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_m2/peak-motifs_positions_7nt_m2.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_m2/peak-motifs_positions_7nt_m2_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_7nt_m2_shift0 (positions_7nt_m2) |
 |
|
|
; positions_7nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; awacTATCGATrgt
; Alignment reference
a 42 38 68 15 4 103 0 0 0 93 6 37 19 25
c 22 15 11 69 9 3 0 109 0 6 8 5 25 24
g 19 16 18 21 1 2 4 0 110 7 4 56 42 18
t 27 41 13 5 96 2 106 1 0 4 92 12 24 43
|
| Dref_rc_shift3 (Dref_rc) |
 |
|
|
; positions_7nt_m2 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.629324; ---yTATCGwTAt-
; cor=; Ncor=
a 0 0 0 0 0 10 0 0 0 6.66667 1.11111 7.77778 2.22222 0
c 0 0 0 6.66667 1.11111 0 0 8.88889 0 0 0 1.11111 0 0
g 0 0 0 0 1.11111 0 0 0 10 0 1.11111 0 1.11111 0
t 0 0 0 3.33333 7.77778 0 10 1.11111 0 3.33333 7.77778 1.11111 6.66667 0
|