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_7nt_mkv2_m2/peak-motifs_oligos_7nt_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_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_ArabidopsisPBM
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |
 |
|
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; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; waACGsCGTtwa
; Alignment reference
a 11 12 23 0 1 2 1 1 1 2 11 10
c 3 5 1 25 0 14 23 0 1 5 0 4
g 1 5 0 0 24 7 1 23 0 3 1 6
t 10 3 1 0 0 2 0 1 23 15 13 5
|
| 7240_MYB52_ArabidopsisPBM_20140210__rc_shift4 (7240_MYB52_ArabidopsisPBM_20140210__rc) |
 |
|
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; oligos_7nt_mkv2_m2 versus 7240_MYB52_ArabidopsisPBM_20140210__rc; m=1/2; ncol2=10; w=0; offset=4; strand=R; shift=4; score=0.418947; ----wCCGTTAg
; cor=; Ncor=
a 0 0 0 0 27 6 7 3 2 3 75 14
c 0 0 0 0 9 79 79 3 1 4 4 10
g 0 0 0 0 18 2 5 92 10 1 11 52
t 0 0 0 0 46 13 9 2 87 92 10 24
|
| 7218_DOF5.7_2_ArabidopsisPBM_20140210__shift4 (7218_DOF5.7_2_ArabidopsisPBM_20140210_) |
 |
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; oligos_7nt_mkv2_m2 versus 7218_DOF5.7_2_ArabidopsisPBM_20140210_; m=2/2; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.406268; ----awCGTTAA
; cor=; Ncor=
a 0 0 0 0 44 47 2 2 2 1 88 87
c 0 0 0 0 8 15 94 0 0 1 3 5
g 0 0 0 0 24 13 2 94 2 2 3 3
t 0 0 0 0 24 25 2 4 96 96 6 5
|