One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m25/peak-motifs_oligos_7nt_mkv4_m25.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/oligos_7nt_mkv4_m25/peak-motifs_oligos_7nt_mkv4_m25_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m25_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv4_m25_shift0 (oligos_7nt_mkv4_m25oligos_7nt_mkv4_m25) |
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; oligos_7nt_mkv4_m25 (oligos_7nt_mkv4_m25oligos_7nt_mkv4_m25); m=0 (reference); ncol1=12; shift=0; ncol=12; ssCAAGCTTGsc
; Alignment reference
a 11 10 2 54 55 2 1 0 0 1 7 10
c 15 18 51 0 2 0 54 0 3 2 22 22
g 21 22 2 3 0 54 0 2 0 52 18 14
t 10 7 2 0 0 1 2 55 54 2 10 11
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| MA0164.1_shift2 (Nr2e3) |
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; oligos_7nt_mkv4_m25 versus MA0164.1 (Nr2e3); m=1/1; ncol2=7; w=7; offset=2; strand=D; shift=2; score=0.569259; --cAAGCTT---
; cor=; Ncor=
a 0 0 4.0 23.0 23.0 0.0 0.0 0.0 0.0 0 0 0
c 0 0 12.0 0.0 0.0 1.0 23.0 0.0 0.0 0 0 0
g 0 0 2.0 0.0 0.0 22.0 0.0 0.0 0.0 0 0 0
t 0 0 5.0 0.0 0.0 0.0 0.0 23.0 23.0 0 0 0
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