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_m2/peak-motifs_dyads_m2.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_m2/peak-motifs_dyads_m2_vs_db_footprintDB
One-to-n matrix alignment; reference matrix: dyads_m2_shift5 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m2_shift5 (dyads_m2) |
 |
|
|
; dyads_m2; m=0 (reference); ncol1=20; shift=5; ncol=25; -----mmGGAmdywabrwymCGAmr
; Alignment reference
a 0 0 0 0 0 13 15 0 1 26 9 9 4 10 15 4 13 9 5 13 0 0 29 11 10
c 0 0 0 0 0 11 9 3 0 5 11 4 16 6 4 9 4 7 10 8 31 0 1 8 6
g 0 0 0 0 0 6 5 24 30 0 4 8 2 6 5 10 10 3 7 7 0 31 1 5 11
t 0 0 0 0 0 1 2 4 0 0 7 10 9 9 7 8 4 12 9 3 0 0 0 7 4
|