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_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.2025-06-19.091929_2025-06-19.091929_ZGCM7J/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_shift3 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift3 (oligos_6-8nt_m4) |
 |
|
|
; oligos_6-8nt_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---yvTACCGTAss
; Alignment reference
a 0 0 0 28 43 5 137 0 9 3 7 133 29 35
c 0 0 0 52 40 8 3 147 124 7 8 7 51 43
g 0 0 0 36 42 5 11 5 15 142 7 12 41 45
t 0 0 0 41 32 139 6 5 9 5 135 5 36 34
|