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_m1/peak-motifs_positions_6nt_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/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; ycyrGACATGCCCagrc ; Alignment reference a 126 136 150 231 81 622 4 698 32 7 19 18 42 444 101 310 160 c 323 337 218 43 48 21 769 19 14 6 658 726 608 67 153 111 417 g 91 181 144 430 634 139 17 14 19 778 10 15 21 193 475 297 135 t 255 141 283 91 32 13 5 64 730 4 108 36 124 91 66 77 83

MA0106.3_shift4 (TP53)
; positions_6nt_m1 versus MA0106.3 (TP53); m=1/3; ncol2=18; w=0; offset=4; strand=D; shift=4; score=0.529999; ----rACATGyCcgGrC ; cor=; Ncor= a 0 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 c 0 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 g 0 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 t 0 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

MA0861.2_shift5 (TP73)
; positions_6nt_m1 versus MA0861.2 (TP73); m=2/3; ncol2=16; w=0; offset=5; strand=D; shift=5; score=0.436945; -----rCATGTcyrrAC ; cor=; Ncor= a 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 9639.0 0.0 c 0 0 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 441.0 145.0 11703.0 g 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 1414.0 0.0 t 0 0 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0 1002.0 442.0 0.0

MA1979.2_rc_shift8 (ZNF416_rc)
; positions_6nt_m1 versus MA1979.2_rc (ZNF416_rc); m=3/3; ncol2=10; w=0; offset=8; strand=R; shift=8; score=0.432019; --------tGCCCAGAt ; cor=; Ncor= a 0 0 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 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 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 0 0 212.0 4.0 0.0 2.0 1.0 2.0 1.0 48.0 197.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; ycyrGACATGCCCagrc ; Alignment reference a 126 136 150 231 81 622 4 698 32 7 19 18 42 444 101 310 160 c 323 337 218 43 48 21 769 19 14 6 658 726 608 67 153 111 417 g 91 181 144 430 634 139 17 14 19 778 10 15 21 193 475 297 135 t 255 141 283 91 32 13 5 64 730 4 108 36 124 91 66 77 83
MA0106.3_shift4 (TP53)				; positions_6nt_m1 versus MA0106.3 (TP53); m=1/3; ncol2=18; w=0; offset=4; strand=D; shift=4; score=0.529999; ----rACATGyCcgGrC ; cor=; Ncor= a 0 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 c 0 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 g 0 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 t 0 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
MA0861.2_shift5 (TP73)				; positions_6nt_m1 versus MA0861.2 (TP73); m=2/3; ncol2=16; w=0; offset=5; strand=D; shift=5; score=0.436945; -----rCATGTcyrrAC ; cor=; Ncor= a 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 9639.0 0.0 c 0 0 0 0 0 429.0 10829.0 124.0 293.0 28.0 2591.0 8161.0 2940.0 2418.0 441.0 145.0 11703.0 g 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 1414.0 0.0 t 0 0 0 0 0 208.0 0.0 198.0 11480.0 1.0 11892.0 2749.0 4242.0 2457.0 1002.0 442.0 0.0
MA1979.2_rc_shift8 (ZNF416_rc)				; positions_6nt_m1 versus MA1979.2_rc (ZNF416_rc); m=3/3; ncol2=10; w=0; offset=8; strand=R; shift=8; score=0.432019; --------tGCCCAGAt ; cor=; Ncor= a 0 0 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 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 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 0 0 212.0 4.0 0.0 2.0 1.0 2.0 1.0 48.0 197.0