One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m20/peak-motifs_oligos_8nt_mkv2_m20.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -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/oligos_8nt_mkv2_m20/peak-motifs_oligos_8nt_mkv2_m20_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m20_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m20_shift4 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)
; oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=0 (reference); ncol1=13; shift=4; ncol=17; ----swGAGGCAGGGrG ; Alignment reference a 0 0 0 0 2 11 1 25 0 0 1 25 0 6 0 8 2 c 0 0 0 0 13 2 2 0 0 0 25 0 0 0 0 1 3 g 0 0 0 0 11 6 23 0 26 25 0 0 26 20 26 14 19 t 0 0 0 0 0 7 0 1 0 1 0 1 0 0 0 3 2

MA1596.1_rc_shift1 (ZNF460_rc)
; oligos_8nt_mkv2_m20 versus MA1596.1_rc (ZNF460_rc); m=1/3; ncol2=16; w=13; offset=-3; strand=R; shift=1; score=0.570564; -CyyGGGAGGCkGAGGy ; cor=; Ncor= a 0 64.0 29.0 56.0 40.0 9.0 10.0 1570.0 6.0 11.0 35.0 85.0 29.0 1284.0 66.0 114.0 46.0 c 0 1147.0 421.0 930.0 27.0 15.0 15.0 17.0 9.0 7.0 1493.0 181.0 47.0 83.0 67.0 185.0 1023.0 g 0 158.0 175.0 110.0 1533.0 1583.0 1584.0 12.0 1596.0 1588.0 23.0 495.0 1519.0 218.0 1460.0 1264.0 131.0 t 0 243.0 987.0 516.0 12.0 5.0 3.0 13.0 1.0 6.0 61.0 851.0 17.0 27.0 19.0 49.0 412.0

MA1102.2_shift8 (CTCFL)
; oligos_8nt_mkv2_m20 versus MA1102.2 (CTCFL); m=2/3; ncol2=12; w=9; offset=4; strand=D; shift=8; score=0.460605; --------rsCAGGGGG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 5825.0 2659.0 1301.0 17270.0 86.0 684.0 349.0 193.0 351.0 c 0 0 0 0 0 0 0 0 4180.0 7033.0 12867.0 413.0 481.0 600.0 1141.0 767.0 270.0 g 0 0 0 0 0 0 0 0 4844.0 7094.0 2033.0 329.0 17285.0 16511.0 15425.0 16819.0 17001.0 t 0 0 0 0 0 0 0 0 3188.0 1251.0 1836.0 25.0 185.0 242.0 1122.0 258.0 415.0

MA0003.4_rc_shift0 (TFAP2A_rc)
; oligos_8nt_mkv2_m20 versus MA0003.4_rc (TFAP2A_rc); m=3/3; ncol2=14; w=10; offset=-4; strand=R; shift=0; score=0.427855; tksCCTGAGGcarb--- ; cor=; Ncor= a 3008.0 3914.0 1204.0 158.0 133.0 433.0 496.0 13767.0 289.0 180.0 1304.0 6701.0 5211.0 3469.0 0 0 0 c 3841.0 3051.0 4098.0 15422.0 15432.0 1229.0 1406.0 750.0 212.0 187.0 9961.0 3791.0 3374.0 4072.0 0 0 0 g 3915.0 4783.0 9445.0 234.0 217.0 739.0 13536.0 1173.0 15351.0 15321.0 3615.0 2634.0 4620.0 4092.0 0 0 0 t 5204.0 4220.0 1221.0 154.0 186.0 13567.0 530.0 278.0 116.0 280.0 1088.0 2842.0 2763.0 4335.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m20_shift4 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20)				; oligos_8nt_mkv2_m20 (oligos_8nt_mkv2_m20oligos_8nt_mkv2_m20); m=0 (reference); ncol1=13; shift=4; ncol=17; ----swGAGGCAGGGrG ; Alignment reference a 0 0 0 0 2 11 1 25 0 0 1 25 0 6 0 8 2 c 0 0 0 0 13 2 2 0 0 0 25 0 0 0 0 1 3 g 0 0 0 0 11 6 23 0 26 25 0 0 26 20 26 14 19 t 0 0 0 0 0 7 0 1 0 1 0 1 0 0 0 3 2
MA1596.1_rc_shift1 (ZNF460_rc)				; oligos_8nt_mkv2_m20 versus MA1596.1_rc (ZNF460_rc); m=1/3; ncol2=16; w=13; offset=-3; strand=R; shift=1; score=0.570564; -CyyGGGAGGCkGAGGy ; cor=; Ncor= a 0 64.0 29.0 56.0 40.0 9.0 10.0 1570.0 6.0 11.0 35.0 85.0 29.0 1284.0 66.0 114.0 46.0 c 0 1147.0 421.0 930.0 27.0 15.0 15.0 17.0 9.0 7.0 1493.0 181.0 47.0 83.0 67.0 185.0 1023.0 g 0 158.0 175.0 110.0 1533.0 1583.0 1584.0 12.0 1596.0 1588.0 23.0 495.0 1519.0 218.0 1460.0 1264.0 131.0 t 0 243.0 987.0 516.0 12.0 5.0 3.0 13.0 1.0 6.0 61.0 851.0 17.0 27.0 19.0 49.0 412.0
MA1102.2_shift8 (CTCFL)				; oligos_8nt_mkv2_m20 versus MA1102.2 (CTCFL); m=2/3; ncol2=12; w=9; offset=4; strand=D; shift=8; score=0.460605; --------rsCAGGGGG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 5825.0 2659.0 1301.0 17270.0 86.0 684.0 349.0 193.0 351.0 c 0 0 0 0 0 0 0 0 4180.0 7033.0 12867.0 413.0 481.0 600.0 1141.0 767.0 270.0 g 0 0 0 0 0 0 0 0 4844.0 7094.0 2033.0 329.0 17285.0 16511.0 15425.0 16819.0 17001.0 t 0 0 0 0 0 0 0 0 3188.0 1251.0 1836.0 25.0 185.0 242.0 1122.0 258.0 415.0
MA0003.4_rc_shift0 (TFAP2A_rc)				; oligos_8nt_mkv2_m20 versus MA0003.4_rc (TFAP2A_rc); m=3/3; ncol2=14; w=10; offset=-4; strand=R; shift=0; score=0.427855; tksCCTGAGGcarb--- ; cor=; Ncor= a 3008.0 3914.0 1204.0 158.0 133.0 433.0 496.0 13767.0 289.0 180.0 1304.0 6701.0 5211.0 3469.0 0 0 0 c 3841.0 3051.0 4098.0 15422.0 15432.0 1229.0 1406.0 750.0 212.0 187.0 9961.0 3791.0 3374.0 4072.0 0 0 0 g 3915.0 4783.0 9445.0 234.0 217.0 739.0 13536.0 1173.0 15351.0 15321.0 3615.0 2634.0 4620.0 4092.0 0 0 0 t 5204.0 4220.0 1221.0 154.0 186.0 13567.0 530.0 278.0 116.0 280.0 1088.0 2842.0 2763.0 4335.0 0 0 0