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.2025-06-19.092718_2025-06-19.092718_Z1kkIg/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5.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.2025-06-19.092718_2025-06-19.092718_Z1kkIg/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift1 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m5_shift1 (oligos_6-8nt_m5) |
 |
|
|
; oligos_6-8nt_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -csCCCATCCCcs
; Alignment reference
a 0 14 14 2 3 1 62 5 1 0 2 16 16
c 0 28 34 70 70 73 7 6 65 67 71 29 20
g 0 16 22 2 0 0 2 7 3 6 2 15 25
t 0 17 5 1 2 1 4 57 6 2 0 15 14
|