One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_6nt_mkv3_m32/peak-motifs_oligos_6nt_mkv3_m32.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_6nt_mkv3_m32/peak-motifs_oligos_6nt_mkv3_m32_vs_db_jaspar_core_nonredundant_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m32_shift1 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv3_m32_shift1 (oligos_6nt_mkv3_m32oligos_6nt_mkv3_m32) |
 |
|
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; oligos_6nt_mkv3_m32 (oligos_6nt_mkv3_m32oligos_6nt_mkv3_m32); m=0 (reference); ncol1=10; shift=1; ncol=12; -cgCGGCCGcg-
; Alignment reference
a 0 35 22 0 0 1 2 0 0 20 37 0
c 0 119 63 254 10 6 245 244 0 149 63 0
g 0 63 149 0 244 245 6 10 254 63 119 0
t 0 37 20 0 0 2 1 0 0 22 35 0
|
| MA0131.2_shift0 (HINFP) |
 |
|
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; oligos_6nt_mkv3_m32 versus MA0131.2 (HINFP); m=1/1; ncol2=12; w=10; offset=-1; strand=D; shift=0; score=0.599456; 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
|