One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.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/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: dyads_m3_shift2 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m3_shift2 (dyads_m3) |
 |
|
|
; dyads_m3; m=0 (reference); ncol1=30; shift=2; ncol=32; --thACCttsctyysmbwyrycrtrkyCAGtr
; Alignment reference
a 0 0 5 12 30 0 0 9 9 5 5 8 9 8 6 15 1 13 5 17 2 6 16 6 15 7 7 0 29 1 6 12
c 0 0 7 13 6 37 35 6 7 12 18 6 11 12 13 11 11 4 15 2 14 13 6 8 5 7 12 34 0 1 5 3
g 0 0 9 1 0 0 1 7 9 13 5 4 4 4 10 6 12 9 1 12 7 9 12 9 15 13 8 0 7 35 8 14
t 0 0 16 11 1 0 1 15 12 7 9 19 13 13 8 5 13 11 16 6 14 9 3 14 2 10 10 3 1 0 18 8
|