One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m29/peak-motifs_dyads_m29.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_Rep2_motifs50/results/discovered_motifs/dyads_m29/peak-motifs_dyads_m29_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m29_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m29_shift2 (dyads_m29dyads_m29)
; dyads_m29 (dyads_m29dyads_m29); m=0 (reference); ncol1=10; shift=2; ncol=14; --ssCACAGAsv-- ; Alignment reference a 0 0 169 158 0 686 0 684 0 686 135 201 0 0 c 0 0 184 256 686 0 686 1 0 0 191 174 0 0 g 0 0 219 184 0 0 0 1 686 0 242 221 0 0 t 0 0 114 88 0 0 0 0 0 0 118 90 0 0

MA0002.2_rc_shift0 (RUNX1_rc)
; dyads_m29 versus MA0002.2_rc (RUNX1_rc); m=1/3; ncol2=11; w=9; offset=-2; strand=R; shift=0; score=0.61476; waaCCACAram--- ; cor=; Ncor= a 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 0 0 0 c 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 0 0 0 g 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 0 0 0 t 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0 0 0 0

MA1646.1_shift3 (OSR2)
; dyads_m29 versus MA1646.1 (OSR2); m=2/3; ncol2=12; w=9; offset=1; strand=D; shift=3; score=0.50295; ---amaCAGAAGCh ; cor=; Ncor= a 0 0 0 4437.0 4244.0 8520.0 254.0 13599.0 216.0 11678.0 13725.0 416.0 666.0 4386.0 c 0 0 0 3641.0 4206.0 2221.0 13937.0 197.0 229.0 703.0 288.0 170.0 12109.0 4274.0 g 0 0 0 3246.0 3006.0 2117.0 406.0 737.0 14206.0 901.0 516.0 13982.0 841.0 2266.0 t 0 0 0 3484.0 3352.0 1950.0 211.0 275.0 157.0 1526.0 279.0 240.0 1192.0 3882.0

MA1618.1_shift3 (Ptf1a)
; dyads_m29 versus MA1618.1 (Ptf1a); m=3/3; ncol2=13; w=9; offset=1; strand=D; shift=3; score=0.455817; ---dmaCAGATGtt ; cor=; Ncor= a 0 0 0 4092.0 4476.0 8554.0 133.0 14064.0 250.0 12132.0 126.0 241.0 965.0 1511.0 c 0 0 0 2989.0 3662.0 2747.0 14006.0 118.0 466.0 1724.0 224.0 122.0 2058.0 2341.0 g 0 0 0 3661.0 3568.0 2414.0 130.0 153.0 13072.0 437.0 118.0 13868.0 2854.0 2295.0 t 0 0 0 3699.0 2735.0 726.0 172.0 106.0 653.0 148.0 13973.0 210.0 8564.0 8294.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m29_shift2 (dyads_m29dyads_m29)				; dyads_m29 (dyads_m29dyads_m29); m=0 (reference); ncol1=10; shift=2; ncol=14; --ssCACAGAsv-- ; Alignment reference a 0 0 169 158 0 686 0 684 0 686 135 201 0 0 c 0 0 184 256 686 0 686 1 0 0 191 174 0 0 g 0 0 219 184 0 0 0 1 686 0 242 221 0 0 t 0 0 114 88 0 0 0 0 0 0 118 90 0 0
MA0002.2_rc_shift0 (RUNX1_rc)				; dyads_m29 versus MA0002.2_rc (RUNX1_rc); m=1/3; ncol2=11; w=9; offset=-2; strand=R; shift=0; score=0.61476; waaCCACAram--- ; cor=; Ncor= a 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 0 0 0 c 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 0 0 0 g 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 0 0 0 t 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0 0 0 0
MA1646.1_shift3 (OSR2)				; dyads_m29 versus MA1646.1 (OSR2); m=2/3; ncol2=12; w=9; offset=1; strand=D; shift=3; score=0.50295; ---amaCAGAAGCh ; cor=; Ncor= a 0 0 0 4437.0 4244.0 8520.0 254.0 13599.0 216.0 11678.0 13725.0 416.0 666.0 4386.0 c 0 0 0 3641.0 4206.0 2221.0 13937.0 197.0 229.0 703.0 288.0 170.0 12109.0 4274.0 g 0 0 0 3246.0 3006.0 2117.0 406.0 737.0 14206.0 901.0 516.0 13982.0 841.0 2266.0 t 0 0 0 3484.0 3352.0 1950.0 211.0 275.0 157.0 1526.0 279.0 240.0 1192.0 3882.0
MA1618.1_shift3 (Ptf1a)				; dyads_m29 versus MA1618.1 (Ptf1a); m=3/3; ncol2=13; w=9; offset=1; strand=D; shift=3; score=0.455817; ---dmaCAGATGtt ; cor=; Ncor= a 0 0 0 4092.0 4476.0 8554.0 133.0 14064.0 250.0 12132.0 126.0 241.0 965.0 1511.0 c 0 0 0 2989.0 3662.0 2747.0 14006.0 118.0 466.0 1724.0 224.0 122.0 2058.0 2341.0 g 0 0 0 3661.0 3568.0 2414.0 130.0 153.0 13072.0 437.0 118.0 13868.0 2854.0 2295.0 t 0 0 0 3699.0 2735.0 726.0 172.0 106.0 653.0 148.0 13973.0 210.0 8564.0 8294.0