One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 transfac -file2 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.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 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_ref
One-to-n matrix alignment; reference matrix: positions_6nt_m1_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_m1_shift0 (positions_6nt_m1) |
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; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
; Alignment reference
a | 338 299 421 1039 1054 828 0 0 0 3 8 840 779 305 274
c | 216 265 122 1 2 15 1 0 0 0 4 1 89 195 240
g | 316 275 453 11 13 223 1073 1071 1074 27 1 232 103 393 287
t | 204 235 78 23 5 8 0 3 0 1044 1061 1 103 181 273
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| MA0452.1_shift1 (Kr_JASPAR) |
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0.953 |
0.699 |
8.659 |
0.701 |
0.950 |
0.608 |
0.972 |
2 |
1 |
1 |
1 |
1 |
1 |
1 |
1.143 |
1 |
; positions_6nt_m1 versus MA0452.1 (Kr_JASPAR); m=1/2; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1.1429; -crAAaGGGTTa---
; cor=0.953; Ncor=0.699; logoDP=8.659; NIcor=0.701; NsEucl=0.950; SSD=0.608; NSW=0.972; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1
a | 0 3 11 24 30 18 0 2 2 0 4 20 0 0 0
c | 0 17 4 0 0 6 0 0 0 1 0 4 0 0 0
g | 0 5 10 7 0 7 31 29 29 7 5 3 0 0 0
t | 0 6 6 0 1 0 0 0 0 23 22 4 0 0 0
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| Kr_FlyReg_FBgn0001325_shift3 (Kr) |
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0.958 |
0.639 |
5.639 |
0.639 |
0.935 |
0.845 |
0.958 |
1 |
2 |
2 |
2 |
2 |
2 |
2 |
1.857 |
2 |
; positions_6nt_m1 versus Kr_FlyReg_FBgn0001325 (Kr); m=2/2; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 1.8571; ---AAmGGGTtaw--
; cor=0.958; Ncor=0.639; logoDP=5.639; NIcor=0.639; NsEucl=0.935; SSD=0.845; NSW=0.958; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=2
a | 0 0 0 37 33 20 2 4 6 1 8 28 16 0 0
c | 0 0 0 0 6 11 0 1 3 3 4 6 8 0 0
g | 0 0 0 4 1 9 40 37 35 4 4 5 5 0 0
t | 0 0 0 3 4 4 2 2 0 36 28 5 15 0 0
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