One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.092836_2025-06-19.092836_d6nk31/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_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/2025/06/19/peak-motifs.2025-06-19.092836_2025-06-19.092836_d6nk31/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift1 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3) |
 |
|
|
; oligos_6-8nt_m3; m=0 (reference); ncol1=15; shift=1; ncol=16; -bsCCCATGCAvmsvc
; Alignment reference
a 0 13 13 3 5 2 74 3 2 1 70 28 24 15 22 10
c 0 26 28 70 71 77 3 1 6 78 5 24 22 25 23 37
g 0 22 24 3 3 3 1 1 74 1 6 22 18 24 23 19
t 0 21 17 6 3 0 4 77 0 2 1 8 18 18 14 16
|