One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; wrATTGCACAAcwy ; Alignment reference a 72 59 190 1 0 11 1 209 3 233 233 4 90 46 c 55 56 14 0 0 2 234 8 223 2 0 153 53 71 g 39 63 26 0 1 213 0 9 2 0 0 22 28 54 t 69 57 5 234 234 9 0 9 7 0 2 56 64 64

MA0102.3_shift2 (CEBPA) 0.946 0.744 9.783 0.734 0.947 0.670 0.970 3 6 7 5 3 3 3 4.286 1
; oligos_7nt_mkv4_m2 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 4.2857; --aTTGCAyAAym- ; cor=0.946; Ncor=0.744; logoDP=9.783; NIcor=0.734; NsEucl=0.947; SSD=0.670; NSW=0.970; rcor=3; rNcor=6; rlogoDP=7; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=4.286; match_rank=1 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0

MA0466.1_shift1 (CEBPB) 0.915 0.719 9.589 0.707 0.936 1.006 0.954 15 8 12 8 14 16 13 12.286 8
; oligos_7nt_mkv4_m2 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score=12.2857; -kATTGCAymAy-- ; cor=0.915; Ncor=0.719; logoDP=9.589; NIcor=0.707; NsEucl=0.936; SSD=1.006; NSW=0.954; rcor=15; rNcor=8; rlogoDP=12; rNIcor=8; rNsEucl=14; rSSD=16; rNSW=13; rank_mean=12.286; match_rank=8 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0

MA0133.1_shift7 (BRCA1) 0.874 0.437 3.092 0.443 0.916 0.700 0.950 24 46 46 35 30 4 19 29.143 28
; oligos_7nt_mkv4_m2 versus MA0133.1 (BRCA1); m=3/3; ncol2=7; w=7; offset=7; strand=D; shift=7; score=29.1429; -------mCAAcms ; cor=0.874; Ncor=0.437; logoDP=3.092; NIcor=0.443; NsEucl=0.916; SSD=0.700; NSW=0.950; rcor=24; rNcor=46; rlogoDP=46; rNIcor=35; rNsEucl=30; rSSD=4; rNSW=19; rank_mean=29.143; match_rank=28 a 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 7 2 0 1 1 3 3

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m2_shift0 (oligos_7nt_mkv4_m2)																	; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; wrATTGCACAAcwy ; Alignment reference a 72 59 190 1 0 11 1 209 3 233 233 4 90 46 c 55 56 14 0 0 2 234 8 223 2 0 153 53 71 g 39 63 26 0 1 213 0 9 2 0 0 22 28 54 t 69 57 5 234 234 9 0 9 7 0 2 56 64 64
MA0102.3_shift2 (CEBPA)	0.946	0.744	9.783	0.734	0.947	0.670	0.970	3	6	7	5	3	3	3	4.286	1	; oligos_7nt_mkv4_m2 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 4.2857; --aTTGCAyAAym- ; cor=0.946; Ncor=0.744; logoDP=9.783; NIcor=0.734; NsEucl=0.947; SSD=0.670; NSW=0.970; rcor=3; rNcor=6; rlogoDP=7; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=4.286; match_rank=1 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift1 (CEBPB)	0.915	0.719	9.589	0.707	0.936	1.006	0.954	15	8	12	8	14	16	13	12.286	8	; oligos_7nt_mkv4_m2 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score=12.2857; -kATTGCAymAy-- ; cor=0.915; Ncor=0.719; logoDP=9.589; NIcor=0.707; NsEucl=0.936; SSD=1.006; NSW=0.954; rcor=15; rNcor=8; rlogoDP=12; rNIcor=8; rNsEucl=14; rSSD=16; rNSW=13; rank_mean=12.286; match_rank=8 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0133.1_shift7 (BRCA1)	0.874	0.437	3.092	0.443	0.916	0.700	0.950	24	46	46	35	30	4	19	29.143	28	; oligos_7nt_mkv4_m2 versus MA0133.1 (BRCA1); m=3/3; ncol2=7; w=7; offset=7; strand=D; shift=7; score=29.1429; -------mCAAcms ; cor=0.874; Ncor=0.437; logoDP=3.092; NIcor=0.443; NsEucl=0.916; SSD=0.700; NSW=0.950; rcor=24; rNcor=46; rlogoDP=46; rNIcor=35; rNsEucl=30; rSSD=4; rNSW=19; rank_mean=29.143; match_rank=28 a 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 7 2 0 1 1 3 3

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ytATTGCACAATmcy ; Alignment reference a 71 70 210 0 2 11 0 253 6 283 282 4 86 69 60 c 78 69 25 0 0 0 282 5 271 3 1 43 76 81 78 g 56 70 36 0 0 260 0 18 0 0 2 22 65 65 62 t 81 77 15 286 284 15 4 10 9 0 1 217 59 71 86

MA0102.3_shift2 (CEBPA) 0.949 0.696 9.638 0.689 0.949 0.627 0.971 2 10 11 9 2 2 2 5.429 2
; oligos_7nt_mkv4_m1 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 5.4286; --aTTGCAyAAym-- ; cor=0.949; Ncor=0.696; logoDP=9.638; NIcor=0.689; NsEucl=0.949; SSD=0.627; NSW=0.971; rcor=2; rNcor=10; rlogoDP=11; rNIcor=9; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=5.429; match_rank=2 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0

MA0466.1_shift1 (CEBPB) 0.931 0.683 9.474 0.676 0.942 0.822 0.963 9 14 14 12 6 7 6 9.714 6
; oligos_7nt_mkv4_m1 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 9.7143; -kATTGCAymAy--- ; cor=0.931; Ncor=0.683; logoDP=9.474; NIcor=0.676; NsEucl=0.942; SSD=0.822; NSW=0.963; rcor=9; rNcor=14; rlogoDP=14; rNIcor=12; rNsEucl=6; rSSD=7; rNSW=6; rank_mean=9.714; match_rank=6 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0

MA0078.1_rc_shift6 (Sox17_rc) 0.856 0.514 2.520 0.171 0.918 1.099 0.939 29 37 53 42 26 22 24 33.286 34
; oligos_7nt_mkv4_m1 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=9; offset=6; strand=R; shift=6; score=33.2857; ------sACAATrdr ; cor=0.856; Ncor=0.514; logoDP=2.520; NIcor=0.171; NsEucl=0.918; SSD=1.099; NSW=0.939; rcor=29; rNcor=37; rlogoDP=53; rNIcor=42; rNsEucl=26; rSSD=22; rNSW=24; rank_mean=33.286; match_rank=34 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)																	; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; ytATTGCACAATmcy ; Alignment reference a 71 70 210 0 2 11 0 253 6 283 282 4 86 69 60 c 78 69 25 0 0 0 282 5 271 3 1 43 76 81 78 g 56 70 36 0 0 260 0 18 0 0 2 22 65 65 62 t 81 77 15 286 284 15 4 10 9 0 1 217 59 71 86
MA0102.3_shift2 (CEBPA)	0.949	0.696	9.638	0.689	0.949	0.627	0.971	2	10	11	9	2	2	2	5.429	2	; oligos_7nt_mkv4_m1 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 5.4286; --aTTGCAyAAym-- ; cor=0.949; Ncor=0.696; logoDP=9.638; NIcor=0.689; NsEucl=0.949; SSD=0.627; NSW=0.971; rcor=2; rNcor=10; rlogoDP=11; rNIcor=9; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=5.429; match_rank=2 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift1 (CEBPB)	0.931	0.683	9.474	0.676	0.942	0.822	0.963	9	14	14	12	6	7	6	9.714	6	; oligos_7nt_mkv4_m1 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 9.7143; -kATTGCAymAy--- ; cor=0.931; Ncor=0.683; logoDP=9.474; NIcor=0.676; NsEucl=0.942; SSD=0.822; NSW=0.963; rcor=9; rNcor=14; rlogoDP=14; rNIcor=12; rNsEucl=6; rSSD=7; rNSW=6; rank_mean=9.714; match_rank=6 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0078.1_rc_shift6 (Sox17_rc)	0.856	0.514	2.520	0.171	0.918	1.099	0.939	29	37	53	42	26	22	24	33.286	34	; oligos_7nt_mkv4_m1 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=9; offset=6; strand=R; shift=6; score=33.2857; ------sACAATrdr ; cor=0.856; Ncor=0.514; logoDP=2.520; NIcor=0.171; NsEucl=0.918; SSD=1.099; NSW=0.939; rcor=29; rNcor=37; rlogoDP=53; rNIcor=42; rNsEucl=26; rSSD=22; rNSW=24; rank_mean=33.286; match_rank=34 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift5 ; 13 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=5; ncol=20; -----yrAGGTCAGar---- ; Alignment reference a 0 0 0 0 0 21 22 85 0 0 0 0 84 1 33 23 0 0 0 0 c 0 0 0 0 0 25 21 0 0 0 0 86 1 2 19 11 0 0 0 0 g 0 0 0 0 0 14 28 1 86 86 0 0 1 75 17 32 0 0 0 0 t 0 0 0 0 0 26 15 0 0 0 86 0 0 8 17 20 0 0 0 0

MA0071.1_shift3 (RORA_1) 0.977 0.601 10.437 0.605 0.960 0.202 0.987 1 21 1 19 1 1 1 6.429 3
; oligos_6nt_mkv3_m2 versus MA0071.1 (RORA_1); m=1/12; ncol2=10; w=8; offset=-2; strand=D; shift=3; score= 6.4286; ---wwcwAGGTCA------- ; cor=0.977; Ncor=0.601; logoDP=10.437; NIcor=0.605; NsEucl=0.960; SSD=0.202; NSW=0.987; rcor=1; rNcor=21; rlogoDP=1; rNIcor=19; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=6.429; match_rank=3 a 0 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 c 0 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 g 0 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 t 0 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0

MA0512.1_shift4 (Rxra) 0.889 0.741 8.430 0.732 0.927 1.056 0.947 21 7 20 6 20 18 21 16.143 11
; oligos_6nt_mkv3_m2 versus MA0512.1 (Rxra); m=2/12; ncol2=11; w=10; offset=-1; strand=D; shift=4; score=16.1429; ----CArAGKTCAgd----- ; cor=0.889; Ncor=0.741; logoDP=8.430; NIcor=0.732; NsEucl=0.927; SSD=1.056; NSW=0.947; rcor=21; rNcor=7; rlogoDP=20; rNIcor=6; rNsEucl=20; rSSD=18; rNSW=21; rank_mean=16.143; match_rank=11 a 0 0 0 0 278 4154 2623 4877 0 0 0 0 5348 1150 1640 0 0 0 0 0 c 0 0 0 0 4521 418 252 0 0 0 583 5348 0 1070 742 0 0 0 0 0 g 0 0 0 0 305 9 2473 471 5348 3882 643 0 0 2336 1569 0 0 0 0 0 t 0 0 0 0 244 767 0 0 0 1466 4122 0 0 792 1397 0 0 0 0 0

