One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_m1.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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_m1_vs_db_ArabidopsisPBM
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |
 |
|
|
; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; ysCTCCTCkk
; Alignment reference
a 2 3 0 0 0 0 0 0 1 4
c 8 9 18 0 18 18 0 18 4 3
g 3 5 0 0 0 0 0 0 6 5
t 5 1 0 18 0 0 18 0 7 6
|
| 7274_TOE2_ArabidopsisPBM_20140210__shift3 (7274_TOE2_ArabidopsisPBM_20140210_) |
 |
|
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; oligos_6nt_mkv1_m1 versus 7274_TOE2_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.405123; ---wCCTCGT
; cor=; Ncor=
a 0 0 0 61 0 13 0 6 1 0
c 0 0 0 2 92 85 0 92 0 0
g 0 0 0 4 0 1 2 1 98 11
t 0 0 0 33 8 1 98 1 1 89
|