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.2025-06-19.093845_2025-06-19.093845_bSfSpH/results/discovered_motifs/oligos_6-8nt_m4/peak-motifs_oligos_6-8nt_m4.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.2025-06-19.093845_2025-06-19.093845_bSfSpH/results/discovered_motifs/oligos_6-8nt_m4/peak-motifs_oligos_6-8nt_m4_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift7 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift7 (oligos_6-8nt_m4) |
 |
|
|
; oligos_6-8nt_m4; m=0 (reference); ncol1=17; shift=7; ncol=24; -------CsCCsCCGCCGCCGCCs
; Alignment reference
a 0 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21
c 0 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33
g 0 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63
t 0 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7
|