One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift2 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_8nt_mkv2_m1_shift2 (oligos_8nt_mkv2_m1) |
 |
|
|
; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --wyCTTACTACww
; Alignment reference
a 0 0 17 9 1 3 1 40 2 2 43 2 17 20
c 0 0 6 12 43 1 3 1 38 1 1 40 8 4
g 0 0 4 5 1 0 0 1 2 1 1 2 2 2
t 0 0 19 20 1 42 42 4 4 42 1 2 19 20
|