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_7nt_m2/peak-motifs_positions_7nt_m2.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_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=16; shift=5; ncol=21; -----gyctGGGCATGTCyrg ; Alignment reference a 0 0 0 0 0 87 95 75 86 98 30 99 7 744 68 11 12 36 94 231 151 c 0 0 0 0 0 149 302 475 169 18 23 12 799 20 17 19 135 612 452 182 198 g 0 0 0 0 0 419 110 166 70 668 740 699 6 18 33 788 19 67 44 240 333 t 0 0 0 0 0 167 315 106 497 38 29 12 10 40 704 4 656 107 232 169 140

MA0106.3_rc_shift0 (TP53_rc)
; positions_7nt_m2 versus MA0106.3_rc (TP53_rc); m=1/4; ncol2=18; w=-5; offset=-5; strand=R; shift=0; score=0.550697; rACATGyCcgGrCATGTy--- ; cor=; Ncor= a 9120.0 17859.0 68.0 17864.0 1155.0 1.0 190.0 1546.0 2118.0 3774.0 2642.0 7106.0 0.0 18893.0 739.0 837.0 735.0 2268.0 0 0 0 c 825.0 116.0 20549.0 89.0 157.0 4.0 8821.0 17846.0 9954.0 2151.0 417.0 109.0 20393.0 137.0 653.0 13.0 2433.0 6563.0 0 0 0 g 9183.0 3338.0 33.0 118.0 250.0 19350.0 26.0 756.0 1474.0 11875.0 17286.0 12014.0 2.0 374.0 204.0 19689.0 116.0 1037.0 0 0 0 t 1472.0 879.0 327.0 1825.0 12925.0 0.0 7104.0 3584.0 3851.0 1145.0 1228.0 244.0 8.0 1710.0 11931.0 45.0 10514.0 7544.0 0 0 0

MA1979.2_shift4 (ZNF416)
; positions_7nt_m2 versus MA1979.2 (ZNF416); m=2/4; ncol2=10; w=-1; offset=-1; strand=D; shift=4; score=0.463425; ----TaTCTGGGCa------- ; cor=; Ncor= a 0 0 0 0 47.0 197.0 48.0 1.0 2.0 1.0 2.0 0.0 4.0 212.0 0 0 0 0 0 0 0 c 0 0 0 0 32.0 25.0 28.0 334.0 6.0 7.0 5.0 1.0 320.0 38.0 0 0 0 0 0 0 0 g 0 0 0 0 26.0 77.0 15.0 7.0 1.0 335.0 335.0 341.0 3.0 29.0 0 0 0 0 0 0 0 t 0 0 0 0 240.0 46.0 254.0 3.0 336.0 2.0 3.0 3.0 18.0 66.0 0 0 0 0 0 0 0

MA0861.2_rc_shift1 (TP73_rc)
; positions_7nt_m2 versus MA0861.2_rc (TP73_rc); m=3/4; ncol2=16; w=-4; offset=-4; strand=R; shift=1; score=0.447563; -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 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 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 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

MA0597.3_shift6 (THAP1)
; positions_7nt_m2 versus MA0597.3 (THAP1); m=4/4; ncol2=8; w=0; offset=1; strand=D; shift=6; score=0.405375; ------gcAGGGCA------- ; cor=; Ncor= a 0 0 0 0 0 0 477.0 553.0 4731.0 22.0 40.0 91.0 98.0 4900.0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 966.0 3351.0 219.0 127.0 183.0 67.0 4861.0 95.0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 3186.0 933.0 220.0 4958.0 4893.0 4942.0 104.0 172.0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 549.0 341.0 8.0 71.0 62.0 78.0 115.0 11.0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=16; shift=5; ncol=21; -----gyctGGGCATGTCyrg ; Alignment reference a 0 0 0 0 0 87 95 75 86 98 30 99 7 744 68 11 12 36 94 231 151 c 0 0 0 0 0 149 302 475 169 18 23 12 799 20 17 19 135 612 452 182 198 g 0 0 0 0 0 419 110 166 70 668 740 699 6 18 33 788 19 67 44 240 333 t 0 0 0 0 0 167 315 106 497 38 29 12 10 40 704 4 656 107 232 169 140
MA0106.3_rc_shift0 (TP53_rc)				; positions_7nt_m2 versus MA0106.3_rc (TP53_rc); m=1/4; ncol2=18; w=-5; offset=-5; strand=R; shift=0; score=0.550697; rACATGyCcgGrCATGTy--- ; cor=; Ncor= a 9120.0 17859.0 68.0 17864.0 1155.0 1.0 190.0 1546.0 2118.0 3774.0 2642.0 7106.0 0.0 18893.0 739.0 837.0 735.0 2268.0 0 0 0 c 825.0 116.0 20549.0 89.0 157.0 4.0 8821.0 17846.0 9954.0 2151.0 417.0 109.0 20393.0 137.0 653.0 13.0 2433.0 6563.0 0 0 0 g 9183.0 3338.0 33.0 118.0 250.0 19350.0 26.0 756.0 1474.0 11875.0 17286.0 12014.0 2.0 374.0 204.0 19689.0 116.0 1037.0 0 0 0 t 1472.0 879.0 327.0 1825.0 12925.0 0.0 7104.0 3584.0 3851.0 1145.0 1228.0 244.0 8.0 1710.0 11931.0 45.0 10514.0 7544.0 0 0 0
MA1979.2_shift4 (ZNF416)				; positions_7nt_m2 versus MA1979.2 (ZNF416); m=2/4; ncol2=10; w=-1; offset=-1; strand=D; shift=4; score=0.463425; ----TaTCTGGGCa------- ; cor=; Ncor= a 0 0 0 0 47.0 197.0 48.0 1.0 2.0 1.0 2.0 0.0 4.0 212.0 0 0 0 0 0 0 0 c 0 0 0 0 32.0 25.0 28.0 334.0 6.0 7.0 5.0 1.0 320.0 38.0 0 0 0 0 0 0 0 g 0 0 0 0 26.0 77.0 15.0 7.0 1.0 335.0 335.0 341.0 3.0 29.0 0 0 0 0 0 0 0 t 0 0 0 0 240.0 46.0 254.0 3.0 336.0 2.0 3.0 3.0 18.0 66.0 0 0 0 0 0 0 0
MA0861.2_rc_shift1 (TP73_rc)				; positions_7nt_m2 versus MA0861.2_rc (TP73_rc); m=3/4; ncol2=16; w=-4; offset=-4; strand=R; shift=1; score=0.447563; -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 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 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 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
MA0597.3_shift6 (THAP1)				; positions_7nt_m2 versus MA0597.3 (THAP1); m=4/4; ncol2=8; w=0; offset=1; strand=D; shift=6; score=0.405375; ------gcAGGGCA------- ; cor=; Ncor= a 0 0 0 0 0 0 477.0 553.0 4731.0 22.0 40.0 91.0 98.0 4900.0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 966.0 3351.0 219.0 127.0 183.0 67.0 4861.0 95.0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 3186.0 933.0 220.0 4958.0 4893.0 4942.0 104.0 172.0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 549.0 341.0 8.0 71.0 62.0 78.0 115.0 11.0 0 0 0 0 0 0 0