One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_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_Rep3_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 ; 3 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=12; shift=2; ncol=14; --AmTGArAAAyry
; Alignment reference
a 0 0 139 98 0 2 163 55 163 162 163 14 104 6
c 0 0 4 43 9 0 0 0 0 0 0 103 6 87
g 0 0 14 19 0 160 0 108 0 0 0 0 48 5
t 0 0 6 3 154 1 0 0 0 1 0 46 5 65
|
| MA1549.1_shift0 (POU6F1(var.2)) |
 |
|
|
; dyads_m29 versus MA1549.1 (POU6F1(var.2)); m=1/2; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=0.42953; rTAATGAGst----
; cor=; Ncor=
a 2756.0 164.0 6413.0 6413.0 0.0 67.0 6413.0 314.0 1972.0 1577.0 0 0 0 0
c 416.0 273.0 179.0 0.0 0.0 206.0 96.0 851.0 3065.0 1238.0 0 0 0 0
g 1930.0 10.0 255.0 0.0 298.0 5799.0 0.0 6413.0 3348.0 1534.0 0 0 0 0
t 1312.0 6413.0 0.0 0.0 6413.0 615.0 411.0 1855.0 1462.0 2064.0 0 0 0 0
|
| MA0033.2_shift6 (FOXL1) |
 |
|
|
; dyads_m29 versus MA0033.2 (FOXL1); m=2/2; ncol2=7; w=7; offset=4; strand=D; shift=6; score=0.40889; ------rTAAACA-
; cor=; Ncor=
a 0 0 0 0 0 0 2102.0 10.0 4780.0 4780.0 4780.0 0.0 4780.0 0
c 0 0 0 0 0 0 13.0 416.0 628.0 38.0 82.0 3723.0 54.0 0
g 0 0 0 0 0 0 2678.0 0.0 57.0 0.0 50.0 0.0 0.0 0
t 0 0 0 0 0 0 140.0 4780.0 0.0 15.0 0.0 1057.0 17.0 0
|