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/positions_6nt_m4/peak-motifs_positions_6nt_m4.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/positions_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift6 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift6 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=16; shift=6; ncol=22; ------ycygGACATGTCcrgr ; Alignment reference a 0 0 0 0 0 0 97 140 122 176 66 547 13 695 31 7 15 32 69 327 139 278 c 0 0 0 0 0 0 272 302 192 31 20 10 714 7 12 11 173 627 469 105 163 98 g 0 0 0 0 0 0 98 164 105 469 627 173 11 12 7 713 10 20 31 192 302 272 t 0 0 0 0 0 0 278 139 326 69 32 15 7 31 695 14 547 66 176 121 141 97

MA0106.3_shift0 (TP53)
; positions_6nt_m4 versus MA0106.3 (TP53); m=1/3; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.485533; rACATGyCcgGrCATGTy---- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA0861.2_rc_shift1 (TP73_rc)
; positions_6nt_m4 versus MA0861.2_rc (TP73_rc); m=2/3; ncol2=16; w=-5; offset=-5; strand=R; shift=1; score=0.47143; -rCrTGTyyrgACATGy----- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA0525.2_shift0 (TP63)
; positions_6nt_m4 versus MA0525.2 (TP63); m=3/3; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.454378; 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 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 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 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 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m4_shift6 (positions_6nt_m4)				; positions_6nt_m4; m=0 (reference); ncol1=16; shift=6; ncol=22; ------ycygGACATGTCcrgr ; Alignment reference a 0 0 0 0 0 0 97 140 122 176 66 547 13 695 31 7 15 32 69 327 139 278 c 0 0 0 0 0 0 272 302 192 31 20 10 714 7 12 11 173 627 469 105 163 98 g 0 0 0 0 0 0 98 164 105 469 627 173 11 12 7 713 10 20 31 192 302 272 t 0 0 0 0 0 0 278 139 326 69 32 15 7 31 695 14 547 66 176 121 141 97
MA0106.3_shift0 (TP53)				; positions_6nt_m4 versus MA0106.3 (TP53); m=1/3; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.485533; rACATGyCcgGrCATGTy---- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA0861.2_rc_shift1 (TP73_rc)				; positions_6nt_m4 versus MA0861.2_rc (TP73_rc); m=2/3; ncol2=16; w=-5; offset=-5; strand=R; shift=1; score=0.47143; -rCrTGTyyrgACATGy----- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA0525.2_shift0 (TP63)				; positions_6nt_m4 versus MA0525.2 (TP63); m=3/3; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.454378; 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 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 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 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 0