One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3.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/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGGCCGss ; Alignment reference a 0 551 731 69 97 117 154 62 81 455 601 c 0 1932 1478 4293 617 724 3674 3891 224 2005 1585 g 0 1587 2004 224 3893 3674 724 617 4296 1476 1932 t 0 599 456 83 62 154 117 99 68 733 551

MA0131.3_rc_shift2 (HINFP_rc)
; oligos_6nt_mkv4_m3 versus MA0131.3_rc (HINFP_rc); m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=2; score=0.573534; --GCGGACGy- ; cor=; Ncor= a 0 0 12.0 21.0 3.0 0.0 470.0 10.0 7.0 17.0 0 c 0 0 15.0 472.0 0.0 13.0 0.0 484.0 97.0 217.0 0 g 0 0 395.0 31.0 413.0 404.0 0.0 14.0 388.0 45.0 0 t 0 0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 276.0 0

MA1959.2_shift4 (KLF7)
; oligos_6nt_mkv4_m3 versus MA1959.2 (KLF7); m=2/4; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.45079; ----GGGCGKg ; cor=; Ncor= a 0 0 0 0 1.0 1.0 1.0 45.0 1.0 1.0 150.0 c 0 0 0 0 1.0 1.0 1.0 788.0 1.0 25.0 42.0 g 0 0 0 0 997.0 997.0 997.0 1.0 997.0 720.0 642.0 t 0 0 0 0 1.0 1.0 1.0 167.0 1.0 254.0 167.0

MA1513.2_shift0 (KLF15)
; oligos_6nt_mkv4_m3 versus MA1513.2 (KLF15); m=3/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.447959; cCCCGCCC--- ; cor=; Ncor= a 937.0 40.0 93.0 0.0 0.0 11.0 55.0 12.0 0 0 0 c 6506.0 11234.0 10940.0 11368.0 0.0 11345.0 10954.0 11254.0 0 0 0 g 2117.0 86.0 333.0 1.0 11369.0 2.0 359.0 100.0 0 0 0 t 1809.0 9.0 3.0 0.0 0.0 11.0 1.0 3.0 0 0 0

MA2126.1_shift4 (Zfp961)
; oligos_6nt_mkv4_m3 versus MA2126.1 (Zfp961); m=4/4; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.447569; ----GGGCGCC ; cor=; Ncor= a 0 0 0 0 18.0 13.0 11.0 8.0 23.0 12.0 9.0 c 0 0 0 0 20.0 22.0 13.0 1219.0 8.0 1367.0 1353.0 g 0 0 0 0 1372.0 1312.0 1278.0 9.0 1372.0 23.0 30.0 t 0 0 0 0 8.0 71.0 116.0 182.0 15.0 16.0 26.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m3_shift1 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCGGCCGss ; Alignment reference a 0 551 731 69 97 117 154 62 81 455 601 c 0 1932 1478 4293 617 724 3674 3891 224 2005 1585 g 0 1587 2004 224 3893 3674 724 617 4296 1476 1932 t 0 599 456 83 62 154 117 99 68 733 551
MA0131.3_rc_shift2 (HINFP_rc)				; oligos_6nt_mkv4_m3 versus MA0131.3_rc (HINFP_rc); m=1/4; ncol2=8; w=0; offset=1; strand=R; shift=2; score=0.573534; --GCGGACGy- ; cor=; Ncor= a 0 0 12.0 21.0 3.0 0.0 470.0 10.0 7.0 17.0 0 c 0 0 15.0 472.0 0.0 13.0 0.0 484.0 97.0 217.0 0 g 0 0 395.0 31.0 413.0 404.0 0.0 14.0 388.0 45.0 0 t 0 0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 276.0 0
MA1959.2_shift4 (KLF7)				; oligos_6nt_mkv4_m3 versus MA1959.2 (KLF7); m=2/4; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.45079; ----GGGCGKg ; cor=; Ncor= a 0 0 0 0 1.0 1.0 1.0 45.0 1.0 1.0 150.0 c 0 0 0 0 1.0 1.0 1.0 788.0 1.0 25.0 42.0 g 0 0 0 0 997.0 997.0 997.0 1.0 997.0 720.0 642.0 t 0 0 0 0 1.0 1.0 1.0 167.0 1.0 254.0 167.0
MA1513.2_shift0 (KLF15)				; oligos_6nt_mkv4_m3 versus MA1513.2 (KLF15); m=3/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.447959; cCCCGCCC--- ; cor=; Ncor= a 937.0 40.0 93.0 0.0 0.0 11.0 55.0 12.0 0 0 0 c 6506.0 11234.0 10940.0 11368.0 0.0 11345.0 10954.0 11254.0 0 0 0 g 2117.0 86.0 333.0 1.0 11369.0 2.0 359.0 100.0 0 0 0 t 1809.0 9.0 3.0 0.0 0.0 11.0 1.0 3.0 0 0 0
MA2126.1_shift4 (Zfp961)				; oligos_6nt_mkv4_m3 versus MA2126.1 (Zfp961); m=4/4; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.447569; ----GGGCGCC ; cor=; Ncor= a 0 0 0 0 18.0 13.0 11.0 8.0 23.0 12.0 9.0 c 0 0 0 0 20.0 22.0 13.0 1219.0 8.0 1367.0 1353.0 g 0 0 0 0 1372.0 1312.0 1278.0 9.0 1372.0 23.0 30.0 t 0 0 0 0 8.0 71.0 116.0 182.0 15.0 16.0 26.0