MA0258.2_shift7 (ESR2) 0.909 0.481 7.498 0.480 0.926 0.898 0.950 16 42 29 29 21 11 18 23.714 21
; oligos_6nt_mkv3_m2 versus MA0258.2 (ESR2); m=3/12; ncol2=15; w=9; offset=2; strand=D; shift=7; score=23.7143; -------rGGTCAsmstGaC ; cor=0.909; Ncor=0.481; logoDP=7.498; NIcor=0.480; NsEucl=0.926; SSD=0.898; NSW=0.950; rcor=16; rNcor=42; rlogoDP=29; rNIcor=29; rNsEucl=21; rSSD=11; rNSW=18; rank_mean=23.714; match_rank=21 a 0 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 c 0 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 g 0 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 t 0 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977

MA0141.2_shift1 (Esrrb) 0.902 0.481 9.026 0.473 0.915 0.918 0.943 19 41 17 30 31 12 23 24.714 24
; oligos_6nt_mkv3_m2 versus MA0141.2 (Esrrb); m=4/12; ncol2=12; w=8; offset=-4; strand=D; shift=1; score=24.7143; -rgsyCAAGGTCA------- ; cor=0.902; Ncor=0.481; logoDP=9.026; NIcor=0.473; NsEucl=0.915; SSD=0.918; NSW=0.943; rcor=19; rNcor=41; rlogoDP=17; rNIcor=30; rNsEucl=31; rSSD=12; rNSW=23; rank_mean=24.714; match_rank=24 a 0 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 c 0 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 g 0 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 t 0 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0

MA0160.1_shift6 (NR4A2) 0.854 0.621 7.578 0.622 0.898 1.342 0.916 31 18 28 17 51 27 43 30.714 31
; oligos_6nt_mkv3_m2 versus MA0160.1 (NR4A2); m=5/12; ncol2=8; w=8; offset=1; strand=D; shift=6; score=30.7143; ------aAGGTCAc------ ; cor=0.854; Ncor=0.621; logoDP=7.578; NIcor=0.622; NsEucl=0.898; SSD=1.342; NSW=0.916; rcor=31; rNcor=18; rlogoDP=28; rNIcor=17; rNsEucl=51; rSSD=27; rNSW=43; rank_mean=30.714; match_rank=31 a 0 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 c 0 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 g 0 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0

MA0592.1_shift4 (ESRRA) 0.822 0.685 9.380 0.666 0.904 1.828 0.909 46 12 15 14 48 48 49 33.143 33
; oligos_6nt_mkv3_m2 versus MA0592.1 (ESRRA); m=6/12; ncol2=11; w=10; offset=-1; strand=D; shift=4; score=33.1429; ----yCAAGGTCAcm----- ; cor=0.822; Ncor=0.685; logoDP=9.380; NIcor=0.666; NsEucl=0.904; SSD=1.828; NSW=0.909; rcor=46; rNcor=12; rlogoDP=15; rNIcor=14; rNsEucl=48; rSSD=48; rNSW=49; rank_mean=33.143; match_rank=33 a 0 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 0 0 0 c 0 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 0 0 0 g 0 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 0 0 0 t 0 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0 0 0 0

MA0072.1_shift0 (RORA_2) 0.838 0.471 10.296 0.463 0.900 1.622 0.910 36 43 3 31 49 38 47 35.286 37
; oligos_6nt_mkv3_m2 versus MA0072.1 (RORA_2); m=7/12; ncol2=14; w=9; offset=-5; strand=D; shift=0; score=35.2857; wwwAwbTAGGTCAr------ ; cor=0.838; Ncor=0.471; logoDP=10.296; NIcor=0.463; NsEucl=0.900; SSD=1.622; NSW=0.910; rcor=36; rNcor=43; rlogoDP=3; rNIcor=31; rNsEucl=49; rSSD=38; rNSW=47; rank_mean=35.286; match_rank=37 a 9 17 15 35 23 2 0 28 0 0 0 0 36 15 0 0 0 0 0 0 c 8 2 0 1 0 12 0 0 0 0 0 36 0 6 0 0 0 0 0 0 g 8 7 3 0 0 13 0 8 36 36 0 0 0 10 0 0 0 0 0 0 t 11 10 18 0 13 9 36 0 0 0 36 0 0 5 0 0 0 0 0 0

MA0504.1_shift5 (NR2C2) 0.797 0.585 6.029 0.552 0.911 1.916 0.913 49 24 35 22 37 50 45 37.429 40
; oligos_6nt_mkv3_m2 versus MA0504.1 (NR2C2); m=8/12; ncol2=15; w=11; offset=0; strand=D; shift=5; score=37.4286; -----mgrGGTCArAGGTCA ; cor=0.797; Ncor=0.585; logoDP=6.029; NIcor=0.552; NsEucl=0.911; SSD=1.916; NSW=0.913; rcor=49; rNcor=24; rlogoDP=35; rNIcor=22; rNsEucl=37; rSSD=50; rNSW=45; rank_mean=37.429; match_rank=40 a 0 0 0 0 0 129 82 193 0 10 3 6 343 187 324 10 11 0 9 290 c 0 0 0 0 0 126 70 6 8 3 0 309 0 0 0 0 0 27 315 0 g 0 0 0 0 0 90 221 195 366 355 79 54 48 208 71 385 336 89 35 92 t 0 0 0 0 0 50 22 1 21 27 313 26 4 0 0 0 48 279 36 13

MA0112.2_shift2 (ESR1) 0.809 0.445 4.397 0.450 0.915 1.754 0.920 48 45 39 33 33 44 39 40.143 45
; oligos_6nt_mkv3_m2 versus MA0112.2 (ESR1); m=9/12; ncol2=20; w=11; offset=-3; strand=D; shift=2; score=40.1429; --vkscmaGGtCAcccTGaC ; cor=0.809; Ncor=0.445; logoDP=4.397; NIcor=0.450; NsEucl=0.915; SSD=1.754; NSW=0.920; rcor=48; rNcor=45; rlogoDP=39; rNIcor=33; rNsEucl=33; rSSD=44; rNSW=39; rank_mean=40.143; match_rank=45 a 0 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 c 0 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 g 0 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 t 0 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17

MA0505.1_shift0 (Nr5a2) 0.790 0.494 7.874 0.460 0.898 2.077 0.896 50 40 25 32 50 53 53 43.286 50
; oligos_6nt_mkv3_m2 versus MA0505.1 (Nr5a2); m=10/12; ncol2=15; w=10; offset=-5; strand=D; shift=0; score=43.2857; ragtTCAAGGyCAgs----- ; cor=0.790; Ncor=0.494; logoDP=7.874; NIcor=0.460; NsEucl=0.898; SSD=2.077; NSW=0.896; rcor=50; rNcor=40; rlogoDP=25; rNIcor=32; rNsEucl=50; rSSD=53; rNSW=53; rank_mean=43.286; match_rank=50 a 645 985 276 122 71 8 1685 1679 39 0 169 0 1437 271 249 0 0 0 0 0 c 224 170 198 378 351 1616 14 0 0 0 584 1568 20 345 693 0 0 0 0 0 g 634 336 990 366 23 74 0 23 1663 1702 61 12 90 740 454 0 0 0 0 0 t 199 211 238 836 1257 4 3 0 0 0 888 122 155 346 306 0 0 0 0 0

MA0066.1_shift5 (PPARG) 0.766 0.421 6.837 0.424 0.905 2.176 0.901 54 50 34 37 47 54 50 46.571 53
; oligos_6nt_mkv3_m2 versus MA0066.1 (PPARG); m=11/12; ncol2=20; w=11; offset=0; strand=D; shift=5; score=46.5714; -----sTrGGTCAcsgTGAC ; cor=0.766; Ncor=0.421; logoDP=6.837; NIcor=0.424; NsEucl=0.905; SSD=2.176; NSW=0.901; rcor=54; rNcor=50; rlogoDP=34; rNIcor=37; rNsEucl=47; rSSD=54; rNSW=50; rank_mean=46.571; match_rank=53 a 0 0 0 0 0 3 3 19 0 1 0 2 26 5 5 4 1 2 22 1 c 0 0 0 0 0 8 0 0 1 0 1 23 1 15 7 2 0 5 5 27 g 0 0 0 0 0 14 0 9 27 26 4 3 0 4 10 18 2 20 0 0 t 0 0 0 0 0 3 25 0 0 1 23 0 1 4 6 4 25 1 1 0

