One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.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/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 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_6nt_m2_shift0 (positions_6nt_m2) |
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; positions_6nt_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; dkATTACGCAAGArw
; Alignment reference
a 203 157 612 2 1 589 32 68 11 677 677 9 629 179 202
c 108 117 23 2 2 3 539 20 645 1 0 57 15 148 142
g 175 199 33 1 11 48 27 575 2 0 1 540 14 185 144
t 192 205 10 673 664 38 80 15 20 0 0 72 20 166 190
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| MA0102.1_shift3 (Cebpa) |
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0.760 |
0.608 |
6.251 |
0.605 |
0.906 |
2.544 |
0.894 |
2 |
1 |
1 |
1 |
1 |
2 |
2 |
1.429 |
1 |
; positions_6nt_m2 versus MA0102.1 (Cebpa); m=1/2; ncol2=12; w=12; offset=3; strand=D; shift=3; score= 1.4286; ---TtkygCAAyvyb
; cor=0.760; Ncor=0.608; logoDP=6.251; NIcor=0.605; NsEucl=0.906; SSD=2.544; NSW=0.894; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.429; match_rank=1
a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1
c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6
g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5
t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
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| MA0102.2_shift3 (CEBPA) |
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0.819 |
0.491 |
6.232 |
0.484 |
0.895 |
1.793 |
0.900 |
1 |
2 |
2 |
2 |
2 |
1 |
1 |
1.571 |
2 |
; positions_6nt_m2 versus MA0102.2 (CEBPA); m=2/2; ncol2=9; w=9; offset=3; strand=D; shift=3; score= 1.5714; ---TtkygCAAy---
; cor=0.819; Ncor=0.491; logoDP=6.232; NIcor=0.484; NsEucl=0.895; SSD=1.793; NSW=0.900; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=2
a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0
c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0
g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0
t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
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