One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_7nt_m1_shift0 (positions_7nt_m1) |
 |
|
|
; positions_7nt_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; awacTATCGATAgtwt
; Alignment reference
a 35 29 51 7 8 77 1 1 0 84 2 65 7 16 33 15
c 17 13 9 56 12 4 2 87 0 1 5 3 18 12 13 21
g 21 13 12 18 3 5 1 0 87 2 4 12 56 9 13 17
t 15 33 16 7 65 2 84 0 1 1 77 8 7 51 29 35
|
| Dref_rc_shift3 (Dref_rc) |
 |
|
|
; positions_7nt_m1 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.554241; ---yTATCGwTAt---
; cor=; Ncor=
a 0 0 0 0 0 10 0 0 0 6.66667 1.11111 7.77778 2.22222 0 0 0
c 0 0 0 6.66667 1.11111 0 0 8.88889 0 0 0 1.11111 0 0 0 0
g 0 0 0 0 1.11111 0 0 0 10 0 1.11111 0 1.11111 0 0 0
t 0 0 0 3.33333 7.77778 0 10 1.11111 0 3.33333 7.77778 1.11111 6.66667 0 0 0
|