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_8nt_m1/peak-motifs_positions_8nt_m1.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_8nt_m1/peak-motifs_positions_8nt_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_8nt_m1_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_8nt_m1_shift0 (positions_8nt_m1) |
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; positions_8nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; wkCAGGCCGATvc
; Alignment reference
a 17 7 1 37 2 1 4 2 2 34 1 10 9
c 7 9 38 0 0 0 27 31 2 1 0 12 17
g 5 12 0 1 36 38 3 1 35 1 0 12 7
t 10 11 0 1 1 0 5 5 0 3 38 5 6
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| MA0035.1_shift7 (Gata1) |
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0.872 |
0.402 |
3.480 |
0.405 |
0.911 |
0.572 |
0.952 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_8nt_m1 versus MA0035.1 (Gata1); m=1/1; ncol2=6; w=6; offset=7; strand=D; shift=7; score= 1; -------sGATgs
; cor=0.872; Ncor=0.402; logoDP=3.480; NIcor=0.405; NsEucl=0.911; SSD=0.572; NSW=0.952; 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 0 0 0 13 0 50 1 13 6
c 0 0 0 0 0 0 0 14 0 2 0 6 16
g 0 0 0 0 0 0 0 15 53 0 1 25 22
t 0 0 0 0 0 0 0 11 0 1 51 9 9
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