One-to-n alignments
Command: compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.162239_oBtCQA/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.tf -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.162239_oBtCQA/compare-matrices.tab
One-to-n matrix alignment; reference matrix: cluster_2_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
|---|
| cluster_2_shift0 (cluster_2) |
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; cluster_2; m=0 (reference); ncol1=16; shift=0; ncol=16; awkkmCACGTGTCcww
; Alignment reference
a 35 27 53 37 93 18 206 8 16 7 6 9 27 51 82 60
c 14 14 34 20 98 182 4 191 2 4 6 7 167 107 36 50
g 20 9 65 102 10 7 1 4 191 4 199 19 7 23 41 34
t 17 36 66 59 17 11 7 15 9 203 7 183 17 37 59 74
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| 7247_PIF3_ArabidopsisPBM_20140210__shift3 (7247_PIF3_ArabidopsisPBM_20140210_) |
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0.776 |
0.485 |
6.943 |
0.891 |
0.882 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; cluster_2 versus 7247_PIF3_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=0; offset=3; strand=D; shift=3; score= 1; ---sCCACGTGGs---
; cor=0.776; Ncor=0.485; logoDP=6.943; NsEucl=0.891; NSW=0.882; rcor=1; rNcor=1; rlogoDP=1; rNsEucl=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 18 0 1 99 0 3 0 0 1 9 0 0 0
c 0 0 0 37 96 99 1 97 0 0 0 3 40 0 0 0
g 0 0 0 37 3 0 0 0 97 1 99 96 35 0 0 0
t 0 0 0 8 1 0 0 3 0 99 1 0 16 0 0 0
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