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_6nt_m1/peak-motifs_positions_6nt_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_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m1_shift0 (positions_6nt_m1) |
 |
|
|
; positions_6nt_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; wacTATCGATAgyw
; Alignment reference
a 34 40 7 11 88 2 0 0 92 2 69 8 19 34
c 13 14 65 15 3 1 97 0 2 4 2 17 25 16
g 17 24 17 2 4 2 0 97 1 3 15 65 14 13
t 33 19 8 69 2 92 0 0 2 88 11 7 39 34
|
| Dref_shift2 (Dref) |
 |
|
|
; positions_6nt_m1 versus Dref; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.632364; --aTAwCGATAr--
; cor=; Ncor=
a 0 0 6.66667 1.11111 7.77778 3.33333 0 1.11111 10 0 7.77778 3.33333 0 0
c 0 0 1.11111 0 1.11111 0 10 0 0 0 1.11111 0 0 0
g 0 0 0 1.11111 0 0 0 8.88889 0 0 1.11111 6.66667 0 0
t 0 0 2.22222 7.77778 1.11111 6.66667 0 0 0 10 0 0 0 0
|