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_7nt_mkv1_m1/peak-motifs_oligos_7nt_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_7nt_mkv1_m1/peak-motifs_oligos_7nt_mkv1_m1_vs_db_ArabidopsisPBM
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |
 |
|
|
; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; raAAAAAAAww
; Alignment reference
a 32 29 69 70 73 71 70 71 74 33 33
c 15 16 3 4 5 3 3 1 0 9 8
g 22 19 7 5 2 5 4 4 4 18 19
t 12 17 2 2 1 2 4 5 3 21 21
|
| 7217_DOF5.7_ArabidopsisPBM_20140210__shift2 (7217_DOF5.7_ArabidopsisPBM_20140210_) |
 |
|
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; oligos_7nt_mkv1_m1 versus 7217_DOF5.7_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.54141; --raAAArrkg
; cor=; Ncor=
a 0 0 39 45 68 97 90 36 48 10 18
c 0 0 21 9 1 0 0 4 6 19 21
g 0 0 27 22 7 1 8 59 44 46 41
t 0 0 13 24 24 2 2 1 2 25 20
|