One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.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/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_8nt_mkv2_m2/peak-motifs_oligos_8nt_mkv2_m2_vs_db_ArabidopsisPBM
One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m2_shift2 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_8nt_mkv2_m2_shift2 (oligos_8nt_mkv2_m2) |
 |
|
|
; oligos_8nt_mkv2_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --ywAACGGCGTtw
; Alignment reference
a 0 0 4 9 15 16 1 0 2 0 0 1 3 5
c 0 0 6 1 1 0 16 1 2 17 0 0 4 1
g 0 0 2 0 2 1 0 16 14 0 18 1 4 3
t 0 0 6 8 0 1 1 1 0 1 0 16 7 9
|
| 7240_MYB52_ArabidopsisPBM_20140210__shift0 (7240_MYB52_ArabidopsisPBM_20140210_) |
 |
|
|
; oligos_8nt_mkv2_m2 versus 7240_MYB52_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.460582; amcTAACGGw----
; cor=; Ncor=
a 64 49 24 10 92 87 2 9 13 46 0 0 0 0
c 8 30 52 11 1 10 92 5 2 18 0 0 0 0
g 17 15 10 4 4 1 3 79 79 9 0 0 0 0
t 11 6 14 75 3 2 3 7 6 27 0 0 0 0
|