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_m4/peak-motifs_oligos_8nt_mkv2_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m4_shift4 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_8nt_mkv2_m4_shift4 (oligos_8nt_mkv2_m4) |
 |
|
|
; oligos_8nt_mkv2_m4; m=0 (reference); ncol1=12; shift=4; ncol=16; ----wwGTGACAGAkw
; Alignment reference
a 0 0 0 0 18 13 3 1 1 34 4 35 3 36 9 13
c 0 0 0 0 4 3 0 2 0 0 30 1 2 1 1 5
g 0 0 0 0 5 6 35 2 37 2 3 2 34 0 15 9
t 0 0 0 0 12 17 1 34 1 3 2 1 0 2 14 12
|