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_m2/peak-motifs_positions_6nt_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_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m2_shift0 (positions_6nt_m2) |
 |
|
|
; positions_6nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; waCTATCGATAstw
; Alignment reference
a 37 37 3 12 83 2 3 1 85 2 73 8 21 32
c 14 14 67 10 3 2 90 0 2 5 2 47 16 16
g 14 22 17 3 5 2 0 91 4 0 12 31 17 13
t 28 20 6 68 2 87 0 1 2 86 6 7 39 32
|
| Dref_rc_shift2 (Dref_rc) |
 |
|
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; positions_6nt_m2 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.634776; --yTATCGwTAt--
; cor=; Ncor=
a 0 0 0 0 10 0 0 0 6.66667 1.11111 7.77778 2.22222 0 0
c 0 0 6.66667 1.11111 0 0 8.88889 0 0 0 1.11111 0 0 0
g 0 0 0 1.11111 0 0 0 10 0 1.11111 0 1.11111 0 0
t 0 0 3.33333 7.77778 0 10 1.11111 0 3.33333 7.77778 1.11111 6.66667 0 0
|