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_m2/peak-motifs_positions_6nt_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_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; crrACATGCCCagrc ; Alignment reference a 187 285 296 736 7 734 37 16 21 45 40 500 88 316 181 c 255 121 111 22 812 36 13 6 725 763 671 68 127 136 454 g 197 310 368 75 18 21 23 809 7 17 12 180 552 296 123 t 207 130 71 13 9 55 773 15 93 21 123 98 79 98 88

MA0106.3_shift2 (TP53)
; positions_6nt_m2 versus MA0106.3 (TP53); m=1/4; ncol2=18; w=0; offset=2; strand=D; shift=2; score=0.594259; --rACATGyCcgGrC ; cor=; Ncor= a 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 c 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 g 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 t 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

MA1979.2_rc_shift6 (ZNF416_rc)
; positions_6nt_m2 versus MA1979.2_rc (ZNF416_rc); m=2/4; ncol2=10; w=0; offset=6; strand=R; shift=6; score=0.494261; ------tGCCCAGAt ; cor=; Ncor= a 0 0 0 0 0 0 66.0 18.0 3.0 3.0 2.0 336.0 3.0 254.0 46.0 c 0 0 0 0 0 0 29.0 3.0 341.0 335.0 335.0 1.0 7.0 15.0 77.0 g 0 0 0 0 0 0 38.0 320.0 1.0 5.0 7.0 6.0 334.0 28.0 25.0 t 0 0 0 0 0 0 212.0 4.0 0.0 2.0 1.0 2.0 1.0 48.0 197.0

MA0861.2_shift3 (TP73)
; positions_6nt_m2 versus MA0861.2 (TP73); m=3/4; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.472395; ---rCATGTcyrrAC ; cor=; Ncor= a 0 0 0 6206.0 0.0 8760.0 3837.0 8.0 130.0 1377.0 2166.0 3488.0 3988.0 9639.0 0.0 c 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 441.0 145.0 11703.0 g 0 0 0 3304.0 0.0 557.0 806.0 11787.0 91.0 783.0 2230.0 3558.0 7797.0 1414.0 0.0 t 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0 1002.0 442.0 0.0

MA0597.3_rc_shift6 (THAP1_rc)
; positions_6nt_m2 versus MA0597.3_rc (THAP1_rc); m=4/4; ncol2=8; w=0; offset=6; strand=R; shift=6; score=0.437377; ------TGCCCTgc- ; cor=; Ncor= a 0 0 0 0 0 0 11.0 115.0 78.0 62.0 71.0 8.0 341.0 549.0 0 c 0 0 0 0 0 0 172.0 104.0 4942.0 4893.0 4958.0 220.0 933.0 3186.0 0 g 0 0 0 0 0 0 95.0 4861.0 67.0 183.0 127.0 219.0 3351.0 966.0 0 t 0 0 0 0 0 0 4900.0 98.0 91.0 40.0 22.0 4731.0 553.0 477.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; crrACATGCCCagrc ; Alignment reference a 187 285 296 736 7 734 37 16 21 45 40 500 88 316 181 c 255 121 111 22 812 36 13 6 725 763 671 68 127 136 454 g 197 310 368 75 18 21 23 809 7 17 12 180 552 296 123 t 207 130 71 13 9 55 773 15 93 21 123 98 79 98 88
MA0106.3_shift2 (TP53)				; positions_6nt_m2 versus MA0106.3 (TP53); m=1/4; ncol2=18; w=0; offset=2; strand=D; shift=2; score=0.594259; --rACATGyCcgGrC ; cor=; Ncor= a 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 c 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 g 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 t 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
MA1979.2_rc_shift6 (ZNF416_rc)				; positions_6nt_m2 versus MA1979.2_rc (ZNF416_rc); m=2/4; ncol2=10; w=0; offset=6; strand=R; shift=6; score=0.494261; ------tGCCCAGAt ; cor=; Ncor= a 0 0 0 0 0 0 66.0 18.0 3.0 3.0 2.0 336.0 3.0 254.0 46.0 c 0 0 0 0 0 0 29.0 3.0 341.0 335.0 335.0 1.0 7.0 15.0 77.0 g 0 0 0 0 0 0 38.0 320.0 1.0 5.0 7.0 6.0 334.0 28.0 25.0 t 0 0 0 0 0 0 212.0 4.0 0.0 2.0 1.0 2.0 1.0 48.0 197.0
MA0861.2_shift3 (TP73)				; positions_6nt_m2 versus MA0861.2 (TP73); m=3/4; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.472395; ---rCATGTcyrrAC ; cor=; Ncor= a 0 0 0 6206.0 0.0 8760.0 3837.0 8.0 130.0 1377.0 2166.0 3488.0 3988.0 9639.0 0.0 c 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 441.0 145.0 11703.0 g 0 0 0 3304.0 0.0 557.0 806.0 11787.0 91.0 783.0 2230.0 3558.0 7797.0 1414.0 0.0 t 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0 1002.0 442.0 0.0
MA0597.3_rc_shift6 (THAP1_rc)				; positions_6nt_m2 versus MA0597.3_rc (THAP1_rc); m=4/4; ncol2=8; w=0; offset=6; strand=R; shift=6; score=0.437377; ------TGCCCTgc- ; cor=; Ncor= a 0 0 0 0 0 0 11.0 115.0 78.0 62.0 71.0 8.0 341.0 549.0 0 c 0 0 0 0 0 0 172.0 104.0 4942.0 4893.0 4958.0 220.0 933.0 3186.0 0 g 0 0 0 0 0 0 95.0 4861.0 67.0 183.0 127.0 219.0 3351.0 966.0 0 t 0 0 0 0 0 0 4900.0 98.0 91.0 40.0 22.0 4731.0 553.0 477.0 0