MA0089.1_rc_shift9 (NFE2L1::MafG_rc) 0.787 0.429 0.090 -0.133 0.860 1.403 0.883 51 48 54 54 54 31 54 49.429 54
; oligos_6nt_mkv3_m2 versus MA0089.1_rc (NFE2L1::MafG_rc); m=12/12; ncol2=6; w=6; offset=4; strand=R; shift=9; score=49.4286; ---------GTCATs----- ; cor=0.787; Ncor=0.429; logoDP=0.090; NIcor=-0.133; NsEucl=0.860; SSD=1.403; NSW=0.883; rcor=51; rNcor=48; rlogoDP=54; rNIcor=54; rNsEucl=54; rSSD=31; rNSW=54; rank_mean=49.429; match_rank=54 a 0 0 0 0 0 0 0 0 0 6 0 1 34 0 6 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 2 0 32 0 3 10 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 26 0 0 0 2 11 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 34 1 0 29 7 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv3_m2_shift5 (oligos_6nt_mkv3_m2)																	; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=5; ncol=20; -----yrAGGTCAGar---- ; Alignment reference a 0 0 0 0 0 21 22 85 0 0 0 0 84 1 33 23 0 0 0 0 c 0 0 0 0 0 25 21 0 0 0 0 86 1 2 19 11 0 0 0 0 g 0 0 0 0 0 14 28 1 86 86 0 0 1 75 17 32 0 0 0 0 t 0 0 0 0 0 26 15 0 0 0 86 0 0 8 17 20 0 0 0 0
MA0071.1_shift3 (RORA_1)	0.977	0.601	10.437	0.605	0.960	0.202	0.987	1	21	1	19	1	1	1	6.429	3	; oligos_6nt_mkv3_m2 versus MA0071.1 (RORA_1); m=1/12; ncol2=10; w=8; offset=-2; strand=D; shift=3; score= 6.4286; ---wwcwAGGTCA------- ; cor=0.977; Ncor=0.601; logoDP=10.437; NIcor=0.605; NsEucl=0.960; SSD=0.202; NSW=0.987; rcor=1; rNcor=21; rlogoDP=1; rNIcor=19; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=6.429; match_rank=3 a 0 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 c 0 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 g 0 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 t 0 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0
MA0512.1_shift4 (Rxra)	0.889	0.741	8.430	0.732	0.927	1.056	0.947	21	7	20	6	20	18	21	16.143	11	; oligos_6nt_mkv3_m2 versus MA0512.1 (Rxra); m=2/12; ncol2=11; w=10; offset=-1; strand=D; shift=4; score=16.1429; ----CArAGKTCAgd----- ; cor=0.889; Ncor=0.741; logoDP=8.430; NIcor=0.732; NsEucl=0.927; SSD=1.056; NSW=0.947; rcor=21; rNcor=7; rlogoDP=20; rNIcor=6; rNsEucl=20; rSSD=18; rNSW=21; rank_mean=16.143; match_rank=11 a 0 0 0 0 278 4154 2623 4877 0 0 0 0 5348 1150 1640 0 0 0 0 0 c 0 0 0 0 4521 418 252 0 0 0 583 5348 0 1070 742 0 0 0 0 0 g 0 0 0 0 305 9 2473 471 5348 3882 643 0 0 2336 1569 0 0 0 0 0 t 0 0 0 0 244 767 0 0 0 1466 4122 0 0 792 1397 0 0 0 0 0
MA0258.2_shift7 (ESR2)	0.909	0.481	7.498	0.480	0.926	0.898	0.950	16	42	29	29	21	11	18	23.714	21	; oligos_6nt_mkv3_m2 versus MA0258.2 (ESR2); m=3/12; ncol2=15; w=9; offset=2; strand=D; shift=7; score=23.7143; -------rGGTCAsmstGaC ; cor=0.909; Ncor=0.481; logoDP=7.498; NIcor=0.480; NsEucl=0.926; SSD=0.898; NSW=0.950; rcor=16; rNcor=42; rlogoDP=29; rNIcor=29; rNsEucl=21; rSSD=11; rNSW=18; rank_mean=23.714; match_rank=21 a 0 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 c 0 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 g 0 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 t 0 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977
MA0141.2_shift1 (Esrrb)	0.902	0.481	9.026	0.473	0.915	0.918	0.943	19	41	17	30	31	12	23	24.714	24	; oligos_6nt_mkv3_m2 versus MA0141.2 (Esrrb); m=4/12; ncol2=12; w=8; offset=-4; strand=D; shift=1; score=24.7143; -rgsyCAAGGTCA------- ; cor=0.902; Ncor=0.481; logoDP=9.026; NIcor=0.473; NsEucl=0.915; SSD=0.918; NSW=0.943; rcor=19; rNcor=41; rlogoDP=17; rNIcor=30; rNsEucl=31; rSSD=12; rNSW=23; rank_mean=24.714; match_rank=24 a 0 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 c 0 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 g 0 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 t 0 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0
MA0160.1_shift6 (NR4A2)	0.854	0.621	7.578	0.622	0.898	1.342	0.916	31	18	28	17	51	27	43	30.714	31	; oligos_6nt_mkv3_m2 versus MA0160.1 (NR4A2); m=5/12; ncol2=8; w=8; offset=1; strand=D; shift=6; score=30.7143; ------aAGGTCAc------ ; cor=0.854; Ncor=0.621; logoDP=7.578; NIcor=0.622; NsEucl=0.898; SSD=1.342; NSW=0.916; rcor=31; rNcor=18; rlogoDP=28; rNIcor=17; rNsEucl=51; rSSD=27; rNSW=43; rank_mean=30.714; match_rank=31 a 0 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 c 0 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 g 0 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0
MA0592.1_shift4 (ESRRA)	0.822	0.685	9.380	0.666	0.904	1.828	0.909	46	12	15	14	48	48	49	33.143	33	; oligos_6nt_mkv3_m2 versus MA0592.1 (ESRRA); m=6/12; ncol2=11; w=10; offset=-1; strand=D; shift=4; score=33.1429; ----yCAAGGTCAcm----- ; cor=0.822; Ncor=0.685; logoDP=9.380; NIcor=0.666; NsEucl=0.904; SSD=1.828; NSW=0.909; rcor=46; rNcor=12; rlogoDP=15; rNIcor=14; rNsEucl=48; rSSD=48; rNSW=49; rank_mean=33.143; match_rank=33 a 0 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 0 0 0 c 0 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 0 0 0 g 0 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 0 0 0 t 0 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0 0 0 0
MA0072.1_shift0 (RORA_2)	0.838	0.471	10.296	0.463	0.900	1.622	0.910	36	43	3	31	49	38	47	35.286	37	; oligos_6nt_mkv3_m2 versus MA0072.1 (RORA_2); m=7/12; ncol2=14; w=9; offset=-5; strand=D; shift=0; score=35.2857; wwwAwbTAGGTCAr------ ; cor=0.838; Ncor=0.471; logoDP=10.296; NIcor=0.463; NsEucl=0.900; SSD=1.622; NSW=0.910; rcor=36; rNcor=43; rlogoDP=3; rNIcor=31; rNsEucl=49; rSSD=38; rNSW=47; rank_mean=35.286; match_rank=37 a 9 17 15 35 23 2 0 28 0 0 0 0 36 15 0 0 0 0 0 0 c 8 2 0 1 0 12 0 0 0 0 0 36 0 6 0 0 0 0 0 0 g 8 7 3 0 0 13 0 8 36 36 0 0 0 10 0 0 0 0 0 0 t 11 10 18 0 13 9 36 0 0 0 36 0 0 5 0 0 0 0 0 0
MA0504.1_shift5 (NR2C2)	0.797	0.585	6.029	0.552	0.911	1.916	0.913	49	24	35	22	37	50	45	37.429	40	; oligos_6nt_mkv3_m2 versus MA0504.1 (NR2C2); m=8/12; ncol2=15; w=11; offset=0; strand=D; shift=5; score=37.4286; -----mgrGGTCArAGGTCA ; cor=0.797; Ncor=0.585; logoDP=6.029; NIcor=0.552; NsEucl=0.911; SSD=1.916; NSW=0.913; rcor=49; rNcor=24; rlogoDP=35; rNIcor=22; rNsEucl=37; rSSD=50; rNSW=45; rank_mean=37.429; match_rank=40 a 0 0 0 0 0 129 82 193 0 10 3 6 343 187 324 10 11 0 9 290 c 0 0 0 0 0 126 70 6 8 3 0 309 0 0 0 0 0 27 315 0 g 0 0 0 0 0 90 221 195 366 355 79 54 48 208 71 385 336 89 35 92 t 0 0 0 0 0 50 22 1 21 27 313 26 4 0 0 0 48 279 36 13
MA0112.2_shift2 (ESR1)	0.809	0.445	4.397	0.450	0.915	1.754	0.920	48	45	39	33	33	44	39	40.143	45	; oligos_6nt_mkv3_m2 versus MA0112.2 (ESR1); m=9/12; ncol2=20; w=11; offset=-3; strand=D; shift=2; score=40.1429; --vkscmaGGtCAcccTGaC ; cor=0.809; Ncor=0.445; logoDP=4.397; NIcor=0.450; NsEucl=0.915; SSD=1.754; NSW=0.920; rcor=48; rNcor=45; rlogoDP=39; rNIcor=33; rNsEucl=33; rSSD=44; rNSW=39; rank_mean=40.143; match_rank=45 a 0 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 c 0 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 g 0 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 t 0 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17
MA0505.1_shift0 (Nr5a2)	0.790	0.494	7.874	0.460	0.898	2.077	0.896	50	40	25	32	50	53	53	43.286	50	; oligos_6nt_mkv3_m2 versus MA0505.1 (Nr5a2); m=10/12; ncol2=15; w=10; offset=-5; strand=D; shift=0; score=43.2857; ragtTCAAGGyCAgs----- ; cor=0.790; Ncor=0.494; logoDP=7.874; NIcor=0.460; NsEucl=0.898; SSD=2.077; NSW=0.896; rcor=50; rNcor=40; rlogoDP=25; rNIcor=32; rNsEucl=50; rSSD=53; rNSW=53; rank_mean=43.286; match_rank=50 a 645 985 276 122 71 8 1685 1679 39 0 169 0 1437 271 249 0 0 0 0 0 c 224 170 198 378 351 1616 14 0 0 0 584 1568 20 345 693 0 0 0 0 0 g 634 336 990 366 23 74 0 23 1663 1702 61 12 90 740 454 0 0 0 0 0 t 199 211 238 836 1257 4 3 0 0 0 888 122 155 346 306 0 0 0 0 0
MA0066.1_shift5 (PPARG)	0.766	0.421	6.837	0.424	0.905	2.176	0.901	54	50	34	37	47	54	50	46.571	53	; oligos_6nt_mkv3_m2 versus MA0066.1 (PPARG); m=11/12; ncol2=20; w=11; offset=0; strand=D; shift=5; score=46.5714; -----sTrGGTCAcsgTGAC ; cor=0.766; Ncor=0.421; logoDP=6.837; NIcor=0.424; NsEucl=0.905; SSD=2.176; NSW=0.901; rcor=54; rNcor=50; rlogoDP=34; rNIcor=37; rNsEucl=47; rSSD=54; rNSW=50; rank_mean=46.571; match_rank=53 a 0 0 0 0 0 3 3 19 0 1 0 2 26 5 5 4 1 2 22 1 c 0 0 0 0 0 8 0 0 1 0 1 23 1 15 7 2 0 5 5 27 g 0 0 0 0 0 14 0 9 27 26 4 3 0 4 10 18 2 20 0 0 t 0 0 0 0 0 3 25 0 0 1 23 0 1 4 6 4 25 1 1 0
MA0089.1_rc_shift9 (NFE2L1::MafG_rc)	0.787	0.429	0.090	-0.133	0.860	1.403	0.883	51	48	54	54	54	31	54	49.429	54	; oligos_6nt_mkv3_m2 versus MA0089.1_rc (NFE2L1::MafG_rc); m=12/12; ncol2=6; w=6; offset=4; strand=R; shift=9; score=49.4286; ---------GTCATs----- ; cor=0.787; Ncor=0.429; logoDP=0.090; NIcor=-0.133; NsEucl=0.860; SSD=1.403; NSW=0.883; rcor=51; rNcor=48; rlogoDP=54; rNIcor=54; rNsEucl=54; rSSD=31; rNSW=54; rank_mean=49.429; match_rank=54 a 0 0 0 0 0 0 0 0 0 6 0 1 34 0 6 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 2 0 32 0 3 10 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 26 0 0 0 2 11 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 34 1 0 29 7 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; rtgATTGCACAATmy- ; Alignment reference a 41 31 23 122 1 1 5 0 129 4 148 147 5 40 31 0 c 30 35 21 8 0 0 0 150 2 143 1 1 18 42 45 0 g 46 29 89 13 0 0 137 0 15 0 0 1 9 36 36 0 t 33 55 17 7 149 149 8 0 4 3 1 1 118 32 38 0

MA0102.3_shift3 (CEBPA) 0.944 0.692 9.686 0.687 0.946 0.704 0.968 4 11 10 10 4 5 4 6.857 4
; oligos_6nt_mkv3_m1 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 6.8571; ---aTTGCAyAAym-- ; cor=0.944; Ncor=0.692; logoDP=9.686; NIcor=0.687; NsEucl=0.946; SSD=0.704; NSW=0.968; rcor=4; rNcor=11; rlogoDP=10; rNIcor=10; rNsEucl=4; rSSD=5; rNSW=4; rank_mean=6.857; match_rank=4 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0

MA0466.1_shift2 (CEBPB) 0.923 0.677 9.579 0.671 0.937 0.960 0.956 12 15 13 13 12 14 11 12.857 9
; oligos_6nt_mkv3_m1 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score=12.8571; --kATTGCAymAy--- ; cor=0.923; Ncor=0.677; logoDP=9.579; NIcor=0.671; NsEucl=0.937; SSD=0.960; NSW=0.956; rcor=12; rNcor=15; rlogoDP=13; rNIcor=13; rNsEucl=12; rSSD=14; rNSW=11; rank_mean=12.857; match_rank=9 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0

