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.2025-04-28.203737_2025-04-28.203737_n2namY/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.2025-04-28.203737_2025-04-28.203737_n2namY/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_shift1 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m1_shift1 (positions_6nt_m1) |
 |
|
|
; positions_6nt_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -haTCGATAGyw
; Alignment reference
a 0 25 45 5 2 0 85 4 74 3 11 31
c 0 24 11 5 84 1 2 2 0 12 27 15
g 0 14 16 4 1 86 0 3 8 69 12 14
t 0 25 16 74 1 1 1 79 6 4 38 28
|
| Dref_shift0 (Dref) |
 |
|
|
; positions_6nt_m1 versus Dref; m=1/1; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.685196; aTAwCGATAr--
; cor=; Ncor=
a 6.66667 1.11111 7.77778 3.33333 0 1.11111 10 0 7.77778 3.33333 0 0
c 1.11111 0 1.11111 0 10 0 0 0 1.11111 0 0 0
g 0 1.11111 0 0 0 8.88889 0 0 1.11111 6.66667 0 0
t 2.22222 7.77778 1.11111 6.66667 0 0 0 10 0 0 0 0
|