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.2025-06-19.093845_2025-06-19.093845_bSfSpH/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2.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.2025-06-19.093845_2025-06-19.093845_bSfSpH/results/discovered_motifs/oligos_6-8nt_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift4 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m2_shift4 (oligos_6-8nt_m2) |
 |
|
|
; oligos_6-8nt_m2; m=0 (reference); ncol1=23; shift=4; ncol=27; ----CgCCsCCryCsCCGCCGCCGCCv
; Alignment reference
a 0 0 0 0 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12
c 0 0 0 0 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11
g 0 0 0 0 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18
t 0 0 0 0 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2
|