One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m16/peak-motifs_oligos_6nt_mkv4_m16.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_m16/peak-motifs_oligos_6nt_mkv4_m16_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m16_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m16_shift0 (oligos_6nt_mkv4_m16oligos_6nt_mkv4_m16) |
 |
|
|
; oligos_6nt_mkv4_m16 (oligos_6nt_mkv4_m16oligos_6nt_mkv4_m16); m=0 (reference); ncol1=10; shift=0; ncol=10; ssAAGCTAvv
; Alignment reference
a 358 370 1540 1537 8 7 0 1540 385 395
c 419 454 0 3 2 1523 0 0 396 397
g 469 513 0 0 1528 6 0 0 485 445
t 294 203 0 0 2 4 1540 0 274 303
|
| MA0164.1_rc_shift2 (Nr2e3_rc) |
 |
|
|
; oligos_6nt_mkv4_m16 versus MA0164.1_rc (Nr2e3_rc); m=1/1; ncol2=7; w=7; offset=2; strand=R; shift=2; score=0.53844; --AAGCTTg-
; cor=; Ncor=
a 0 0 23.0 23.0 0.0 0.0 0.0 0.0 5.0 0
c 0 0 0.0 0.0 0.0 22.0 0.0 0.0 2.0 0
g 0 0 0.0 0.0 23.0 1.0 0.0 0.0 12.0 0
t 0 0 0.0 0.0 0.0 0.0 23.0 23.0 4.0 0
|