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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_vs_db_footprintDB-plants
One-to-n matrix alignment; reference matrix: dyads_m3_shift7 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m3_shift7 (dyads_m3) |
 |
|
|
; dyads_m3; m=0 (reference); ncol1=18; shift=7; ncol=25; -------mmCTThtwthhwwTTCwt
; Alignment reference
a 0 0 0 0 0 0 0 24 23 1 0 1 21 13 22 16 18 21 25 20 1 3 0 25 14
c 0 0 0 0 0 0 0 17 18 64 1 1 19 16 11 15 17 20 14 14 0 0 66 15 13
g 0 0 0 0 0 0 0 10 9 0 2 0 7 10 6 9 7 8 9 8 0 1 0 5 11
t 0 0 0 0 0 0 0 15 16 1 63 64 19 27 27 26 24 17 18 24 65 62 0 21 28
|