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.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_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.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/oligos_6nt_mkv3_m3/peak-motifs_oligos_6nt_mkv3_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift7 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=14; shift=7; ncol=21; -------cyrGACATGTCyrg ; Alignment reference a 0 0 0 0 0 0 0 144 170 237 64 626 9 750 38 5 14 26 105 243 175 c 0 0 0 0 0 0 0 323 259 42 25 8 791 8 19 10 167 700 431 143 172 g 0 0 0 0 0 0 0 173 143 431 700 167 10 19 8 790 8 25 42 260 323 t 0 0 0 0 0 0 0 175 243 105 26 14 5 38 750 10 626 64 237 169 145

MA0861.2_shift11 (TP73)
; oligos_6nt_mkv3_m3 versus MA0861.2 (TP73); m=1/3; ncol2=16; w=0; offset=4; strand=D; shift=11; score=0.474352; -----------rCATGTcyrr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6206.0 0.0 8760.0 3837.0 8.0 130.0 1377.0 2166.0 3488.0 3988.0 c 0 0 0 0 0 0 0 0 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 441.0 g 0 0 0 0 0 0 0 0 0 0 0 3304.0 0.0 557.0 806.0 11787.0 91.0 783.0 2230.0 3558.0 7797.0 t 0 0 0 0 0 0 0 0 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0 1002.0

MA0106.3_rc_shift10 (TP53_rc)
; oligos_6nt_mkv3_m3 versus MA0106.3_rc (TP53_rc); m=2/3; ncol2=18; w=0; offset=3; strand=R; shift=10; score=0.47031; ----------rACATGyCcgG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 9120.0 17859.0 68.0 17864.0 1155.0 1.0 190.0 1546.0 2118.0 3774.0 2642.0 c 0 0 0 0 0 0 0 0 0 0 825.0 116.0 20549.0 89.0 157.0 4.0 8821.0 17846.0 9954.0 2151.0 417.0 g 0 0 0 0 0 0 0 0 0 0 9183.0 3338.0 33.0 118.0 250.0 19350.0 26.0 756.0 1474.0 11875.0 17286.0 t 0 0 0 0 0 0 0 0 0 0 1472.0 879.0 327.0 1825.0 12925.0 0.0 7104.0 3584.0 3851.0 1145.0 1228.0

MA0525.2_shift0 (TP63)
; oligos_6nt_mkv3_m3 versus MA0525.2 (TP63); m=3/3; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.465853; rACATGTygkrACATGTc--- ; cor=; Ncor= a 1586.0 2261.0 0.0 2246.0 692.0 0.0 14.0 97.0 649.0 112.0 993.0 2192.0 0.0 2151.0 75.0 0.0 49.0 701.0 0 0 0 c 26.0 1.0 2533.0 0.0 33.0 0.0 85.0 1025.0 478.0 681.0 1.0 0.0 2788.0 0.0 617.0 0.0 202.0 2099.0 0 0 0 g 997.0 185.0 0.0 76.0 0.0 4021.0 0.0 26.0 2070.0 1656.0 2132.0 48.0 0.0 1.0 8.0 3532.0 1.0 198.0 0 0 0 t 115.0 21.0 0.0 4.0 2353.0 0.0 3025.0 1961.0 13.0 829.0 47.0 45.0 0.0 192.0 2823.0 0.0 3126.0 606.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift7 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=14; shift=7; ncol=21; -------cyrGACATGTCyrg ; Alignment reference a 0 0 0 0 0 0 0 144 170 237 64 626 9 750 38 5 14 26 105 243 175 c 0 0 0 0 0 0 0 323 259 42 25 8 791 8 19 10 167 700 431 143 172 g 0 0 0 0 0 0 0 173 143 431 700 167 10 19 8 790 8 25 42 260 323 t 0 0 0 0 0 0 0 175 243 105 26 14 5 38 750 10 626 64 237 169 145
MA0861.2_shift11 (TP73)				; oligos_6nt_mkv3_m3 versus MA0861.2 (TP73); m=1/3; ncol2=16; w=0; offset=4; strand=D; shift=11; score=0.474352; -----------rCATGTcyrr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6206.0 0.0 8760.0 3837.0 8.0 130.0 1377.0 2166.0 3488.0 3988.0 c 0 0 0 0 0 0 0 0 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 441.0 g 0 0 0 0 0 0 0 0 0 0 0 3304.0 0.0 557.0 806.0 11787.0 91.0 783.0 2230.0 3558.0 7797.0 t 0 0 0 0 0 0 0 0 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0 1002.0
MA0106.3_rc_shift10 (TP53_rc)				; oligos_6nt_mkv3_m3 versus MA0106.3_rc (TP53_rc); m=2/3; ncol2=18; w=0; offset=3; strand=R; shift=10; score=0.47031; ----------rACATGyCcgG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 9120.0 17859.0 68.0 17864.0 1155.0 1.0 190.0 1546.0 2118.0 3774.0 2642.0 c 0 0 0 0 0 0 0 0 0 0 825.0 116.0 20549.0 89.0 157.0 4.0 8821.0 17846.0 9954.0 2151.0 417.0 g 0 0 0 0 0 0 0 0 0 0 9183.0 3338.0 33.0 118.0 250.0 19350.0 26.0 756.0 1474.0 11875.0 17286.0 t 0 0 0 0 0 0 0 0 0 0 1472.0 879.0 327.0 1825.0 12925.0 0.0 7104.0 3584.0 3851.0 1145.0 1228.0
MA0525.2_shift0 (TP63)				; oligos_6nt_mkv3_m3 versus MA0525.2 (TP63); m=3/3; ncol2=18; w=-7; offset=-7; strand=D; shift=0; score=0.465853; rACATGTygkrACATGTc--- ; cor=; Ncor= a 1586.0 2261.0 0.0 2246.0 692.0 0.0 14.0 97.0 649.0 112.0 993.0 2192.0 0.0 2151.0 75.0 0.0 49.0 701.0 0 0 0 c 26.0 1.0 2533.0 0.0 33.0 0.0 85.0 1025.0 478.0 681.0 1.0 0.0 2788.0 0.0 617.0 0.0 202.0 2099.0 0 0 0 g 997.0 185.0 0.0 76.0 0.0 4021.0 0.0 26.0 2070.0 1656.0 2132.0 48.0 0.0 1.0 8.0 3532.0 1.0 198.0 0 0 0 t 115.0 21.0 0.0 4.0 2353.0 0.0 3025.0 1961.0 13.0 829.0 47.0 45.0 0.0 192.0 2823.0 0.0 3126.0 606.0 0 0 0