One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_6nt_mkv2_m3/peak-motifs_oligos_6nt_mkv2_m3_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift2 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3) |
 |
|
|
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --wrAGATAGwd
; Alignment reference
a 0 0 16 19 48 0 52 0 46 0 21 15
c 0 0 5 3 2 0 0 0 5 0 5 7
g 0 0 12 18 2 52 0 1 0 52 10 15
t 0 0 19 12 0 0 0 51 1 0 16 15
|