One-to-n alignments
Command: compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.162148_IHTZdU/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_2026-01-09.162148_IHTZdU/compare-matrices.tab
One-to-n matrix alignment; reference matrix: cluster_1_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_1_shift0 (cluster_1) |
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; cluster_1; m=0 (reference); ncol1=16; shift=0; ncol=16; wwwdTGGACCAmwwww
; Alignment reference
a 73 770 745 656 271 94 156 2109 109 89 2178 691 1111 580 681 373
c 39 422 457 271 102 71 67 73 1862 2325 149 1161 239 304 289 190
g 20 404 429 665 205 2266 2236 172 30 57 78 143 214 234 338 194
t 75 849 933 972 1986 133 105 210 563 93 159 569 582 1028 719 316
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| 7267_TCP16_ArabidopsisPBM_20140210__rc_shift2 (7267_TCP16_ArabidopsisPBM_20140210__rc) |
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0.702 |
0.439 |
2.031 |
0.879 |
0.854 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; cluster_1 versus 7267_TCP16_ArabidopsisPBM_20140210__rc; m=1/1; ncol2=10; w=0; offset=2; strand=R; shift=2; score= 1; --kGTGGACCCR----
; cor=0.702; Ncor=0.439; logoDP=2.031; NsEucl=0.879; NSW=0.854; rcor=1; rNcor=1; rlogoDP=1; rNsEucl=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 12 1 0 0 0 74 0 1 1 70 0 0 0 0
c 0 0 1 1 2 0 0 2 100 99 87 3 0 0 0 0
g 0 0 42 98 0 100 100 12 0 0 0 25 0 0 0 0
t 0 0 45 0 98 0 0 12 0 0 12 2 0 0 0 0
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