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_m2/peak-motifs_dyads_m2.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_m2/peak-motifs_dyads_m2_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: dyads_m2_shift1 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m2_shift1 (dyads_m2) |
 |
|
|
; dyads_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -adGGAGAGAAGGrd
; Alignment reference
a 0 24 19 10 10 46 4 48 3 49 51 2 9 25 17
c 0 5 5 2 5 1 3 1 3 1 0 1 3 7 6
g 0 14 15 41 39 5 44 4 49 6 5 48 43 15 15
t 0 14 18 4 3 5 6 4 2 1 1 6 2 10 19
|