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_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.2025-06-19.092836_2025-06-19.092836_d6nk31/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_shift5 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m2_shift5 (oligos_6-8nt_m2) |
 |
|
|
; oligos_6-8nt_m2; m=0 (reference); ncol1=12; shift=5; ncol=17; -----msAACCTGCCrs
; Alignment reference
a 0 0 0 0 0 15 11 40 42 1 3 1 0 1 3 15 7
c 0 0 0 0 0 15 17 4 2 44 44 2 3 43 40 11 16
g 0 0 0 0 0 6 12 1 3 2 0 2 44 3 2 14 13
t 0 0 0 0 0 11 7 2 0 0 0 42 0 0 2 7 11
|