One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/04/peak-motifs.2026-03-04.105925_2026-03-04.105925_GBNx32/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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 $RSAT/public_html/tmp/www-data/2026/03/04/peak-motifs.2026-03-04.105925_2026-03-04.105925_GBNx32/results/discovered_motifs/oligos_6nt_mkv3_m1/peak-motifs_oligos_6nt_mkv3_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=22; shift=0; ncol=22; yryaTwTGCATATGCAwAtryr ; Alignment reference a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86

MA0507.3_rc_shift0 (POU2F2_rc)
; oligos_6nt_mkv3_m1 versus MA0507.3_rc (POU2F2_rc); m=1/5; ncol2=13; w=0; offset=0; strand=R; shift=0; score= 0.509; cTmATTTGCATAw--------- ; cor=; Ncor= a 788.0 1065.0 5505.0 9207.0 8.0 57.0 1929.0 1193.0 111.0 9207.0 0.0 9207.0 3315.0 0 0 0 0 0 0 0 0 0 c 5392.0 851.0 3703.0 35.0 0.0 23.0 0.0 127.0 9207.0 2.0 0.0 4.0 2020.0 0 0 0 0 0 0 0 0 0 g 1301.0 648.0 862.0 8.0 5.0 7.0 0.0 8014.0 0.0 13.0 0.0 100.0 435.0 0 0 0 0 0 0 0 0 0 t 1726.0 6644.0 1399.0 56.0 9207.0 9207.0 7279.0 2.0 0.0 0.0 9207.0 34.0 5892.0 0 0 0 0 0 0 0 0 0

MA0142.1_rc_shift3 (Pou5f1::Sox2_rc)
; oligos_6nt_mkv3_m1 versus MA0142.1_rc (Pou5f1::Sox2_rc); m=2/5; ncol2=15; w=0; offset=3; strand=R; shift=3; score=0.487543; ---aTtTGCATrwsAAwr---- ; cor=; Ncor= a 0 0 0 837.0 53.0 92.0 269.0 196.0 104.0 1332.0 80.0 612.0 907.0 63.0 1231.0 1270.0 701.0 389.0 0 0 0 0 c 0 0 0 207.0 75.0 315.0 30.0 129.0 1239.0 15.0 24.0 186.0 29.0 825.0 79.0 36.0 28.0 66.0 0 0 0 0 g 0 0 0 119.0 33.0 68.0 16.0 1029.0 16.0 5.0 30.0 365.0 18.0 363.0 12.0 50.0 58.0 846.0 0 0 0 0 t 0 0 0 198.0 1200.0 887.0 1050.0 14.0 10.0 17.0 1235.0 206.0 415.0 118.0 47.0 11.0 579.0 63.0 0 0 0 0

MA0784.3_rc_shift8 (POU1F1_rc)
; oligos_6nt_mkv3_m1 versus MA0784.3_rc (POU1F1_rc); m=3/5; ncol2=14; w=0; offset=8; strand=R; shift=8; score=0.456527; --------awTATGCwAATkAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3278.0 1804.0 59.0 4127.0 17.0 3.0 16.0 2563.0 4127.0 4127.0 31.0 262.0 3907.0 504.0 c 0 0 0 0 0 0 0 0 384.0 57.0 5.0 0.0 5.0 1.0 3708.0 0.0 2.0 1.0 28.0 192.0 220.0 372.0 g 0 0 0 0 0 0 0 0 702.0 165.0 5.0 3.0 9.0 4127.0 67.0 0.0 13.0 0.0 7.0 1846.0 126.0 3623.0 t 0 0 0 0 0 0 0 0 849.0 2323.0 4127.0 3.0 4127.0 54.0 419.0 1564.0 91.0 0.0 4127.0 2281.0 106.0 131.0

MA0787.1_shift9 (POU3F2)
; oligos_6nt_mkv3_m1 versus MA0787.1 (POU3F2); m=4/5; ncol2=12; w=0; offset=9; strand=D; shift=9; score=0.446048; ---------wTATGCwAATka- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 591.0 163.0 1292.0 28.0 19.0 68.0 688.0 1292.0 1292.0 63.0 137.0 1292.0 0 c 0 0 0 0 0 0 0 0 0 61.0 65.0 16.0 30.0 9.0 1292.0 4.0 16.0 6.0 19.0 165.0 262.0 0 g 0 0 0 0 0 0 0 0 0 171.0 40.0 25.0 12.0 1292.0 153.0 1.0 32.0 0.0 28.0 452.0 261.0 0 t 0 0 0 0 0 0 0 0 0 700.0 1292.0 0.0 1292.0 60.0 372.0 604.0 45.0 13.0 1292.0 840.0 562.0 0