MA0078.1_rc_shift7 (Sox17_rc) 0.857 0.428 2.551 0.146 0.908 1.094 0.932 28 49 52 44 43 21 28 37.857 42
; oligos_6nt_mkv3_m1 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=8; offset=7; strand=R; shift=7; score=37.8571; -------sACAATrdr ; cor=0.857; Ncor=0.428; logoDP=2.551; NIcor=0.146; NsEucl=0.908; SSD=1.094; NSW=0.932; rcor=28; rNcor=49; rlogoDP=52; rNIcor=44; rNsEucl=43; rSSD=21; rNSW=28; rank_mean=37.857; match_rank=42 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)																	; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; rtgATTGCACAATmy- ; Alignment reference a 41 31 23 122 1 1 5 0 129 4 148 147 5 40 31 0 c 30 35 21 8 0 0 0 150 2 143 1 1 18 42 45 0 g 46 29 89 13 0 0 137 0 15 0 0 1 9 36 36 0 t 33 55 17 7 149 149 8 0 4 3 1 1 118 32 38 0
MA0102.3_shift3 (CEBPA)	0.944	0.692	9.686	0.687	0.946	0.704	0.968	4	11	10	10	4	5	4	6.857	4	; oligos_6nt_mkv3_m1 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 6.8571; ---aTTGCAyAAym-- ; cor=0.944; Ncor=0.692; logoDP=9.686; NIcor=0.687; NsEucl=0.946; SSD=0.704; NSW=0.968; rcor=4; rNcor=11; rlogoDP=10; rNIcor=10; rNsEucl=4; rSSD=5; rNSW=4; rank_mean=6.857; match_rank=4 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift2 (CEBPB)	0.923	0.677	9.579	0.671	0.937	0.960	0.956	12	15	13	13	12	14	11	12.857	9	; oligos_6nt_mkv3_m1 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score=12.8571; --kATTGCAymAy--- ; cor=0.923; Ncor=0.677; logoDP=9.579; NIcor=0.671; NsEucl=0.937; SSD=0.960; NSW=0.956; rcor=12; rNcor=15; rlogoDP=13; rNIcor=13; rNsEucl=12; rSSD=14; rNSW=11; rank_mean=12.857; match_rank=9 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0078.1_rc_shift7 (Sox17_rc)	0.857	0.428	2.551	0.146	0.908	1.094	0.932	28	49	52	44	43	21	28	37.857	42	; oligos_6nt_mkv3_m1 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=8; offset=7; strand=R; shift=7; score=37.8571; -------sACAATrdr ; cor=0.857; Ncor=0.428; logoDP=2.551; NIcor=0.146; NsEucl=0.908; SSD=1.094; NSW=0.932; rcor=28; rNcor=49; rlogoDP=52; rNIcor=44; rNsEucl=43; rSSD=21; rNSW=28; rank_mean=37.857; match_rank=42 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=16; shift=0; ncol=16; aktgATTGCACAACay ; Alignment reference a 31 15 18 11 69 0 0 2 0 74 0 79 79 1 30 14 c 15 19 7 10 2 0 0 1 79 1 74 0 0 57 17 28 g 16 23 9 48 7 0 0 74 0 4 0 0 0 5 13 11 t 17 22 45 10 1 79 79 2 0 0 5 0 0 16 19 26

MA0102.3_shift4 (CEBPA) 0.941 0.647 10.317 0.636 0.943 0.792 0.964 5 16 2 16 5 6 5 7.857 5
; positions_6nt_m5 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 7.8571; ----aTTGCAyAAym- ; cor=0.941; Ncor=0.647; logoDP=10.317; NIcor=0.636; NsEucl=0.943; SSD=0.792; NSW=0.964; rcor=5; rNcor=16; rlogoDP=2; rNIcor=16; rNsEucl=5; rSSD=6; rNSW=5; rank_mean=7.857; match_rank=5 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0

MA0466.1_shift3 (CEBPB) 0.907 0.623 10.152 0.609 0.930 1.201 0.945 18 17 4 18 19 25 22 17.571 13
; positions_6nt_m5 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=17.5714; ---kATTGCAymAy-- ; cor=0.907; Ncor=0.623; logoDP=10.152; NIcor=0.609; NsEucl=0.930; SSD=1.201; NSW=0.945; rcor=18; rNcor=17; rlogoDP=4; rNIcor=18; rNsEucl=19; rSSD=25; rNSW=22; rank_mean=17.571; match_rank=13 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m5_shift0 (positions_6nt_m5)																	; positions_6nt_m5; m=0 (reference); ncol1=16; shift=0; ncol=16; aktgATTGCACAACay ; Alignment reference a 31 15 18 11 69 0 0 2 0 74 0 79 79 1 30 14 c 15 19 7 10 2 0 0 1 79 1 74 0 0 57 17 28 g 16 23 9 48 7 0 0 74 0 4 0 0 0 5 13 11 t 17 22 45 10 1 79 79 2 0 0 5 0 0 16 19 26
MA0102.3_shift4 (CEBPA)	0.941	0.647	10.317	0.636	0.943	0.792	0.964	5	16	2	16	5	6	5	7.857	5	; positions_6nt_m5 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 7.8571; ----aTTGCAyAAym- ; cor=0.941; Ncor=0.647; logoDP=10.317; NIcor=0.636; NsEucl=0.943; SSD=0.792; NSW=0.964; rcor=5; rNcor=16; rlogoDP=2; rNIcor=16; rNsEucl=5; rSSD=6; rNSW=5; rank_mean=7.857; match_rank=5 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift3 (CEBPB)	0.907	0.623	10.152	0.609	0.930	1.201	0.945	18	17	4	18	19	25	22	17.571	13	; positions_6nt_m5 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=17.5714; ---kATTGCAymAy-- ; cor=0.907; Ncor=0.623; logoDP=10.152; NIcor=0.609; NsEucl=0.930; SSD=1.201; NSW=0.945; rcor=18; rNcor=17; rlogoDP=4; rNIcor=18; rNsEucl=19; rSSD=25; rNSW=22; rank_mean=17.571; match_rank=13 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; ryTgATTGCACAACtyy ; Alignment reference a 30 15 9 10 58 0 0 0 0 64 0 71 72 1 17 12 15 c 11 23 5 9 1 0 0 1 72 2 69 1 0 52 10 24 19 g 18 15 7 44 10 0 0 68 0 3 0 0 0 2 9 13 13 t 13 19 51 9 3 72 72 3 0 3 3 0 0 17 36 23 25

MA0102.3_shift4 (CEBPA) 0.934 0.604 10.138 0.595 0.941 0.852 0.961 8 20 5 20 8 9 8 11.143 7
; positions_7nt_m4 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score=11.1429; ----aTTGCAyAAym-- ; cor=0.934; Ncor=0.604; logoDP=10.138; NIcor=0.595; NsEucl=0.941; SSD=0.852; NSW=0.961; rcor=8; rNcor=20; rlogoDP=5; rNIcor=20; rNsEucl=8; rSSD=9; rNSW=8; rank_mean=11.143; match_rank=7 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0

MA0466.1_shift3 (CEBPB) 0.908 0.588 9.999 0.572 0.931 1.149 0.948 17 23 6 21 18 24 20 18.429 14
; positions_7nt_m4 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=18.4286; ---kATTGCAymAy--- ; cor=0.908; Ncor=0.588; logoDP=9.999; NIcor=0.572; NsEucl=0.931; SSD=1.149; NSW=0.948; rcor=17; rNcor=23; rlogoDP=6; rNIcor=21; rNsEucl=18; rSSD=24; rNSW=20; rank_mean=18.429; match_rank=14 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)																	; positions_7nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; ryTgATTGCACAACtyy ; Alignment reference a 30 15 9 10 58 0 0 0 0 64 0 71 72 1 17 12 15 c 11 23 5 9 1 0 0 1 72 2 69 1 0 52 10 24 19 g 18 15 7 44 10 0 0 68 0 3 0 0 0 2 9 13 13 t 13 19 51 9 3 72 72 3 0 3 3 0 0 17 36 23 25
MA0102.3_shift4 (CEBPA)	0.934	0.604	10.138	0.595	0.941	0.852	0.961	8	20	5	20	8	9	8	11.143	7	; positions_7nt_m4 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score=11.1429; ----aTTGCAyAAym-- ; cor=0.934; Ncor=0.604; logoDP=10.138; NIcor=0.595; NsEucl=0.941; SSD=0.852; NSW=0.961; rcor=8; rNcor=20; rlogoDP=5; rNIcor=20; rNsEucl=8; rSSD=9; rNSW=8; rank_mean=11.143; match_rank=7 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)	0.908	0.588	9.999	0.572	0.931	1.149	0.948	17	23	6	21	18	24	20	18.429	14	; positions_7nt_m4 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=18.4286; ---kATTGCAymAy--- ; cor=0.908; Ncor=0.588; logoDP=9.999; NIcor=0.572; NsEucl=0.931; SSD=1.149; NSW=0.948; rcor=17; rNcor=23; rlogoDP=6; rNIcor=21; rNsEucl=18; rSSD=24; rNSW=20; rank_mean=18.429; match_rank=14 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; yrTTGCGyAAtm ; Alignment reference a 42 81 1 1 15 0 4 23 151 164 16 51 c 45 32 2 2 2 165 3 50 13 2 42 45 g 38 43 0 0 150 1 162 2 4 2 28 33 t 46 15 168 168 4 5 2 96 3 3 85 42

MA0043.1_rc_shift0 (HLF_rc) 0.876 0.876 5.172 0.789 0.937 1.131 0.953 23 1 38 1 11 23 14 15.857 10
; oligos_7nt_mkv4_m5 versus MA0043.1_rc (HLF_rc); m=1/3; ncol2=12; w=12; offset=0; strand=R; shift=0; score=15.8571; daTTryGTAAym ; cor=0.876; Ncor=0.876; logoDP=5.172; NIcor=0.789; NsEucl=0.937; SSD=1.131; NSW=0.953; rcor=23; rNcor=1; rlogoDP=38; rNIcor=1; rNsEucl=11; rSSD=23; rNSW=14; rank_mean=15.857; match_rank=10 a 5 12 2 0 9 0 2 2 15 17 0 5 c 3 1 1 1 0 12 1 2 3 0 12 8 g 5 3 0 4 9 0 15 1 0 0 0 4 t 5 2 15 13 0 6 0 13 0 1 6 1

MA0102.3_shift1 (CEBPA) 0.828 0.759 7.867 0.756 0.917 1.652 0.925 39 4 26 4 27 39 31 24.286 22
; oligos_7nt_mkv4_m5 versus MA0102.3 (CEBPA); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score=24.2857; -aTTGCAyAAym ; cor=0.828; Ncor=0.759; logoDP=7.867; NIcor=0.756; NsEucl=0.917; SSD=1.652; NSW=0.925; rcor=39; rNcor=4; rlogoDP=26; rNIcor=4; rNsEucl=27; rSSD=39; rNSW=31; rank_mean=24.286; match_rank=22 a 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661

