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_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.2025-06-19.092322_2025-06-19.092322_shBOom/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_shift4 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1) |
 |
|
|
; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----ccCCCCGCCCcy
; Alignment reference
a 0 0 0 0 32 37 9 4 6 3 6 4 5 9 40 31
c 0 0 0 0 81 87 179 190 183 179 50 192 185 182 89 91
g 0 0 0 0 50 44 6 5 10 8 144 5 8 10 33 30
t 0 0 0 0 40 35 9 4 4 13 3 2 5 2 41 51
|