One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.194903_2014-09-05.194903_oebJl9/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| positions_7nt_m5_shift0 (positions_7nt_m5) |
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; positions_7nt_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wkCACTCCAsg
; Alignment reference
a 2 1 0 6 0 0 0 0 6 0 1
c 0 0 6 0 6 0 6 6 0 2 1
g 0 2 0 0 0 0 0 0 0 4 3
t 4 3 0 0 0 6 0 0 0 0 1
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| MA0130.1_shift4 (ZNF354C) |
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0.800 |
0.437 |
6.779 |
0.396 |
0.856 |
1.496 |
0.875 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m5 versus MA0130.1 (ZNF354C); m=1/1; ncol2=6; w=6; offset=4; strand=D; shift=4; score= 1; ----mTCCAC-
; cor=0.800; Ncor=0.437; logoDP=6.779; NIcor=0.396; NsEucl=0.856; SSD=1.496; NSW=0.875; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 0 7 3 0 0 16 0 0
c 0 0 0 0 6 2 16 16 0 15 0
g 0 0 0 0 3 0 0 0 0 1 0
t 0 0 0 0 0 11 0 0 0 0 0
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