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_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/2026/01/05/peak-motifs.2026-01-05.052000_2026-01-05.052000_2qIqyX/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 ; 5 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=24; shift=0; ncol=24; skrGrCATGyCCrGrCATGyCyms ; Alignment reference a 110 103 155 91 354 5 435 53 5 15 25 27 331 33 196 3 497 106 20 26 44 66 171 123 c 149 139 33 22 15 542 20 8 2 387 508 390 16 7 6 565 22 17 11 196 420 315 154 180 g 202 163 304 416 178 9 17 22 563 4 5 13 192 513 358 3 10 28 535 22 25 38 136 156 t 112 168 81 44 26 17 101 490 3 167 35 143 34 20 13 2 44 422 7 329 84 154 112 114

MA0106.3_shift3 (TP53)
; oligos_6nt_mkv3_m1 versus MA0106.3 (TP53); m=1/4; ncol2=18; w=0; offset=3; strand=D; shift=3; score=0.70851; ---rACATGyCcgGrCATGTy--- ; cor=; Ncor= a 0 0 0 7544.0 10514.0 45.0 11931.0 1710.0 8.0 244.0 1228.0 1145.0 3851.0 3584.0 7104.0 0.0 12925.0 1825.0 327.0 879.0 1472.0 0 0 0 c 0 0 0 1037.0 116.0 19689.0 204.0 374.0 2.0 12014.0 17286.0 11875.0 1474.0 756.0 26.0 19350.0 250.0 118.0 33.0 3338.0 9183.0 0 0 0 g 0 0 0 6563.0 2433.0 13.0 653.0 137.0 20393.0 109.0 417.0 2151.0 9954.0 17846.0 8821.0 4.0 157.0 89.0 20549.0 116.0 825.0 0 0 0 t 0 0 0 2268.0 735.0 837.0 739.0 18893.0 0.0 7106.0 2642.0 3774.0 2118.0 1546.0 190.0 1.0 1155.0 17864.0 68.0 17859.0 9120.0 0 0 0

MA0861.2_rc_shift4 (TP73_rc)
; oligos_6nt_mkv3_m1 versus MA0861.2_rc (TP73_rc); m=2/4; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.568857; ----rCrTGTyyrgACATGy---- ; cor=; Ncor= a 0 0 0 0 6995.0 39.0 8476.0 2302.0 0.0 442.0 1002.0 2457.0 4242.0 2749.0 11892.0 1.0 11480.0 198.0 0.0 208.0 0 0 0 0 c 0 0 0 0 181.0 13026.0 130.0 279.0 0.0 1414.0 7797.0 3558.0 2230.0 783.0 91.0 11787.0 806.0 557.0 0.0 3304.0 0 0 0 0 g 0 0 0 0 6944.0 170.0 5965.0 143.0 11703.0 145.0 441.0 2418.0 2940.0 8161.0 2591.0 28.0 293.0 124.0 10829.0 429.0 0 0 0 0 t 0 0 0 0 993.0 16.0 256.0 10125.0 0.0 9639.0 3988.0 3488.0 2166.0 1377.0 130.0 8.0 3837.0 8760.0 0.0 6206.0 0 0 0 0

MA0525.2_rc_shift3 (TP63_rc)
; oligos_6nt_mkv3_m1 versus MA0525.2_rc (TP63_rc); m=3/4; ncol2=18; w=0; offset=3; strand=R; shift=3; score=0.561194; ---gACATGTymcrACATGTy--- ; cor=; Ncor= a 0 0 0 606.0 3126.0 0.0 2823.0 192.0 0.0 45.0 47.0 829.0 13.0 1961.0 3025.0 0.0 2353.0 4.0 0.0 21.0 115.0 0 0 0 c 0 0 0 198.0 1.0 3532.0 8.0 1.0 0.0 48.0 2132.0 1656.0 2070.0 26.0 0.0 4021.0 0.0 76.0 0.0 185.0 997.0 0 0 0 g 0 0 0 2099.0 202.0 0.0 617.0 0.0 2788.0 0.0 1.0 681.0 478.0 1025.0 85.0 0.0 33.0 0.0 2533.0 1.0 26.0 0 0 0 t 0 0 0 701.0 49.0 0.0 75.0 2151.0 0.0 2192.0 993.0 112.0 649.0 97.0 14.0 0.0 692.0 2246.0 0.0 2261.0 1586.0 0 0 0

MA1719.2_rc_shift10 (ZNF816_rc)
; oligos_6nt_mkv3_m1 versus MA1719.2_rc (ZNF816_rc); m=4/4; ncol2=15; w=0; offset=10; strand=R; shift=10; score=0.400896; ----------cCcwgCATGTCCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 118.0 82.0 193.0 265.0 252.0 39.0 810.0 35.0 6.0 3.0 6.0 5.0 4.0 12.0 c 0 0 0 0 0 0 0 0 0 0 683.0 732.0 508.0 174.0 53.0 949.0 111.0 89.0 13.0 10.0 1020.0 1035.0 1033.0 1006.0 g 0 0 0 0 0 0 0 0 0 0 126.0 90.0 106.0 210.0 612.0 27.0 85.0 143.0 1015.0 3.0 12.0 6.0 6.0 4.0 t 0 0 0 0 0 0 0 0 0 0 126.0 149.0 246.0 404.0 136.0 38.0 47.0 786.0 19.0 1037.0 15.0 7.0 10.0 31.0

