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_m1/peak-motifs_positions_7nt_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_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift2 ; 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_m1_shift2 (positions_7nt_m1) |
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; positions_7nt_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --vsAGGGGCCgg
; Alignment reference
a 0 0 2 1 6 0 0 0 0 0 0 1 1
c 0 0 2 3 0 0 0 0 0 6 6 1 1
g 0 0 2 2 0 6 6 6 6 0 0 4 4
t 0 0 0 0 0 0 0 0 0 0 0 0 0
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MA0155.1_shift0 (INSM1) |
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0.762 |
0.586 |
8.805 |
0.613 |
0.889 |
2.465 |
0.877 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m1 versus MA0155.1 (INSM1); m=1/1; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 1; TGymwGGGGkcr-
; cor=0.762; Ncor=0.586; logoDP=8.805; NIcor=0.613; NsEucl=0.889; SSD=2.465; NSW=0.877; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 1 0 0 6 16 0 0 0 0 0 3 10 0
c 0 0 8 15 0 0 1 0 0 2 16 0 0
g 4 20 3 0 0 24 23 24 24 16 0 12 0
t 19 4 13 3 8 0 0 0 0 6 5 2 0
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