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/dyads_m4/peak-motifs_dyads_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/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: dyads_m4_shift7 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m4_shift7 (dyads_m4) |
 |
|
|
; dyads_m4; m=0 (reference); ncol1=10; shift=7; ncol=17; -------whACCAAAww
; Alignment reference
a 0 0 0 0 0 0 0 18 19 63 0 0 61 63 63 25 25
c 0 0 0 0 0 0 0 12 16 0 63 62 0 0 0 9 12
g 0 0 0 0 0 0 0 13 10 0 0 1 2 0 0 11 4
t 0 0 0 0 0 0 0 20 18 0 0 0 0 0 0 18 22
|