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_m4/peak-motifs_positions_7nt_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_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift7 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift7 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=15; shift=7; ncol=22; -------cyrGGCATGTCTggr ; Alignment reference a 0 0 0 0 0 0 0 87 99 288 33 94 7 571 24 9 8 17 45 86 141 191 c 0 0 0 0 0 0 0 265 237 22 10 7 587 13 14 6 79 507 112 64 84 55 g 0 0 0 0 0 0 0 146 82 255 553 507 12 7 14 593 7 37 30 372 280 296 t 0 0 0 0 0 0 0 118 198 51 20 8 10 25 564 8 522 55 429 94 111 74

MA0861.2_shift11 (TP73)
; positions_7nt_m4 versus MA0861.2 (TP73); m=1/6; ncol2=16; w=0; offset=4; strand=D; shift=11; score=0.463236; -----------rCATGTcyrrA ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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

MA0106.3_rc_shift0 (TP53_rc)
; positions_7nt_m4 versus MA0106.3_rc (TP53_rc); m=2/6; ncol2=18; w=-7; offset=-7; strand=R; shift=0; score=0.457527; 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 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 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 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 0

MA0090.4_rc_shift8 (TEAD1_rc)
; positions_7nt_m4 versus MA0090.4_rc (TEAD1_rc); m=3/6; ncol2=9; w=0; offset=1; strand=R; shift=8; score=0.426799; --------CTGGAATGT----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7203.0 9428.0 1687.0 1332.0 63590.0 68517.0 700.0 1103.0 1941.0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 47856.0 2051.0 374.0 765.0 1210.0 646.0 946.0 1923.0 9179.0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 6215.0 1729.0 67635.0 66953.0 622.0 700.0 646.0 61276.0 1248.0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 9124.0 57190.0 702.0 1348.0 4976.0 535.0 68106.0 6096.0 58030.0 0 0 0 0 0

MA0739.2_rc_shift7 (Hic1_rc)
; positions_7nt_m4 versus MA0739.2_rc (Hic1_rc); m=4/6; ncol2=8; w=0; offset=0; strand=R; shift=7; score=0.409433; -------GtTGGCAy------- ; cor=; Ncor= a 0 0 0 0 0 0 0 1488.0 614.0 317.0 68.0 0.0 183.0 11007.0 666.0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1629.0 2267.0 3.0 31.0 121.0 11007.0 73.0 4670.0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 11007.0 1986.0 1999.0 11007.0 11007.0 588.0 422.0 719.0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 1220.0 6140.0 9008.0 88.0 50.0 950.0 62.0 6337.0 0 0 0 0 0 0 0

MA0808.1_rc_shift9 (TEAD3_rc)
; positions_7nt_m4 versus MA0808.1_rc (TEAD3_rc); m=5/6; ncol2=8; w=0; offset=2; strand=R; shift=9; score=0.403587; ---------wGGAATGy----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 13663.0 4.0 0.0 16878.0 21444.0 0.0 0.0 1109.0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 8654.0 0.0 0.0 969.0 0.0 0.0 441.0 8913.0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 1039.0 21444.0 21444.0 23.0 0.0 0.0 18920.0 66.0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 21444.0 0.0 0.0 4566.0 0.0 21444.0 2524.0 12530.0 0 0 0 0 0

MA1153.2_shift14 (Smad4)
; positions_7nt_m4 versus MA1153.2 (Smad4); m=6/6; ncol2=7; w=0; offset=7; strand=D; shift=14; score=0.403531; --------------yGTCTrG- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88.0 0.0 0.0 0.0 0.0 596.0 0.0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 250.0 0.0 0.0 1000.0 0.0 0.0 0.0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 81.0 1000.0 0.0 0.0 0.0 404.0 1000.0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 581.0 0.0 1000.0 0.0 1000.0 0.0 0.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift7 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=15; shift=7; ncol=22; -------cyrGGCATGTCTggr ; Alignment reference a 0 0 0 0 0 0 0 87 99 288 33 94 7 571 24 9 8 17 45 86 141 191 c 0 0 0 0 0 0 0 265 237 22 10 7 587 13 14 6 79 507 112 64 84 55 g 0 0 0 0 0 0 0 146 82 255 553 507 12 7 14 593 7 37 30 372 280 296 t 0 0 0 0 0 0 0 118 198 51 20 8 10 25 564 8 522 55 429 94 111 74
MA0861.2_shift11 (TP73)				; positions_7nt_m4 versus MA0861.2 (TP73); m=1/6; ncol2=16; w=0; offset=4; strand=D; shift=11; score=0.463236; -----------rCATGTcyrrA ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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
MA0106.3_rc_shift0 (TP53_rc)				; positions_7nt_m4 versus MA0106.3_rc (TP53_rc); m=2/6; ncol2=18; w=-7; offset=-7; strand=R; shift=0; score=0.457527; 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 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 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 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 0
MA0090.4_rc_shift8 (TEAD1_rc)				; positions_7nt_m4 versus MA0090.4_rc (TEAD1_rc); m=3/6; ncol2=9; w=0; offset=1; strand=R; shift=8; score=0.426799; --------CTGGAATGT----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 7203.0 9428.0 1687.0 1332.0 63590.0 68517.0 700.0 1103.0 1941.0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 47856.0 2051.0 374.0 765.0 1210.0 646.0 946.0 1923.0 9179.0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 6215.0 1729.0 67635.0 66953.0 622.0 700.0 646.0 61276.0 1248.0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 9124.0 57190.0 702.0 1348.0 4976.0 535.0 68106.0 6096.0 58030.0 0 0 0 0 0
MA0739.2_rc_shift7 (Hic1_rc)				; positions_7nt_m4 versus MA0739.2_rc (Hic1_rc); m=4/6; ncol2=8; w=0; offset=0; strand=R; shift=7; score=0.409433; -------GtTGGCAy------- ; cor=; Ncor= a 0 0 0 0 0 0 0 1488.0 614.0 317.0 68.0 0.0 183.0 11007.0 666.0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1629.0 2267.0 3.0 31.0 121.0 11007.0 73.0 4670.0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 11007.0 1986.0 1999.0 11007.0 11007.0 588.0 422.0 719.0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 1220.0 6140.0 9008.0 88.0 50.0 950.0 62.0 6337.0 0 0 0 0 0 0 0
MA0808.1_rc_shift9 (TEAD3_rc)				; positions_7nt_m4 versus MA0808.1_rc (TEAD3_rc); m=5/6; ncol2=8; w=0; offset=2; strand=R; shift=9; score=0.403587; ---------wGGAATGy----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 13663.0 4.0 0.0 16878.0 21444.0 0.0 0.0 1109.0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 8654.0 0.0 0.0 969.0 0.0 0.0 441.0 8913.0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 1039.0 21444.0 21444.0 23.0 0.0 0.0 18920.0 66.0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 21444.0 0.0 0.0 4566.0 0.0 21444.0 2524.0 12530.0 0 0 0 0 0
MA1153.2_shift14 (Smad4)				; positions_7nt_m4 versus MA1153.2 (Smad4); m=6/6; ncol2=7; w=0; offset=7; strand=D; shift=14; score=0.403531; --------------yGTCTrG- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88.0 0.0 0.0 0.0 0.0 596.0 0.0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 250.0 0.0 0.0 1000.0 0.0 0.0 0.0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 81.0 1000.0 0.0 0.0 0.0 404.0 1000.0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 581.0 0.0 1000.0 0.0 1000.0 0.0 0.0 0