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=24; shift=0; ncol=24; skrGrCATGyCCrGrCATGyCyms ; Alignment reference a 110 103 155 91 354 5 435 53 5 15 25 27 331 33 196 3 497 106 20 26 44 66 171 123 c 149 139 33 22 15 542 20 8 2 387 508 390 16 7 6 565 22 17 11 196 420 315 154 180 g 202 163 304 416 178 9 17 22 563 4 5 13 192 513 358 3 10 28 535 22 25 38 136 156 t 112 168 81 44 26 17 101 490 3 167 35 143 34 20 13 2 44 422 7 329 84 154 112 114
MA0106.3_shift3 (TP53)				; oligos_6nt_mkv3_m1 versus MA0106.3 (TP53); m=1/4; ncol2=18; w=0; offset=3; strand=D; shift=3; score=0.70851; ---rACATGyCcgGrCATGTy--- ; cor=; Ncor= a 0 0 0 7544.0 10514.0 45.0 11931.0 1710.0 8.0 244.0 1228.0 1145.0 3851.0 3584.0 7104.0 0.0 12925.0 1825.0 327.0 879.0 1472.0 0 0 0 c 0 0 0 1037.0 116.0 19689.0 204.0 374.0 2.0 12014.0 17286.0 11875.0 1474.0 756.0 26.0 19350.0 250.0 118.0 33.0 3338.0 9183.0 0 0 0 g 0 0 0 6563.0 2433.0 13.0 653.0 137.0 20393.0 109.0 417.0 2151.0 9954.0 17846.0 8821.0 4.0 157.0 89.0 20549.0 116.0 825.0 0 0 0 t 0 0 0 2268.0 735.0 837.0 739.0 18893.0 0.0 7106.0 2642.0 3774.0 2118.0 1546.0 190.0 1.0 1155.0 17864.0 68.0 17859.0 9120.0 0 0 0
MA0861.2_rc_shift4 (TP73_rc)				; oligos_6nt_mkv3_m1 versus MA0861.2_rc (TP73_rc); m=2/4; ncol2=16; w=0; offset=4; strand=R; shift=4; score=0.568857; ----rCrTGTyyrgACATGy---- ; cor=; Ncor= a 0 0 0 0 6995.0 39.0 8476.0 2302.0 0.0 442.0 1002.0 2457.0 4242.0 2749.0 11892.0 1.0 11480.0 198.0 0.0 208.0 0 0 0 0 c 0 0 0 0 181.0 13026.0 130.0 279.0 0.0 1414.0 7797.0 3558.0 2230.0 783.0 91.0 11787.0 806.0 557.0 0.0 3304.0 0 0 0 0 g 0 0 0 0 6944.0 170.0 5965.0 143.0 11703.0 145.0 441.0 2418.0 2940.0 8161.0 2591.0 28.0 293.0 124.0 10829.0 429.0 0 0 0 0 t 0 0 0 0 993.0 16.0 256.0 10125.0 0.0 9639.0 3988.0 3488.0 2166.0 1377.0 130.0 8.0 3837.0 8760.0 0.0 6206.0 0 0 0 0
MA0525.2_rc_shift3 (TP63_rc)				; oligos_6nt_mkv3_m1 versus MA0525.2_rc (TP63_rc); m=3/4; ncol2=18; w=0; offset=3; strand=R; shift=3; score=0.561194; ---gACATGTymcrACATGTy--- ; cor=; Ncor= a 0 0 0 606.0 3126.0 0.0 2823.0 192.0 0.0 45.0 47.0 829.0 13.0 1961.0 3025.0 0.0 2353.0 4.0 0.0 21.0 115.0 0 0 0 c 0 0 0 198.0 1.0 3532.0 8.0 1.0 0.0 48.0 2132.0 1656.0 2070.0 26.0 0.0 4021.0 0.0 76.0 0.0 185.0 997.0 0 0 0 g 0 0 0 2099.0 202.0 0.0 617.0 0.0 2788.0 0.0 1.0 681.0 478.0 1025.0 85.0 0.0 33.0 0.0 2533.0 1.0 26.0 0 0 0 t 0 0 0 701.0 49.0 0.0 75.0 2151.0 0.0 2192.0 993.0 112.0 649.0 97.0 14.0 0.0 692.0 2246.0 0.0 2261.0 1586.0 0 0 0
MA1719.2_rc_shift10 (ZNF816_rc)				; oligos_6nt_mkv3_m1 versus MA1719.2_rc (ZNF816_rc); m=4/4; ncol2=15; w=0; offset=10; strand=R; shift=10; score=0.400896; ----------cCcwgCATGTCCCC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 118.0 82.0 193.0 265.0 252.0 39.0 810.0 35.0 6.0 3.0 6.0 5.0 4.0 12.0 c 0 0 0 0 0 0 0 0 0 0 683.0 732.0 508.0 174.0 53.0 949.0 111.0 89.0 13.0 10.0 1020.0 1035.0 1033.0 1006.0 g 0 0 0 0 0 0 0 0 0 0 126.0 90.0 106.0 210.0 612.0 27.0 85.0 143.0 1015.0 3.0 12.0 6.0 6.0 4.0 t 0 0 0 0 0 0 0 0 0 0 126.0 149.0 246.0 404.0 136.0 38.0 47.0 786.0 19.0 1037.0 15.0 7.0 10.0 31.0