 0 c 0 5 22 9 5 0 57 0 0 57 0 1 15 15 9 0 0 0 0 g 0 22 17 14 43 1 0 0 57 0 0 56 6 18 20 0 0 0 0 t 0 13 4 19 1 0 0 0 0 0 57 0 4 12 14 0 0 0 0
oligos_8nt_mkv2_m7_rc_shift4 (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc)				; dyads_m25 versus oligos_8nt_mkv2_m7_rc (oligos_8nt_mkv2_m7oligos_8nt_mkv2_m7_rc); m=23/24; ncol2=12; w=12; offset=2; strand=R; shift=4; score=0.549659; ----asCACCTGCTky--- ; cor=; Ncor= a 0 0 0 0 10 3 0 16 0 0 0 1 0 0 1 1 0 0 0 c 0 0 0 0 1 5 16 0 17 17 1 0 17 0 3 5 0 0 0 g 0 0 0 0 4 7 1 1 0 0 1 16 0 1 8 3 0 0 0 t 0 0 0 0 2 2 0 0 0 0 15 0 0 16 5 8 0 0 0
oligos_8nt_mkv2_m25_shift2 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25)				; dyads_m25 versus oligos_8nt_mkv2_m25 (oligos_8nt_mkv2_m25oligos_8nt_mkv2_m25); m=24/24; ncol2=12; w=12; offset=0; strand=D; shift=2; score=0.547102; --gvAACAGTTGcr----- ; cor=; Ncor= a 0 0 1 2 6 6 0 6 0 0 0 0 0 3 0 0 0 0 0 c 0 0 1 2 0 0 6 0 0 1 0 0 4 0 0 0 0 0 0 g 0 0 3 2 0 0 0 0 6 0 0 6 1 2 0 0 0 0 0 t 0 0 1 0 0 0 0 0 0 5 6 0 1 1 0 0 0 0 0