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_m4/peak-motifs_positions_8nt_m4.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_m4/peak-motifs_positions_8nt_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_8nt_m4_shift5 ; 3 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_m4_shift5 (positions_8nt_m4) |
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; positions_8nt_m4; m=0 (reference); ncol1=14; shift=5; ncol=19; -----sgAAGGGGGrGAya
; Alignment reference
a 0 0 0 0 0 4 5 19 20 1 2 2 0 1 15 2 22 6 7
c 0 0 0 0 0 10 5 2 1 0 1 0 0 0 1 0 0 7 6
g 0 0 0 0 0 7 11 4 4 23 22 21 24 21 7 22 1 5 6
t 0 0 0 0 0 4 4 0 0 1 0 2 1 3 2 1 2 7 6
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| MA0163.1_shift0 (PLAG1) |
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0.884 |
0.419 |
4.896 |
0.422 |
0.925 |
0.910 |
0.949 |
1 |
2 |
1 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; positions_8nt_m4 versus MA0163.1 (PLAG1); m=1/2; ncol2=14; w=9; offset=-5; strand=D; shift=0; score= 1.2857; GGGGCCcwmGGGGG-----
; cor=0.884; Ncor=0.419; logoDP=4.896; NIcor=0.422; NsEucl=0.925; SSD=0.910; NSW=0.949; rcor=1; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 3 0 0 0 0 4 12 11 2 0 0 0 2 0 0 0 0 0
c 0 0 0 0 14 15 10 0 5 0 0 0 0 0 0 0 0 0 0
g 18 14 18 17 4 1 1 0 2 14 18 18 16 16 0 0 0 0 0
t 0 1 0 1 0 2 3 6 0 2 0 0 2 0 0 0 0 0 0
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| MA0057.1_shift6 (MZF1_5-13) |
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0.783 |
0.559 |
4.017 |
0.548 |
0.908 |
1.701 |
0.915 |
2 |
1 |
2 |
1 |
2 |
2 |
2 |
1.714 |
2 |
; positions_8nt_m4 versus MA0057.1 (MZF1_5-13); m=2/2; ncol2=10; w=10; offset=1; strand=D; shift=6; score= 1.7143; ------bkAKGGGkrr---
; cor=0.783; Ncor=0.559; logoDP=4.017; NIcor=0.548; NsEucl=0.908; SSD=1.701; NSW=0.915; rcor=2; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
a 0 0 0 0 0 0 1 2 15 0 0 0 0 3 10 8 0 0 0
c 0 0 0 0 0 0 4 0 1 0 0 2 0 1 0 2 0 0 0
g 0 0 0 0 0 0 7 7 0 11 15 14 14 8 4 4 0 0 0
t 0 0 0 0 0 0 4 7 0 5 1 0 2 4 2 2 0 0 0
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