MA0466.1_shift0 (CEBPB) 0.813 0.745 7.739 0.732 0.913 1.814 0.918 47 5 27 7 35 46 42 29.857 29
; oligos_7nt_mkv4_m5 versus MA0466.1 (CEBPB); m=3/3; ncol2=11; w=11; offset=0; strand=D; shift=0; score=29.8571; kATTGCAymAy- ; cor=0.813; Ncor=0.745; logoDP=7.739; NIcor=0.732; NsEucl=0.913; SSD=1.814; NSW=0.918; rcor=47; rNcor=5; rlogoDP=27; rNIcor=7; rNsEucl=35; rSSD=46; rNSW=42; rank_mean=29.857; match_rank=29 a 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)																	; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; yrTTGCGyAAtm ; Alignment reference a 42 81 1 1 15 0 4 23 151 164 16 51 c 45 32 2 2 2 165 3 50 13 2 42 45 g 38 43 0 0 150 1 162 2 4 2 28 33 t 46 15 168 168 4 5 2 96 3 3 85 42
MA0043.1_rc_shift0 (HLF_rc)	0.876	0.876	5.172	0.789	0.937	1.131	0.953	23	1	38	1	11	23	14	15.857	10	; oligos_7nt_mkv4_m5 versus MA0043.1_rc (HLF_rc); m=1/3; ncol2=12; w=12; offset=0; strand=R; shift=0; score=15.8571; daTTryGTAAym ; cor=0.876; Ncor=0.876; logoDP=5.172; NIcor=0.789; NsEucl=0.937; SSD=1.131; NSW=0.953; rcor=23; rNcor=1; rlogoDP=38; rNIcor=1; rNsEucl=11; rSSD=23; rNSW=14; rank_mean=15.857; match_rank=10 a 5 12 2 0 9 0 2 2 15 17 0 5 c 3 1 1 1 0 12 1 2 3 0 12 8 g 5 3 0 4 9 0 15 1 0 0 0 4 t 5 2 15 13 0 6 0 13 0 1 6 1
MA0102.3_shift1 (CEBPA)	0.828	0.759	7.867	0.756	0.917	1.652	0.925	39	4	26	4	27	39	31	24.286	22	; oligos_7nt_mkv4_m5 versus MA0102.3 (CEBPA); m=2/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score=24.2857; -aTTGCAyAAym ; cor=0.828; Ncor=0.759; logoDP=7.867; NIcor=0.756; NsEucl=0.917; SSD=1.652; NSW=0.925; rcor=39; rNcor=4; rlogoDP=26; rNIcor=4; rNsEucl=27; rSSD=39; rNSW=31; rank_mean=24.286; match_rank=22 a 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
MA0466.1_shift0 (CEBPB)	0.813	0.745	7.739	0.732	0.913	1.814	0.918	47	5	27	7	35	46	42	29.857	29	; oligos_7nt_mkv4_m5 versus MA0466.1 (CEBPB); m=3/3; ncol2=11; w=11; offset=0; strand=D; shift=0; score=29.8571; kATTGCAymAy- ; cor=0.813; Ncor=0.745; logoDP=7.739; NIcor=0.732; NsEucl=0.913; SSD=1.814; NSW=0.918; rcor=47; rNcor=5; rlogoDP=27; rNIcor=7; rNsEucl=35; rSSD=46; rNSW=42; rank_mean=29.857; match_rank=29 a 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; rwkATTTCACAAym ; Alignment reference a 62 57 19 194 1 5 23 0 176 9 201 195 25 70 c 40 46 26 4 0 1 5 210 12 190 4 1 64 58 g 69 41 101 10 2 9 33 0 15 2 0 8 32 39 t 39 66 64 2 207 195 149 0 7 9 5 6 89 43

MA0102.3_shift3 (CEBPA) 0.895 0.703 8.236 0.685 0.933 1.078 0.951 20 9 22 11 17 20 17 16.571 12
; oligos_7nt_mkv4_m3 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=16.5714; ---aTTGCAyAAym ; cor=0.895; Ncor=0.703; logoDP=8.236; NIcor=0.685; NsEucl=0.933; SSD=1.078; NSW=0.951; rcor=20; rNcor=9; rlogoDP=22; rNIcor=11; rNsEucl=17; rSSD=20; rNSW=17; rank_mean=16.571; match_rank=12 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661

MA0466.1_shift2 (CEBPB) 0.870 0.684 8.100 0.661 0.925 1.355 0.938 26 13 24 15 22 28 25 21.857 18
; oligos_7nt_mkv4_m3 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=2; strand=D; shift=2; score=21.8571; --kATTGCAymAy- ; cor=0.870; Ncor=0.684; logoDP=8.100; NIcor=0.661; NsEucl=0.925; SSD=1.355; NSW=0.938; rcor=26; rNcor=13; rlogoDP=24; rNIcor=15; rNsEucl=22; rSSD=28; rNSW=25; rank_mean=21.857; match_rank=18 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)																	; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; rwkATTTCACAAym ; Alignment reference a 62 57 19 194 1 5 23 0 176 9 201 195 25 70 c 40 46 26 4 0 1 5 210 12 190 4 1 64 58 g 69 41 101 10 2 9 33 0 15 2 0 8 32 39 t 39 66 64 2 207 195 149 0 7 9 5 6 89 43
MA0102.3_shift3 (CEBPA)	0.895	0.703	8.236	0.685	0.933	1.078	0.951	20	9	22	11	17	20	17	16.571	12	; oligos_7nt_mkv4_m3 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=16.5714; ---aTTGCAyAAym ; cor=0.895; Ncor=0.703; logoDP=8.236; NIcor=0.685; NsEucl=0.933; SSD=1.078; NSW=0.951; rcor=20; rNcor=9; rlogoDP=22; rNIcor=11; rNsEucl=17; rSSD=20; rNSW=17; rank_mean=16.571; match_rank=12 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
MA0466.1_shift2 (CEBPB)	0.870	0.684	8.100	0.661	0.925	1.355	0.938	26	13	24	15	22	28	25	21.857	18	; oligos_7nt_mkv4_m3 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=2; strand=D; shift=2; score=21.8571; --kATTGCAymAy- ; cor=0.870; Ncor=0.684; logoDP=8.100; NIcor=0.661; NsEucl=0.925; SSD=1.355; NSW=0.938; rcor=26; rNcor=13; rlogoDP=24; rNIcor=15; rNsEucl=22; rSSD=28; rNSW=25; rank_mean=21.857; match_rank=18 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; krTTGCkCAAyw ; Alignment reference a 34 80 0 2 1 0 10 4 168 170 11 61 c 33 28 0 4 0 172 3 165 0 1 53 30 g 44 49 0 0 170 0 58 0 3 1 29 32 t 61 15 172 166 1 0 101 3 1 0 79 49

MA0102.3_shift1 (CEBPA) 0.855 0.784 9.115 0.785 0.921 1.497 0.932 30 2 16 2 23 35 26 19.143 16
; oligos_7nt_mkv4_m4 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=1; strand=D; shift=1; score=19.1429; -aTTGCAyAAym ; cor=0.855; Ncor=0.784; logoDP=9.115; NIcor=0.785; NsEucl=0.921; SSD=1.497; NSW=0.932; rcor=30; rNcor=2; rlogoDP=16; rNIcor=2; rNsEucl=23; rSSD=35; rNSW=26; rank_mean=19.143; match_rank=16 a 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661

MA0466.1_shift0 (CEBPB) 0.836 0.766 8.926 0.759 0.916 1.695 0.923 37 3 18 3 28 41 34 23.429 20
; oligos_7nt_mkv4_m4 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=0; strand=D; shift=0; score=23.4286; kATTGCAymAy- ; cor=0.836; Ncor=0.766; logoDP=8.926; NIcor=0.759; NsEucl=0.916; SSD=1.695; NSW=0.923; rcor=37; rNcor=3; rlogoDP=18; rNIcor=3; rNsEucl=28; rSSD=41; rNSW=34; rank_mean=23.429; match_rank=20 a 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)																	; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; krTTGCkCAAyw ; Alignment reference a 34 80 0 2 1 0 10 4 168 170 11 61 c 33 28 0 4 0 172 3 165 0 1 53 30 g 44 49 0 0 170 0 58 0 3 1 29 32 t 61 15 172 166 1 0 101 3 1 0 79 49
MA0102.3_shift1 (CEBPA)	0.855	0.784	9.115	0.785	0.921	1.497	0.932	30	2	16	2	23	35	26	19.143	16	; oligos_7nt_mkv4_m4 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=1; strand=D; shift=1; score=19.1429; -aTTGCAyAAym ; cor=0.855; Ncor=0.784; logoDP=9.115; NIcor=0.785; NsEucl=0.921; SSD=1.497; NSW=0.932; rcor=30; rNcor=2; rlogoDP=16; rNIcor=2; rNsEucl=23; rSSD=35; rNSW=26; rank_mean=19.143; match_rank=16 a 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
MA0466.1_shift0 (CEBPB)	0.836	0.766	8.926	0.759	0.916	1.695	0.923	37	3	18	3	28	41	34	23.429	20	; oligos_7nt_mkv4_m4 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=0; strand=D; shift=0; score=23.4286; kATTGCAymAy- ; cor=0.836; Ncor=0.766; logoDP=8.926; NIcor=0.759; NsEucl=0.916; SSD=1.695; NSW=0.923; rcor=37; rNcor=3; rlogoDP=18; rNIcor=3; rNsEucl=28; rSSD=41; rNSW=34; rank_mean=23.429; match_rank=20 a 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; rdgATTGTGCAATcAtt ; Alignment reference a 23 21 11 66 0 0 3 3 0 6 74 75 5 7 52 17 18 c 17 11 10 1 0 0 0 4 0 69 0 0 8 48 10 18 17 g 22 24 43 6 0 0 71 2 75 0 0 0 5 11 6 17 16 t 13 19 11 2 75 75 1 66 0 0 1 0 57 9 7 23 24

MA0102.3_rc_shift2 (CEBPA_rc) 0.936 0.606 4.313 0.051 0.941 0.849 0.961 7 19 40 46 7 8 7 19.143 15
; positions_7nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score=19.1429; --krTTrTGCAAt---- ; cor=0.936; Ncor=0.606; logoDP=4.313; NIcor=0.051; NsEucl=0.941; SSD=0.849; NSW=0.961; rcor=7; rNcor=19; rlogoDP=40; rNIcor=46; rNsEucl=7; rSSD=8; rNSW=7; rank_mean=19.143; match_rank=15 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0

MA0466.1_rc_shift3 (CEBPB_rc) 0.919 0.594 2.935 -0.034 0.934 1.053 0.952 14 22 48 52 15 17 15 26.143 26
; positions_7nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=26.1429; ---rTkrTGCAATm--- ; cor=0.919; Ncor=0.594; logoDP=2.935; NIcor=-0.034; NsEucl=0.934; SSD=1.053; NSW=0.952; rcor=14; rNcor=22; rlogoDP=48; rNIcor=52; rNsEucl=15; rSSD=17; rNSW=15; rank_mean=26.143; match_rank=26 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0

