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.2025-06-19.092322_2025-06-19.092322_shBOom/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3.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.2025-06-19.092322_2025-06-19.092322_shBOom/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift1 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3) |
 |
|
|
; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -cgCCAGCAGCms
; Alignment reference
a 0 20 33 3 6 129 6 3 119 5 1 36 21
c 0 60 32 113 127 5 6 137 7 4 131 38 46
g 0 34 47 21 6 3 125 2 9 133 6 35 52
t 0 28 30 5 3 5 5 0 7 0 4 33 23
|