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_m1/peak-motifs_oligos_6-8nt_m1.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_m1/peak-motifs_oligos_6-8nt_m1_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift1 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift1 (oligos_6-8nt_m1) |
 |
|
|
; oligos_6-8nt_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -ssCCCATGCAAks
; Alignment reference
a 0 8 8 1 4 2 43 0 2 0 42 32 11 10
c 0 12 19 42 40 39 0 0 5 42 2 4 9 14
g 0 15 12 1 1 3 0 1 38 0 1 8 12 13
t 0 10 6 1 0 1 2 44 0 3 0 1 13 8
|