One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/dyads_m42/peak-motifs_dyads_m42.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -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 Myogenin_Rep1_motifs50/results/discovered_motifs/dyads_m42/peak-motifs_dyads_m42_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m42_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m42_shift3 (dyads_m42dyads_m42)
; dyads_m42 (dyads_m42dyads_m42); m=0 (reference); ncol1=10; shift=3; ncol=15; ---ssAGTGTGks-- ; Alignment reference a 0 0 0 1252 1197 6177 0 0 0 0 0 1163 1165 0 0 c 0 0 0 1711 2638 0 0 0 0 0 0 1342 1639 0 0 g 0 0 0 1813 1775 0 6177 0 6177 0 6177 2117 2138 0 0 t 0 0 0 1401 567 0 0 6177 0 6177 0 1555 1235 0 0

MA1566.1_shift3 (TBX3)
; dyads_m42 versus MA1566.1 (TBX3); m=1/3; ncol2=10; w=10; offset=0; strand=D; shift=3; score=0.70927; ---ragGTGTsaa-- ; cor=; Ncor= a 0 0 0 644.0 2544.0 427.0 6.0 16.0 0.0 115.0 170.0 2544.0 760.0 0 0 c 0 0 0 399.0 481.0 862.0 45.0 735.0 0.0 634.0 1471.0 410.0 586.0 0 0 g 0 0 0 1003.0 1207.0 2544.0 2544.0 0.0 2544.0 155.0 2544.0 947.0 620.0 0 0 t 0 0 0 497.0 760.0 302.0 0.0 2544.0 0.0 2544.0 1112.0 484.0 578.0 0 0

MA1155.1_rc_shift0 (ZSCAN4_rc)
; dyads_m42 versus MA1155.1_rc (ZSCAN4_rc); m=2/3; ncol2=15; w=10; offset=-3; strand=R; shift=0; score=0.531551; tTTtCAGkGTGTGCa ; cor=; Ncor= a 229.0 1.0 6.0 362.0 218.0 1699.0 2.0 8.0 73.0 2.0 0.0 2.0 0.0 0.0 1373.0 c 365.0 2.0 0.0 230.0 1873.0 75.0 0.0 320.0 0.0 2.0 0.0 0.0 1.0 1737.0 112.0 g 200.0 0.0 279.0 107.0 50.0 11.0 1684.0 374.0 1702.0 0.0 1665.0 0.0 1676.0 2.0 383.0 t 1000.0 1269.0 1225.0 1118.0 3.0 8.0 7.0 772.0 3.0 1281.0 0.0 1292.0 0.0 290.0 257.0

MA0673.1_rc_shift1 (NKX2-8_rc)
; dyads_m42 versus MA0673.1_rc (NKX2-8_rc); m=3/3; ncol2=9; w=7; offset=-2; strand=R; shift=1; score=0.454645; -yTsRAGTGs----- ; cor=; Ncor= a 0 811.0 2158.0 271.0 8562.0 8562.0 110.0 516.0 2155.0 249.0 0 0 0 0 0 c 0 2593.0 696.0 4286.0 0.0 0.0 0.0 0.0 0.0 2843.0 0 0 0 0 0 g 0 1964.0 908.0 2267.0 3197.0 91.0 8562.0 595.0 8562.0 3529.0 0 0 0 0 0 t 0 3194.0 8562.0 1738.0 23.0 0.0 14.0 8562.0 70.0 1942.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m42_shift3 (dyads_m42dyads_m42)				; dyads_m42 (dyads_m42dyads_m42); m=0 (reference); ncol1=10; shift=3; ncol=15; ---ssAGTGTGks-- ; Alignment reference a 0 0 0 1252 1197 6177 0 0 0 0 0 1163 1165 0 0 c 0 0 0 1711 2638 0 0 0 0 0 0 1342 1639 0 0 g 0 0 0 1813 1775 0 6177 0 6177 0 6177 2117 2138 0 0 t 0 0 0 1401 567 0 0 6177 0 6177 0 1555 1235 0 0
MA1566.1_shift3 (TBX3)				; dyads_m42 versus MA1566.1 (TBX3); m=1/3; ncol2=10; w=10; offset=0; strand=D; shift=3; score=0.70927; ---ragGTGTsaa-- ; cor=; Ncor= a 0 0 0 644.0 2544.0 427.0 6.0 16.0 0.0 115.0 170.0 2544.0 760.0 0 0 c 0 0 0 399.0 481.0 862.0 45.0 735.0 0.0 634.0 1471.0 410.0 586.0 0 0 g 0 0 0 1003.0 1207.0 2544.0 2544.0 0.0 2544.0 155.0 2544.0 947.0 620.0 0 0 t 0 0 0 497.0 760.0 302.0 0.0 2544.0 0.0 2544.0 1112.0 484.0 578.0 0 0
MA1155.1_rc_shift0 (ZSCAN4_rc)				; dyads_m42 versus MA1155.1_rc (ZSCAN4_rc); m=2/3; ncol2=15; w=10; offset=-3; strand=R; shift=0; score=0.531551; tTTtCAGkGTGTGCa ; cor=; Ncor= a 229.0 1.0 6.0 362.0 218.0 1699.0 2.0 8.0 73.0 2.0 0.0 2.0 0.0 0.0 1373.0 c 365.0 2.0 0.0 230.0 1873.0 75.0 0.0 320.0 0.0 2.0 0.0 0.0 1.0 1737.0 112.0 g 200.0 0.0 279.0 107.0 50.0 11.0 1684.0 374.0 1702.0 0.0 1665.0 0.0 1676.0 2.0 383.0 t 1000.0 1269.0 1225.0 1118.0 3.0 8.0 7.0 772.0 3.0 1281.0 0.0 1292.0 0.0 290.0 257.0
MA0673.1_rc_shift1 (NKX2-8_rc)				; dyads_m42 versus MA0673.1_rc (NKX2-8_rc); m=3/3; ncol2=9; w=7; offset=-2; strand=R; shift=1; score=0.454645; -yTsRAGTGs----- ; cor=; Ncor= a 0 811.0 2158.0 271.0 8562.0 8562.0 110.0 516.0 2155.0 249.0 0 0 0 0 0 c 0 2593.0 696.0 4286.0 0.0 0.0 0.0 0.0 0.0 2843.0 0 0 0 0 0 g 0 1964.0 908.0 2267.0 3197.0 91.0 8562.0 595.0 8562.0 3529.0 0 0 0 0 0 t 0 3194.0 8562.0 1738.0 23.0 0.0 14.0 8562.0 70.0 1942.0 0 0 0 0 0