One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203809_2026-03-30.203809_WvTw0s/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_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/2026/03/30/peak-motifs.2026-03-30.203809_2026-03-30.203809_WvTw0s/results/discovered_motifs/oligos_7nt_mkv4_m1/peak-motifs_oligos_7nt_mkv4_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -mgCCACTGCmc ; Alignment reference a 0 109 73 14 5 257 5 18 11 13 105 71 c 0 77 75 252 282 10 282 19 15 266 81 95 g 0 68 103 8 4 20 8 8 266 7 44 72 t 0 48 51 28 11 15 7 257 10 16 72 64

MA0130.1_shift1 (ZNF354C)
; oligos_7nt_mkv4_m1 versus MA0130.1 (ZNF354C); m=1/3; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.502344; -mTCCAC----- ; cor=; Ncor= a 0 7.0 3.0 0.0 0.0 16.0 0.0 0 0 0 0 0 c 0 6.0 2.0 16.0 16.0 0.0 15.0 0 0 0 0 0 g 0 3.0 0.0 0.0 0.0 0.0 1.0 0 0 0 0 0 t 0 0.0 11.0 0.0 0.0 0.0 0.0 0 0 0 0 0

MA0002.3_rc_shift0 (Runx1_rc)
; oligos_7nt_mkv4_m1 versus MA0002.3_rc (Runx1_rc); m=2/3; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.467345; waaCCACAr--- ; cor=; Ncor= a 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 0 0 0 c 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 0 0 0 g 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 0 0 0 t 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 0 0 0

MA0100.4_shift3 (MYB)
; oligos_7nt_mkv4_m1 versus MA0100.4 (MYB); m=3/3; ncol2=6; w=0; offset=2; strand=D; shift=3; score=0.412412; ---CAACTG--- ; cor=; Ncor= a 0 0 0 0.0 1478.0 1519.0 0.0 1.0 8.0 0 0 0 c 0 0 0 1513.0 3.0 2.0 1527.0 60.0 3.0 0 0 0 g 0 0 0 5.0 39.0 0.0 0.0 68.0 1516.0 0 0 0 t 0 0 0 9.0 7.0 6.0 0.0 1398.0 0.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift1 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -mgCCACTGCmc ; Alignment reference a 0 109 73 14 5 257 5 18 11 13 105 71 c 0 77 75 252 282 10 282 19 15 266 81 95 g 0 68 103 8 4 20 8 8 266 7 44 72 t 0 48 51 28 11 15 7 257 10 16 72 64
MA0130.1_shift1 (ZNF354C)				; oligos_7nt_mkv4_m1 versus MA0130.1 (ZNF354C); m=1/3; ncol2=6; w=0; offset=0; strand=D; shift=1; score=0.502344; -mTCCAC----- ; cor=; Ncor= a 0 7.0 3.0 0.0 0.0 16.0 0.0 0 0 0 0 0 c 0 6.0 2.0 16.0 16.0 0.0 15.0 0 0 0 0 0 g 0 3.0 0.0 0.0 0.0 0.0 1.0 0 0 0 0 0 t 0 0.0 11.0 0.0 0.0 0.0 0.0 0 0 0 0 0
MA0002.3_rc_shift0 (Runx1_rc)				; oligos_7nt_mkv4_m1 versus MA0002.3_rc (Runx1_rc); m=2/3; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.467345; waaCCACAr--- ; cor=; Ncor= a 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 0 0 0 c 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 0 0 0 g 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 0 0 0 t 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 0 0 0
MA0100.4_shift3 (MYB)				; oligos_7nt_mkv4_m1 versus MA0100.4 (MYB); m=3/3; ncol2=6; w=0; offset=2; strand=D; shift=3; score=0.412412; ---CAACTG--- ; cor=; Ncor= a 0 0 0 0.0 1478.0 1519.0 0.0 1.0 8.0 0 0 0 c 0 0 0 1513.0 3.0 2.0 1527.0 60.0 3.0 0 0 0 g 0 0 0 5.0 39.0 0.0 0.0 68.0 1516.0 0 0 0 t 0 0 0 9.0 7.0 6.0 0.0 1398.0 0.0 0 0 0