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.2025-06-19.085523_2025-06-19.085523_UdMRwA/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.2025-06-19.085523_2025-06-19.085523_UdMRwA/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_shift1 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift1 (oligos_6-8nt_m1) |
 |
|
|
; oligos_6-8nt_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -ccCCCtCCCCycc
; Alignment reference
a 0 180 140 33 14 25 49 17 11 25 84 127 130 152
c 0 412 461 868 940 902 227 895 916 900 709 379 428 426
g 0 222 218 54 20 27 77 39 46 37 105 148 238 246
t 0 175 170 34 15 35 636 38 16 27 91 335 193 165
|