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.2025-06-19.091929_2025-06-19.091929_ZGCM7J/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.2025-06-19.091929_2025-06-19.091929_ZGCM7J/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_shift5 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m3_shift5 (oligos_6-8nt_m3) |
 |
|
|
; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=5; ncol=17; -----ssCCCCGCCCcs
; Alignment reference
a 0 0 0 0 0 58 58 11 14 14 13 15 6 7 7 61 48
c 0 0 0 0 0 110 114 282 280 281 275 42 292 286 291 121 118
g 0 0 0 0 0 91 94 14 15 11 9 244 11 10 14 58 95
t 0 0 0 0 0 56 49 8 6 9 18 14 6 12 3 75 54
|