One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/positions_6nt/peak-motifs_positions_6nt.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/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/positions_6nt/peak-motifs_positions_6nt_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_shift1 ; 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_6nt_shift1 (positions_6nt) |
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; positions_6nt; m=0 (reference); ncol1=10; shift=1; ncol=11; -CGCGCGCGCG
; Alignment reference
a 0 0 0 0 0 0 0 0 0 0 0
c 0 6 0 6 0 6 0 6 0 6 0
g 0 0 6 0 6 0 6 0 6 0 6
t 0 0 0 0 0 0 0 0 0 0 0
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| MA0506.1_shift0 (NRF1) |
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0.760 |
0.691 |
10.568 |
0.669 |
0.874 |
3.190 |
0.840 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt versus MA0506.1 (NRF1); m=1/1; ncol2=11; w=10; offset=-1; strand=D; shift=0; score= 1; GCGCmTGCGCr
; cor=0.760; Ncor=0.691; logoDP=10.568; NIcor=0.669; NsEucl=0.874; SSD=3.190; NSW=0.840; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 602 623 196 0 1514 0 0 0 0 74 2245
c 375 4001 189 4016 1862 403 0 4338 349 4550 804
g 3647 0 4239 468 935 528 4624 0 4275 0 1575
t 0 0 0 140 313 3693 0 286 0 0 0
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