MA0788.1_shift8 (POU3F3)
; oligos_6nt_mkv3_m1 versus MA0788.1 (POU3F3); m=5/5; ncol2=13; w=0; offset=8; strand=D; shift=8; score=0.419029; --------wwTATGCwAATtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 576.0 440.0 129.0 1078.0 25.0 22.0 28.0 506.0 1078.0 1078.0 53.0 240.0 536.0 0 c 0 0 0 0 0 0 0 0 75.0 41.0 57.0 11.0 33.0 10.0 1078.0 4.0 11.0 6.0 20.0 141.0 85.0 0 g 0 0 0 0 0 0 0 0 137.0 131.0 64.0 12.0 49.0 1078.0 118.0 1.0 77.0 15.0 12.0 237.0 115.0 0 t 0 0 0 0 0 0 0 0 290.0 637.0 1078.0 30.0 1078.0 86.0 343.0 572.0 79.0 14.0 1078.0 1078.0 542.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift0 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=22; shift=0; ncol=22; yryaTwTGCATATGCAwAtryr ; Alignment reference a 86 142 55 241 36 111 17 47 27 397 25 375 20 20 76 370 226 296 59 148 97 131 c 118 78 162 80 88 35 40 16 362 5 21 13 12 25 295 7 62 14 54 69 117 99 g 99 117 69 54 14 62 7 295 25 12 13 21 5 362 16 40 35 88 80 162 78 118 t 131 97 148 59 296 226 370 76 20 20 375 25 397 27 47 17 111 36 241 55 142 86
MA0507.3_rc_shift0 (POU2F2_rc)				; oligos_6nt_mkv3_m1 versus MA0507.3_rc (POU2F2_rc); m=1/5; ncol2=13; w=0; offset=0; strand=R; shift=0; score= 0.509; cTmATTTGCATAw--------- ; cor=; Ncor= a 788.0 1065.0 5505.0 9207.0 8.0 57.0 1929.0 1193.0 111.0 9207.0 0.0 9207.0 3315.0 0 0 0 0 0 0 0 0 0 c 5392.0 851.0 3703.0 35.0 0.0 23.0 0.0 127.0 9207.0 2.0 0.0 4.0 2020.0 0 0 0 0 0 0 0 0 0 g 1301.0 648.0 862.0 8.0 5.0 7.0 0.0 8014.0 0.0 13.0 0.0 100.0 435.0 0 0 0 0 0 0 0 0 0 t 1726.0 6644.0 1399.0 56.0 9207.0 9207.0 7279.0 2.0 0.0 0.0 9207.0 34.0 5892.0 0 0 0 0 0 0 0 0 0
MA0142.1_rc_shift3 (Pou5f1::Sox2_rc)				; oligos_6nt_mkv3_m1 versus MA0142.1_rc (Pou5f1::Sox2_rc); m=2/5; ncol2=15; w=0; offset=3; strand=R; shift=3; score=0.487543; ---aTtTGCATrwsAAwr---- ; cor=; Ncor= a 0 0 0 837.0 53.0 92.0 269.0 196.0 104.0 1332.0 80.0 612.0 907.0 63.0 1231.0 1270.0 701.0 389.0 0 0 0 0 c 0 0 0 207.0 75.0 315.0 30.0 129.0 1239.0 15.0 24.0 186.0 29.0 825.0 79.0 36.0 28.0 66.0 0 0 0 0 g 0 0 0 119.0 33.0 68.0 16.0 1029.0 16.0 5.0 30.0 365.0 18.0 363.0 12.0 50.0 58.0 846.0 0 0 0 0 t 0 0 0 198.0 1200.0 887.0 1050.0 14.0 10.0 17.0 1235.0 206.0 415.0 118.0 47.0 11.0 579.0 63.0 0 0 0 0
MA0784.3_rc_shift8 (POU1F1_rc)				; oligos_6nt_mkv3_m1 versus MA0784.3_rc (POU1F1_rc); m=3/5; ncol2=14; w=0; offset=8; strand=R; shift=8; score=0.456527; --------awTATGCwAATkAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 3278.0 1804.0 59.0 4127.0 17.0 3.0 16.0 2563.0 4127.0 4127.0 31.0 262.0 3907.0 504.0 c 0 0 0 0 0 0 0 0 384.0 57.0 5.0 0.0 5.0 1.0 3708.0 0.0 2.0 1.0 28.0 192.0 220.0 372.0 g 0 0 0 0 0 0 0 0 702.0 165.0 5.0 3.0 9.0 4127.0 67.0 0.0 13.0 0.0 7.0 1846.0 126.0 3623.0 t 0 0 0 0 0 0 0 0 849.0 2323.0 4127.0 3.0 4127.0 54.0 419.0 1564.0 91.0 0.0 4127.0 2281.0 106.0 131.0
MA0787.1_shift9 (POU3F2)				; oligos_6nt_mkv3_m1 versus MA0787.1 (POU3F2); m=4/5; ncol2=12; w=0; offset=9; strand=D; shift=9; score=0.446048; ---------wTATGCwAATka- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 591.0 163.0 1292.0 28.0 19.0 68.0 688.0 1292.0 1292.0 63.0 137.0 1292.0 0 c 0 0 0 0 0 0 0 0 0 61.0 65.0 16.0 30.0 9.0 1292.0 4.0 16.0 6.0 19.0 165.0 262.0 0 g 0 0 0 0 0 0 0 0 0 171.0 40.0 25.0 12.0 1292.0 153.0 1.0 32.0 0.0 28.0 452.0 261.0 0 t 0 0 0 0 0 0 0 0 0 700.0 1292.0 0.0 1292.0 60.0 372.0 604.0 45.0 13.0 1292.0 840.0 562.0 0
MA0788.1_shift8 (POU3F3)				; oligos_6nt_mkv3_m1 versus MA0788.1 (POU3F3); m=5/5; ncol2=13; w=0; offset=8; strand=D; shift=8; score=0.419029; --------wwTATGCwAATtw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 576.0 440.0 129.0 1078.0 25.0 22.0 28.0 506.0 1078.0 1078.0 53.0 240.0 536.0 0 c 0 0 0 0 0 0 0 0 75.0 41.0 57.0 11.0 33.0 10.0 1078.0 4.0 11.0 6.0 20.0 141.0 85.0 0 g 0 0 0 0 0 0 0 0 137.0 131.0 64.0 12.0 49.0 1078.0 118.0 1.0 77.0 15.0 12.0 237.0 115.0 0 t 0 0 0 0 0 0 0 0 290.0 637.0 1078.0 30.0 1078.0 86.0 343.0 572.0 79.0 14.0 1078.0 1078.0 542.0 0