MA0078.1_shift0 (Sox17) 0.824 0.436 7.119 0.442 0.907 1.416 0.921 45 47 32 36 44 32 36 38.857 44
; positions_7nt_m1 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=0; strand=D; shift=0; score=38.8571; yhyATTGTs-------- ; cor=0.824; Ncor=0.436; logoDP=7.119; NIcor=0.442; NsEucl=0.907; SSD=1.416; NSW=0.921; rcor=45; rNcor=47; rlogoDP=32; rNIcor=36; rNsEucl=44; rSSD=32; rNSW=36; rank_mean=38.857; match_rank=44 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)																	; positions_7nt_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; rdgATTGTGCAATcAtt ; Alignment reference a 23 21 11 66 0 0 3 3 0 6 74 75 5 7 52 17 18 c 17 11 10 1 0 0 0 4 0 69 0 0 8 48 10 18 17 g 22 24 43 6 0 0 71 2 75 0 0 0 5 11 6 17 16 t 13 19 11 2 75 75 1 66 0 0 1 0 57 9 7 23 24
MA0102.3_rc_shift2 (CEBPA_rc)	0.936	0.606	4.313	0.051	0.941	0.849	0.961	7	19	40	46	7	8	7	19.143	15	; positions_7nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score=19.1429; --krTTrTGCAAt---- ; cor=0.936; Ncor=0.606; logoDP=4.313; NIcor=0.051; NsEucl=0.941; SSD=0.849; NSW=0.961; rcor=7; rNcor=19; rlogoDP=40; rNIcor=46; rNsEucl=7; rSSD=8; rNSW=7; rank_mean=19.143; match_rank=15 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0
MA0466.1_rc_shift3 (CEBPB_rc)	0.919	0.594	2.935	-0.034	0.934	1.053	0.952	14	22	48	52	15	17	15	26.143	26	; positions_7nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=26.1429; ---rTkrTGCAATm--- ; cor=0.919; Ncor=0.594; logoDP=2.935; NIcor=-0.034; NsEucl=0.934; SSD=1.053; NSW=0.952; rcor=14; rNcor=22; rlogoDP=48; rNIcor=52; rNsEucl=15; rSSD=17; rNSW=15; rank_mean=26.143; match_rank=26 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0
MA0078.1_shift0 (Sox17)	0.824	0.436	7.119	0.442	0.907	1.416	0.921	45	47	32	36	44	32	36	38.857	44	; positions_7nt_m1 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=0; strand=D; shift=0; score=38.8571; yhyATTGTs-------- ; cor=0.824; Ncor=0.436; logoDP=7.119; NIcor=0.442; NsEucl=0.907; SSD=1.416; NSW=0.921; rcor=45; rNcor=47; rlogoDP=32; rNIcor=36; rNsEucl=44; rSSD=32; rNSW=36; rank_mean=38.857; match_rank=44 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=18; shift=0; ncol=18; aakgATTGTGCAATcawt ; Alignment reference a 18 18 9 6 48 1 0 3 2 0 4 54 55 3 6 36 14 13 c 13 13 7 6 2 0 0 0 3 0 51 0 0 3 36 9 12 9 g 12 13 14 30 4 0 0 52 2 55 0 0 0 1 5 6 11 13 t 12 11 25 13 1 54 55 0 48 0 0 1 0 48 8 4 18 20

MA0102.3_rc_shift3 (CEBPA_rc) 0.938 0.573 4.109 0.042 0.941 0.852 0.961 6 25 42 48 9 10 9 21.286 17
; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=21.2857; ---krTTrTGCAAt---- ; cor=0.938; Ncor=0.573; logoDP=4.109; NIcor=0.042; NsEucl=0.941; SSD=0.852; NSW=0.961; rcor=6; rNcor=25; rlogoDP=42; rNIcor=48; rNsEucl=9; rSSD=10; rNSW=9; rank_mean=21.286; match_rank=17 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0

MA0466.1_rc_shift4 (CEBPB_rc) 0.920 0.562 2.945 -0.032 0.934 1.069 0.951 13 28 47 51 16 19 16 27.143 27
; positions_6nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=4; strand=R; shift=4; score=27.1429; ----rTkrTGCAATm--- ; cor=0.920; Ncor=0.562; logoDP=2.945; NIcor=-0.032; NsEucl=0.934; SSD=1.069; NSW=0.951; rcor=13; rNcor=28; rlogoDP=47; rNIcor=51; rNsEucl=16; rSSD=19; rNSW=16; rank_mean=27.143; match_rank=27 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0

MA0078.1_shift1 (Sox17) 0.828 0.414 6.943 0.418 0.908 1.372 0.924 38 52 33 39 41 29 32 37.714 41
; positions_6nt_m1 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=1; strand=D; shift=1; score=37.7143; -yhyATTGTs-------- ; cor=0.828; Ncor=0.414; logoDP=6.943; NIcor=0.418; NsEucl=0.908; SSD=1.372; NSW=0.924; rcor=38; rNcor=52; rlogoDP=33; rNIcor=39; rNsEucl=41; rSSD=29; rNSW=32; rank_mean=37.714; match_rank=41 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)																	; positions_6nt_m1; m=0 (reference); ncol1=18; shift=0; ncol=18; aakgATTGTGCAATcawt ; Alignment reference a 18 18 9 6 48 1 0 3 2 0 4 54 55 3 6 36 14 13 c 13 13 7 6 2 0 0 0 3 0 51 0 0 3 36 9 12 9 g 12 13 14 30 4 0 0 52 2 55 0 0 0 1 5 6 11 13 t 12 11 25 13 1 54 55 0 48 0 0 1 0 48 8 4 18 20
MA0102.3_rc_shift3 (CEBPA_rc)	0.938	0.573	4.109	0.042	0.941	0.852	0.961	6	25	42	48	9	10	9	21.286	17	; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=21.2857; ---krTTrTGCAAt---- ; cor=0.938; Ncor=0.573; logoDP=4.109; NIcor=0.042; NsEucl=0.941; SSD=0.852; NSW=0.961; rcor=6; rNcor=25; rlogoDP=42; rNIcor=48; rNsEucl=9; rSSD=10; rNSW=9; rank_mean=21.286; match_rank=17 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0
MA0466.1_rc_shift4 (CEBPB_rc)	0.920	0.562	2.945	-0.032	0.934	1.069	0.951	13	28	47	51	16	19	16	27.143	27	; positions_6nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=4; strand=R; shift=4; score=27.1429; ----rTkrTGCAATm--- ; cor=0.920; Ncor=0.562; logoDP=2.945; NIcor=-0.032; NsEucl=0.934; SSD=1.069; NSW=0.951; rcor=13; rNcor=28; rlogoDP=47; rNIcor=51; rNsEucl=16; rSSD=19; rNSW=16; rank_mean=27.143; match_rank=27 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0
MA0078.1_shift1 (Sox17)	0.828	0.414	6.943	0.418	0.908	1.372	0.924	38	52	33	39	41	29	32	37.714	41	; positions_6nt_m1 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=1; strand=D; shift=1; score=37.7143; -yhyATTGTs-------- ; cor=0.828; Ncor=0.414; logoDP=6.943; NIcor=0.418; NsEucl=0.908; SSD=1.372; NSW=0.924; rcor=38; rNcor=52; rlogoDP=33; rNIcor=39; rNsEucl=41; rSSD=29; rNSW=32; rank_mean=37.714; match_rank=41 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; catgATTGTGCAATartt ; Alignment reference a 12 17 7 4 46 0 0 1 1 0 4 51 53 0 29 25 12 13 c 16 12 5 7 3 0 0 0 4 0 45 0 0 2 6 5 12 9 g 13 13 9 31 2 0 0 51 0 53 1 1 0 5 9 14 12 11 t 12 11 32 11 2 53 53 1 48 0 3 1 0 46 9 9 17 20

MA0102.3_rc_shift3 (CEBPA_rc) 0.931 0.569 4.054 0.043 0.938 0.924 0.958 10 26 43 47 10 13 10 22.714 19
; positions_6nt_m3 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=22.7143; ---krTTrTGCAAt---- ; cor=0.931; Ncor=0.569; logoDP=4.054; NIcor=0.043; NsEucl=0.938; SSD=0.924; NSW=0.958; rcor=10; rNcor=26; rlogoDP=43; rNIcor=47; rNsEucl=10; rSSD=13; rNSW=10; rank_mean=22.714; match_rank=19 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0

MA0466.1_rc_shift4 (CEBPB_rc) 0.924 0.565 2.825 -0.025 0.936 0.984 0.955 11 27 50 49 13 15 12 25.286 25
; positions_6nt_m3 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=4; strand=R; shift=4; score=25.2857; ----rTkrTGCAATm--- ; cor=0.924; Ncor=0.565; logoDP=2.825; NIcor=-0.025; NsEucl=0.936; SSD=0.984; NSW=0.955; rcor=11; rNcor=27; rlogoDP=50; rNIcor=49; rNsEucl=13; rSSD=15; rNSW=12; rank_mean=25.286; match_rank=25 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0

MA0078.1_shift1 (Sox17) 0.825 0.413 7.295 0.415 0.905 1.449 0.919 42 54 31 40 46 34 41 41.143 46
; positions_6nt_m3 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=1; strand=D; shift=1; score=41.1429; -yhyATTGTs-------- ; cor=0.825; Ncor=0.413; logoDP=7.295; NIcor=0.415; NsEucl=0.905; SSD=1.449; NSW=0.919; rcor=42; rNcor=54; rlogoDP=31; rNIcor=40; rNsEucl=46; rSSD=34; rNSW=41; rank_mean=41.143; match_rank=46 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)																	; positions_6nt_m3; m=0 (reference); ncol1=18; shift=0; ncol=18; catgATTGTGCAATartt ; Alignment reference a 12 17 7 4 46 0 0 1 1 0 4 51 53 0 29 25 12 13 c 16 12 5 7 3 0 0 0 4 0 45 0 0 2 6 5 12 9 g 13 13 9 31 2 0 0 51 0 53 1 1 0 5 9 14 12 11 t 12 11 32 11 2 53 53 1 48 0 3 1 0 46 9 9 17 20
MA0102.3_rc_shift3 (CEBPA_rc)	0.931	0.569	4.054	0.043	0.938	0.924	0.958	10	26	43	47	10	13	10	22.714	19	; positions_6nt_m3 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=22.7143; ---krTTrTGCAAt---- ; cor=0.931; Ncor=0.569; logoDP=4.054; NIcor=0.043; NsEucl=0.938; SSD=0.924; NSW=0.958; rcor=10; rNcor=26; rlogoDP=43; rNIcor=47; rNsEucl=10; rSSD=13; rNSW=10; rank_mean=22.714; match_rank=19 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0
MA0466.1_rc_shift4 (CEBPB_rc)	0.924	0.565	2.825	-0.025	0.936	0.984	0.955	11	27	50	49	13	15	12	25.286	25	; positions_6nt_m3 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=4; strand=R; shift=4; score=25.2857; ----rTkrTGCAATm--- ; cor=0.924; Ncor=0.565; logoDP=2.825; NIcor=-0.025; NsEucl=0.936; SSD=0.984; NSW=0.955; rcor=11; rNcor=27; rlogoDP=50; rNIcor=49; rNsEucl=13; rSSD=15; rNSW=12; rank_mean=25.286; match_rank=25 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0
MA0078.1_shift1 (Sox17)	0.825	0.413	7.295	0.415	0.905	1.449	0.919	42	54	31	40	46	34	41	41.143	46	; positions_6nt_m3 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=1; strand=D; shift=1; score=41.1429; -yhyATTGTs-------- ; cor=0.825; Ncor=0.413; logoDP=7.295; NIcor=0.415; NsEucl=0.905; SSD=1.449; NSW=0.919; rcor=42; rNcor=54; rlogoDP=31; rNIcor=40; rNsEucl=46; rSSD=34; rNSW=41; rank_mean=41.143; match_rank=46 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; mwgTGTTGCACAATcacw ; Alignment reference a 12 13 6 4 5 0 0 2 0 37 1 41 41 0 5 26 9 15 c 14 1 7 2 4 0 0 0 42 1 40 0 0 1 24 6 16 8 g 7 8 27 5 31 0 0 39 0 3 0 0 1 3 9 3 9 7 t 9 20 2 31 2 42 42 1 0 1 1 1 0 38 4 7 8 12

