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_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.2025-06-19.085523_2025-06-19.085523_UdMRwA/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=11; shift=1; ncol=12; -gcCAAAATGgm
; Alignment reference
a 0 161 157 46 553 573 579 583 8 32 160 162
c 0 159 189 521 27 12 21 23 24 35 157 171
g 0 188 151 51 39 33 23 24 20 556 182 153
t 0 137 148 27 26 27 22 15 593 22 146 159
|