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_m5/peak-motifs_dyads_m5.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_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: dyads_m5_shift2 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m5_shift2 (dyads_m5) |
 |
|
|
; dyads_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwCGAwyACAha
; Alignment reference
a 0 0 21 18 1 0 52 24 12 48 4 54 19 22
c 0 0 10 13 58 0 3 13 15 3 49 2 15 14
g 0 0 13 11 1 57 2 8 12 1 2 2 8 10
t 0 0 16 18 0 3 3 15 21 8 5 2 18 14
|