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/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_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.2025-04-28.203737_2025-04-28.203737_n2namY/results/discovered_motifs/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_vs_db_DMMPMM_drosophila
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |
 |
|
|
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=21; shift=0; ncol=21; swwmyaTCGATAsTATCGAth
; Alignment reference
a 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6
c 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6
g 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5
t 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6
|
| Dref_shift3 (Dref) |
 |
|
|
; oligos_6nt_mkv2_m2 versus Dref; m=1/1; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.420742; ---aTAwCGATAr--------
; cor=; Ncor=
a 0 0 0 6.66667 1.11111 7.77778 3.33333 0 1.11111 10 0 7.77778 3.33333 0 0 0 0 0 0 0 0
c 0 0 0 1.11111 0 1.11111 0 10 0 0 0 1.11111 0 0 0 0 0 0 0 0 0
g 0 0 0 0 1.11111 0 0 0 8.88889 0 0 1.11111 6.66667 0 0 0 0 0 0 0 0
t 0 0 0 2.22222 7.77778 1.11111 6.66667 0 0 0 10 0 0 0 0 0 0 0 0 0 0
|