One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m30/peak-motifs_oligos_6nt_mkv4_m30.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/oligos_6nt_mkv4_m30/peak-motifs_oligos_6nt_mkv4_m30_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m30_shift1 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m30_shift1 (oligos_6nt_mkv4_m30oligos_6nt_mkv4_m30) |
 |
|
|
; oligos_6nt_mkv4_m30 (oligos_6nt_mkv4_m30oligos_6nt_mkv4_m30); m=0 (reference); ncol1=10; shift=1; ncol=12; -ssCGACCGss-
; Alignment reference
a 0 205 152 0 0 1270 0 0 0 222 219 0
c 0 414 424 1270 0 0 1260 1269 0 580 400 0
g 0 477 583 0 1270 0 0 1 1270 330 450 0
t 0 174 111 0 0 0 10 0 0 138 201 0
|
| MA0131.2_shift0 (HINFP) |
 |
|
|
; oligos_6nt_mkv4_m30 versus MA0131.2 (HINFP); m=1/1; ncol2=12; w=10; offset=-1; strand=D; shift=0; score=0.583426; carCGTCCGCgk
; cor=; Ncor=
a 23.0 285.0 276.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 85.0 77.0
c 340.0 131.0 45.0 388.0 14.0 0.0 404.0 413.0 31.0 395.0 55.0 84.0
g 106.0 113.0 217.0 97.0 484.0 0.0 13.0 0.0 472.0 15.0 188.0 154.0
t 100.0 53.0 17.0 7.0 10.0 470.0 0.0 3.0 21.0 12.0 97.0 107.0
|