MA0102.3_shift4 (CEBPA) 0.878 0.536 9.783 0.527 0.921 1.497 0.932 22 30 8 24 24 36 27 24.429 23
; positions_6nt_m2 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=24.4286; ----aTTGCAyAAym--- ; cor=0.878; Ncor=0.536; logoDP=9.783; NIcor=0.527; NsEucl=0.921; SSD=1.497; NSW=0.932; rcor=22; rNcor=30; rlogoDP=8; rNIcor=24; rNsEucl=24; rSSD=36; rNSW=27; rank_mean=24.429; match_rank=23 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0

MA0466.1_shift3 (CEBPB) 0.858 0.524 9.688 0.511 0.915 1.763 0.920 27 33 9 25 34 45 40 30.429 30
; positions_6nt_m2 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score=30.4286; ---kATTGCAymAy---- ; cor=0.858; Ncor=0.524; logoDP=9.688; NIcor=0.511; NsEucl=0.915; SSD=1.763; NSW=0.920; rcor=27; rNcor=33; rlogoDP=9; rNIcor=25; rNsEucl=34; rSSD=45; rNSW=40; rank_mean=30.429; match_rank=30 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0

MA0078.1_rc_shift8 (Sox17_rc) 0.827 0.414 3.180 0.149 0.906 1.417 0.921 41 53 45 43 45 33 37 42.429 48
; positions_6nt_m2 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=9; offset=8; strand=R; shift=8; score=42.4286; --------sACAATrdr- ; cor=0.827; Ncor=0.414; logoDP=3.180; NIcor=0.149; NsEucl=0.906; SSD=1.417; NSW=0.921; rcor=41; rNcor=53; rlogoDP=45; rNIcor=43; rNsEucl=45; rSSD=33; rNSW=37; rank_mean=42.429; match_rank=48 a 0 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 0 c 0 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 0 g 0 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)																	; positions_6nt_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; mwgTGTTGCACAATcacw ; Alignment reference a 12 13 6 4 5 0 0 2 0 37 1 41 41 0 5 26 9 15 c 14 1 7 2 4 0 0 0 42 1 40 0 0 1 24 6 16 8 g 7 8 27 5 31 0 0 39 0 3 0 0 1 3 9 3 9 7 t 9 20 2 31 2 42 42 1 0 1 1 1 0 38 4 7 8 12
MA0102.3_shift4 (CEBPA)	0.878	0.536	9.783	0.527	0.921	1.497	0.932	22	30	8	24	24	36	27	24.429	23	; positions_6nt_m2 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=24.4286; ----aTTGCAyAAym--- ; cor=0.878; Ncor=0.536; logoDP=9.783; NIcor=0.527; NsEucl=0.921; SSD=1.497; NSW=0.932; rcor=22; rNcor=30; rlogoDP=8; rNIcor=24; rNsEucl=24; rSSD=36; rNSW=27; rank_mean=24.429; match_rank=23 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0
MA0466.1_shift3 (CEBPB)	0.858	0.524	9.688	0.511	0.915	1.763	0.920	27	33	9	25	34	45	40	30.429	30	; positions_6nt_m2 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score=30.4286; ---kATTGCAymAy---- ; cor=0.858; Ncor=0.524; logoDP=9.688; NIcor=0.511; NsEucl=0.915; SSD=1.763; NSW=0.920; rcor=27; rNcor=33; rlogoDP=9; rNIcor=25; rNsEucl=34; rSSD=45; rNSW=40; rank_mean=30.429; match_rank=30 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0
MA0078.1_rc_shift8 (Sox17_rc)	0.827	0.414	3.180	0.149	0.906	1.417	0.921	41	53	45	43	45	33	37	42.429	48	; positions_6nt_m2 versus MA0078.1_rc (Sox17_rc); m=3/3; ncol2=9; w=9; offset=8; strand=R; shift=8; score=42.4286; --------sACAATrdr- ; cor=0.827; Ncor=0.414; logoDP=3.180; NIcor=0.149; NsEucl=0.906; SSD=1.417; NSW=0.921; rcor=41; rNcor=53; rlogoDP=45; rNIcor=43; rNsEucl=45; rSSD=33; rNSW=37; rank_mean=42.429; match_rank=48 a 0 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 0 c 0 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 0 g 0 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; ayttATTGCGCAATaarw ; Alignment reference a 35 28 19 17 94 0 1 3 4 19 5 113 114 5 56 51 29 29 c 27 33 27 18 10 1 0 0 90 2 107 1 0 6 23 18 26 25 g 25 25 18 23 6 0 1 108 2 90 0 0 1 10 19 27 32 26 t 28 29 51 57 5 114 113 4 19 4 3 1 0 94 17 19 28 35

MA0102.3_shift4 (CEBPA) 0.844 0.516 8.280 0.501 0.916 1.709 0.922 33 35 21 26 29 42 35 31.571 32
; positions_7nt_m2 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score=31.5714; ----aTTGCAyAAym--- ; cor=0.844; Ncor=0.516; logoDP=8.280; NIcor=0.501; NsEucl=0.916; SSD=1.709; NSW=0.922; rcor=33; rNcor=35; rlogoDP=21; rNIcor=26; rNsEucl=29; rSSD=42; rNSW=35; rank_mean=31.571; match_rank=32 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0

MA0466.1_shift3 (CEBPB) 0.842 0.515 8.223 0.498 0.915 1.736 0.921 34 36 23 27 32 43 38 33.286 36
; positions_7nt_m2 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=33.2857; ---kATTGCAymAy---- ; cor=0.842; Ncor=0.515; logoDP=8.223; NIcor=0.498; NsEucl=0.915; SSD=1.736; NSW=0.921; rcor=34; rNcor=36; rlogoDP=23; rNIcor=27; rNsEucl=32; rSSD=43; rNSW=38; rank_mean=33.286; match_rank=36 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)																	; positions_7nt_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; ayttATTGCGCAATaarw ; Alignment reference a 35 28 19 17 94 0 1 3 4 19 5 113 114 5 56 51 29 29 c 27 33 27 18 10 1 0 0 90 2 107 1 0 6 23 18 26 25 g 25 25 18 23 6 0 1 108 2 90 0 0 1 10 19 27 32 26 t 28 29 51 57 5 114 113 4 19 4 3 1 0 94 17 19 28 35
MA0102.3_shift4 (CEBPA)	0.844	0.516	8.280	0.501	0.916	1.709	0.922	33	35	21	26	29	42	35	31.571	32	; positions_7nt_m2 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score=31.5714; ----aTTGCAyAAym--- ; cor=0.844; Ncor=0.516; logoDP=8.280; NIcor=0.501; NsEucl=0.916; SSD=1.709; NSW=0.922; rcor=33; rNcor=35; rlogoDP=21; rNIcor=26; rNsEucl=29; rSSD=42; rNSW=35; rank_mean=31.571; match_rank=32 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0
MA0466.1_shift3 (CEBPB)	0.842	0.515	8.223	0.498	0.915	1.736	0.921	34	36	23	27	32	43	38	33.286	36	; positions_7nt_m2 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score=33.2857; ---kATTGCAymAy---- ; cor=0.842; Ncor=0.515; logoDP=8.223; NIcor=0.498; NsEucl=0.915; SSD=1.736; NSW=0.921; rcor=34; rNcor=36; rlogoDP=23; rNIcor=27; rNsEucl=32; rSSD=43; rNSW=38; rank_mean=33.286; match_rank=36 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)
; positions_7nt_m5; m=0 (reference); ncol1=18; shift=0; ncol=18; gwgATTGTGCAACAchkr ; Alignment reference a 11 18 8 49 0 0 1 3 0 1 53 54 2 42 5 22 12 18 c 13 7 12 3 0 0 0 3 0 50 1 0 41 7 29 15 6 11 g 21 10 29 1 0 0 53 2 54 1 0 0 5 2 10 3 17 15 t 9 19 5 1 54 54 0 46 0 2 0 0 6 3 10 14 19 10

MA0102.3_rc_shift2 (CEBPA_rc) 0.873 0.534 4.210 0.055 0.920 1.563 0.929 25 31 41 45 25 37 29 33.286 35
; positions_7nt_m5 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score=33.2857; --krTTrTGCAAt----- ; cor=0.873; Ncor=0.534; logoDP=4.210; NIcor=0.055; NsEucl=0.920; SSD=1.563; NSW=0.929; rcor=25; rNcor=31; rlogoDP=41; rNIcor=45; rNsEucl=25; rSSD=37; rNSW=29; rank_mean=33.286; match_rank=35 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0 0

MA0078.1_shift0 (Sox17) 0.839 0.420 7.380 0.423 0.910 1.307 0.927 35 51 30 38 38 26 30 35.429 38
; positions_7nt_m5 versus MA0078.1 (Sox17); m=2/3; ncol2=9; w=9; offset=0; strand=D; shift=0; score=35.4286; yhyATTGTs--------- ; cor=0.839; Ncor=0.420; logoDP=7.380; NIcor=0.423; NsEucl=0.910; SSD=1.307; NSW=0.927; rcor=35; rNcor=51; rlogoDP=30; rNIcor=38; rNsEucl=38; rSSD=26; rNSW=30; rank_mean=35.429; match_rank=38 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0 0

