One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m26/peak-motifs_oligos_6nt_mkv4_m26.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_m26/peak-motifs_oligos_6nt_mkv4_m26_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m26_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m26_shift0 (oligos_6nt_mkv4_m26oligos_6nt_mkv4_m26) |
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; oligos_6nt_mkv4_m26 (oligos_6nt_mkv4_m26oligos_6nt_mkv4_m26); m=0 (reference); ncol1=10; shift=0; ncol=10; ssAAGCTTss
; Alignment reference
a 511 544 2228 2228 0 0 0 0 263 409
c 610 702 0 0 0 2228 0 0 719 698
g 698 719 0 0 2228 0 0 0 702 610
t 409 263 0 0 0 0 2228 2228 544 511
|
| MA0164.1_shift1 (Nr2e3) |
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; oligos_6nt_mkv4_m26 versus MA0164.1 (Nr2e3); m=1/1; ncol2=7; w=7; offset=1; strand=D; shift=1; score=0.690961; -cAAGCTT--
; cor=; Ncor=
a 0 4.0 23.0 23.0 0.0 0.0 0.0 0.0 0 0
c 0 12.0 0.0 0.0 1.0 23.0 0.0 0.0 0 0
g 0 2.0 0.0 0.0 22.0 0.0 0.0 0.0 0 0
t 0 5.0 0.0 0.0 0.0 0.0 23.0 23.0 0 0
|