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_m3/peak-motifs_oligos_6nt_mkv1_m3.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_m3/peak-motifs_oligos_6nt_mkv1_m3_vs_db_ArabidopsisPBM
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |
 |
|
|
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; rtATATATat
; Alignment reference
a 14 7 30 0 32 0 33 0 18 5
c 8 8 3 1 1 2 1 2 3 8
g 9 3 2 0 2 1 1 3 8 8
t 4 17 0 34 0 32 0 30 6 14
|
| 7186_AHL20_ArabidopsisPBM_20140210__shift0 (7186_AHL20_ArabidopsisPBM_20140210_) |
 |
|
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; oligos_6nt_mkv1_m3 versus 7186_AHL20_ArabidopsisPBM_20140210_; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.76704; wAATATATTw
; cor=; Ncor=
a 44 95 88 8 87 13 90 11 3 44
c 16 1 0 1 0 0 1 1 1 10
g 11 1 1 0 0 0 1 0 1 21
t 29 3 11 91 13 87 8 88 95 25
|
| 7185_AHL12_3_ArabidopsisPBM_20140210__shift1 (7185_AHL12_3_ArabidopsisPBM_20140210_) |
 |
|
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; oligos_6nt_mkv1_m3 versus 7185_AHL12_3_ArabidopsisPBM_20140210_; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.578425; -wAwwwwwwT
; cor=; Ncor=
a 0 42 83 44 55 36 64 43 54 11
c 0 11 2 1 1 0 0 1 1 4
g 0 11 5 1 1 0 0 1 0 2
t 0 36 10 54 43 64 36 55 45 83
|