MA0466.1_rc_shift3 (CEBPB_rc) 0.852 0.521 2.820 -0.035 0.912 1.869 0.915 32 34 51 53 36 49 44 42.714 49
; positions_7nt_m5 versus MA0466.1_rc (CEBPB_rc); m=3/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=42.7143; ---rTkrTGCAATm---- ; cor=0.852; Ncor=0.521; logoDP=2.820; NIcor=-0.035; NsEucl=0.912; SSD=1.869; NSW=0.915; rcor=32; rNcor=34; rlogoDP=51; rNIcor=53; rNsEucl=36; rSSD=49; rNSW=44; rank_mean=42.714; match_rank=49 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)																	; positions_7nt_m5; m=0 (reference); ncol1=18; shift=0; ncol=18; gwgATTGTGCAACAchkr ; Alignment reference a 11 18 8 49 0 0 1 3 0 1 53 54 2 42 5 22 12 18 c 13 7 12 3 0 0 0 3 0 50 1 0 41 7 29 15 6 11 g 21 10 29 1 0 0 53 2 54 1 0 0 5 2 10 3 17 15 t 9 19 5 1 54 54 0 46 0 2 0 0 6 3 10 14 19 10
MA0102.3_rc_shift2 (CEBPA_rc)	0.873	0.534	4.210	0.055	0.920	1.563	0.929	25	31	41	45	25	37	29	33.286	35	; positions_7nt_m5 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score=33.2857; --krTTrTGCAAt----- ; cor=0.873; Ncor=0.534; logoDP=4.210; NIcor=0.055; NsEucl=0.920; SSD=1.563; NSW=0.929; rcor=25; rNcor=31; rlogoDP=41; rNIcor=45; rNsEucl=25; rSSD=37; rNSW=29; rank_mean=33.286; match_rank=35 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0 0
MA0078.1_shift0 (Sox17)	0.839	0.420	7.380	0.423	0.910	1.307	0.927	35	51	30	38	38	26	30	35.429	38	; positions_7nt_m5 versus MA0078.1 (Sox17); m=2/3; ncol2=9; w=9; offset=0; strand=D; shift=0; score=35.4286; yhyATTGTs--------- ; cor=0.839; Ncor=0.420; logoDP=7.380; NIcor=0.423; NsEucl=0.910; SSD=1.307; NSW=0.927; rcor=35; rNcor=51; rlogoDP=30; rNIcor=38; rNsEucl=38; rSSD=26; rNSW=30; rank_mean=35.429; match_rank=38 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0 0
MA0466.1_rc_shift3 (CEBPB_rc)	0.852	0.521	2.820	-0.035	0.912	1.869	0.915	32	34	51	53	36	49	44	42.714	49	; positions_7nt_m5 versus MA0466.1_rc (CEBPB_rc); m=3/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score=42.7143; ---rTkrTGCAATm---- ; cor=0.852; Ncor=0.521; logoDP=2.820; NIcor=-0.035; NsEucl=0.912; SSD=1.869; NSW=0.915; rcor=32; rNcor=34; rlogoDP=51; rNIcor=53; rNsEucl=36; rSSD=49; rNSW=44; rank_mean=42.714; match_rank=49 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; mbtgATTGCGCAATcavk ; Alignment reference a 14 9 6 4 40 0 0 0 3 6 3 46 46 1 5 24 12 9 c 13 13 7 6 3 0 0 0 35 2 43 0 0 2 31 9 12 10 g 10 12 9 31 2 0 0 43 2 35 0 0 0 3 6 7 13 13 t 9 12 24 5 1 46 46 3 6 3 0 0 0 40 4 6 9 14

MA0102.3_shift4 (CEBPA) 0.828 0.506 8.679 0.490 0.910 1.975 0.910 40 38 19 28 39 51 46 37.286 39
; positions_6nt_m4 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score=37.2857; ----aTTGCAyAAym--- ; cor=0.828; Ncor=0.506; logoDP=8.679; NIcor=0.490; NsEucl=0.910; SSD=1.975; NSW=0.910; rcor=40; rNcor=38; rlogoDP=19; rNIcor=28; rNsEucl=39; rSSD=51; rNSW=46; rank_mean=37.286; match_rank=39 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0

MA0466.1_rc_shift4 (CEBPB_rc) 0.825 0.504 2.931 -0.028 0.909 2.009 0.909 43 39 49 50 40 52 48 45.857 52
; positions_6nt_m4 versus MA0466.1_rc (CEBPB_rc); m=2/2; ncol2=11; w=11; offset=4; strand=R; shift=4; score=45.8571; ----rTkrTGCAATm--- ; cor=0.825; Ncor=0.504; logoDP=2.931; NIcor=-0.028; NsEucl=0.909; SSD=2.009; NSW=0.909; rcor=43; rNcor=39; rlogoDP=49; rNIcor=50; rNsEucl=40; rSSD=52; rNSW=48; rank_mean=45.857; match_rank=52 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)																	; positions_6nt_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; mbtgATTGCGCAATcavk ; Alignment reference a 14 9 6 4 40 0 0 0 3 6 3 46 46 1 5 24 12 9 c 13 13 7 6 3 0 0 0 35 2 43 0 0 2 31 9 12 10 g 10 12 9 31 2 0 0 43 2 35 0 0 0 3 6 7 13 13 t 9 12 24 5 1 46 46 3 6 3 0 0 0 40 4 6 9 14
MA0102.3_shift4 (CEBPA)	0.828	0.506	8.679	0.490	0.910	1.975	0.910	40	38	19	28	39	51	46	37.286	39	; positions_6nt_m4 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score=37.2857; ----aTTGCAyAAym--- ; cor=0.828; Ncor=0.506; logoDP=8.679; NIcor=0.490; NsEucl=0.910; SSD=1.975; NSW=0.910; rcor=40; rNcor=38; rlogoDP=19; rNIcor=28; rNsEucl=39; rSSD=51; rNSW=46; rank_mean=37.286; match_rank=39 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0
MA0466.1_rc_shift4 (CEBPB_rc)	0.825	0.504	2.931	-0.028	0.909	2.009	0.909	43	39	49	50	40	52	48	45.857	52	; positions_6nt_m4 versus MA0466.1_rc (CEBPB_rc); m=2/2; ncol2=11; w=11; offset=4; strand=R; shift=4; score=45.8571; ----rTkrTGCAATm--- ; cor=0.825; Ncor=0.504; logoDP=2.931; NIcor=-0.028; NsEucl=0.909; SSD=2.009; NSW=0.909; rcor=43; rNcor=39; rlogoDP=49; rNIcor=50; rNsEucl=40; rSSD=52; rNSW=48; rank_mean=45.857; match_rank=52 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=0; ncol=14; dhGATTGCGhm--- ; Alignment reference a 20 21 2 60 0 5 6 0 0 21 38 0 0 0 c 8 17 1 2 1 2 1 65 2 18 18 0 0 0 g 20 12 54 4 1 0 59 0 62 3 5 0 0 0 t 19 17 10 1 65 60 1 2 3 25 6 0 0 0

MA0043.1_rc_shift2 (HLF_rc) 0.824 0.530 3.854 0.414 0.908 1.376 0.924 44 32 44 41 42 30 33 38.000 43
; oligos_6nt_mkv3_m3 versus MA0043.1_rc (HLF_rc); m=1/3; ncol2=12; w=9; offset=2; strand=R; shift=2; score= 38; --daTTryGTAAym ; cor=0.824; Ncor=0.530; logoDP=3.854; NIcor=0.414; NsEucl=0.908; SSD=1.376; NSW=0.924; rcor=44; rNcor=32; rlogoDP=44; rNIcor=41; rNsEucl=42; rSSD=30; rNSW=33; rank_mean=38.000; match_rank=43 a 0 0 5 12 2 0 9 0 2 2 15 17 0 5 c 0 0 3 1 1 1 0 12 1 2 3 0 12 8 g 0 0 5 3 0 4 9 0 15 1 0 0 0 4 t 0 0 5 2 15 13 0 6 0 13 0 1 6 1

MA0466.1_shift2 (CEBPB) 0.777 0.538 5.698 0.529 0.894 1.818 0.899 53 29 36 23 52 47 51 41.571 47
; oligos_6nt_mkv3_m3 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=9; offset=2; strand=D; shift=2; score=41.5714; --kATTGCAymAy- ; cor=0.777; Ncor=0.538; logoDP=5.698; NIcor=0.529; NsEucl=0.894; SSD=1.818; NSW=0.899; rcor=53; rNcor=29; rlogoDP=36; rNIcor=23; rNsEucl=52; rSSD=47; rNSW=51; rank_mean=41.571; match_rank=47 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0

MA0102.3_shift3 (CEBPA) 0.783 0.448 5.527 0.444 0.886 1.660 0.896 52 44 37 34 53 40 52 44.571 51
; oligos_6nt_mkv3_m3 versus MA0102.3 (CEBPA); m=3/3; ncol2=11; w=8; offset=3; strand=D; shift=3; score=44.5714; ---aTTGCAyAAym ; cor=0.783; Ncor=0.448; logoDP=5.527; NIcor=0.444; NsEucl=0.886; SSD=1.660; NSW=0.896; rcor=52; rNcor=44; rlogoDP=37; rNIcor=34; rNsEucl=53; rSSD=40; rNSW=52; rank_mean=44.571; match_rank=51 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)																	; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=0; ncol=14; dhGATTGCGhm--- ; Alignment reference a 20 21 2 60 0 5 6 0 0 21 38 0 0 0 c 8 17 1 2 1 2 1 65 2 18 18 0 0 0 g 20 12 54 4 1 0 59 0 62 3 5 0 0 0 t 19 17 10 1 65 60 1 2 3 25 6 0 0 0
MA0043.1_rc_shift2 (HLF_rc)	0.824	0.530	3.854	0.414	0.908	1.376	0.924	44	32	44	41	42	30	33	38.000	43	; oligos_6nt_mkv3_m3 versus MA0043.1_rc (HLF_rc); m=1/3; ncol2=12; w=9; offset=2; strand=R; shift=2; score= 38; --daTTryGTAAym ; cor=0.824; Ncor=0.530; logoDP=3.854; NIcor=0.414; NsEucl=0.908; SSD=1.376; NSW=0.924; rcor=44; rNcor=32; rlogoDP=44; rNIcor=41; rNsEucl=42; rSSD=30; rNSW=33; rank_mean=38.000; match_rank=43 a 0 0 5 12 2 0 9 0 2 2 15 17 0 5 c 0 0 3 1 1 1 0 12 1 2 3 0 12 8 g 0 0 5 3 0 4 9 0 15 1 0 0 0 4 t 0 0 5 2 15 13 0 6 0 13 0 1 6 1
MA0466.1_shift2 (CEBPB)	0.777	0.538	5.698	0.529	0.894	1.818	0.899	53	29	36	23	52	47	51	41.571	47	; oligos_6nt_mkv3_m3 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=9; offset=2; strand=D; shift=2; score=41.5714; --kATTGCAymAy- ; cor=0.777; Ncor=0.538; logoDP=5.698; NIcor=0.529; NsEucl=0.894; SSD=1.818; NSW=0.899; rcor=53; rNcor=29; rlogoDP=36; rNIcor=23; rNsEucl=52; rSSD=47; rNSW=51; rank_mean=41.571; match_rank=47 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
MA0102.3_shift3 (CEBPA)	0.783	0.448	5.527	0.444	0.886	1.660	0.896	52	44	37	34	53	40	52	44.571	51	; oligos_6nt_mkv3_m3 versus MA0102.3 (CEBPA); m=3/3; ncol2=11; w=8; offset=3; strand=D; shift=3; score=44.5714; ---aTTGCAyAAym ; cor=0.783; Ncor=0.448; logoDP=5.527; NIcor=0.444; NsEucl=0.886; SSD=1.660; NSW=0.896; rcor=52; rNcor=44; rlogoDP=37; rNIcor=34; rNsEucl=53; rSSD=40; rNSW=52; rank_mean=44.571; match_rank=51 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661