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_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.2025-06-19.093845_2025-06-19.093845_bSfSpH/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_shift6 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift6 (oligos_6-8nt_m1) |
 |
|
|
; oligos_6-8nt_m1; m=0 (reference); ncol1=15; shift=6; ncol=21; ------scCGCCGCCGCCscC
; Alignment reference
a 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5
c 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83
g 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18
t 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9
|