One-to-n alignments
Command: compare-matrices -v 1 -mode matches -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 -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/data/ref_motifs/peak-motifs_ref_motifs.tf -format2 transfac -file2 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_ref/peak-motifs_motifs_vs_ref
One-to-n matrix alignment; reference matrix: MA0452.1_shift1 ; 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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| MA0452.1_shift1 (Kr_JASPAR) |
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; MA0452.1 (Kr_JASPAR); m=0 (reference); ncol1=11; shift=1; ncol=15; -crAAaGGGTTa---
; Alignment reference
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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| positions_6nt_m1_shift0 (positions_6nt_m1) |
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0.953 |
0.699 |
8.659 |
0.701 |
0.950 |
0.608 |
0.972 |
2 |
1 |
2 |
1 |
1 |
1 |
1 |
1.286 |
1 |
; MA0452.1 versus positions_6nt_m1; m=1/2; ncol2=15; w=11; offset=-1; strand=D; shift=0; score= 1.2857; rrrAAAGGGTTAArd
; 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=2; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
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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| positions_7nt_m1_shift0 (positions_7nt_m1) |
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0.953 |
0.699 |
8.685 |
0.699 |
0.950 |
0.614 |
0.972 |
3 |
2 |
1 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; MA0452.1 versus positions_7nt_m1; m=2/2; ncol2=15; w=11; offset=-1; strand=D; shift=0; score= 2; rrrAAAGGGTTAArd
; cor=0.953; Ncor=0.699; logoDP=8.685; NIcor=0.699; NsEucl=0.950; SSD=0.614; NSW=0.972; rcor=3; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a | 325 287 388 918 991 801 0 0 0 1 1 821 814 317 252
c | 201 244 235 0 1 5 0 0 0 0 0 0 49 162 228
g | 288 256 319 72 12 200 1008 1008 1008 10 0 187 73 370 271
t | 194 221 66 18 4 2 0 0 0 997 1007 0 72 159 257
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One-to-n matrix alignment; reference matrix: Kr_FlyReg_FBgn0001325_shift3 ; 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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| Kr_FlyReg_FBgn0001325_shift3 (Kr) |
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; Kr_FlyReg_FBgn0001325 (Kr); m=0 (reference); ncol1=10; shift=3; ncol=15; ---AAmGGGTtaw--
; Alignment reference
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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| positions_6nt_m1_shift0 (positions_6nt_m1) |
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0.958 |
0.639 |
5.639 |
0.639 |
0.935 |
0.845 |
0.958 |
1 |
3 |
3 |
3 |
3 |
3 |
3 |
2.714 |
3 |
; Kr_FlyReg_FBgn0001325 versus positions_6nt_m1; m=1/2; ncol2=15; w=10; offset=-3; strand=D; shift=0; score= 2.7143; rrrAAAGGGTTAArd
; cor=0.958; Ncor=0.639; logoDP=5.639; NIcor=0.639; NsEucl=0.935; SSD=0.845; NSW=0.958; rcor=1; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=3
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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| positions_7nt_m1_shift0 (positions_7nt_m1) |
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0.950 |
0.634 |
5.608 |
0.630 |
0.931 |
0.965 |
0.952 |
4 |
4 |
4 |
4 |
4 |
4 |
4 |
4.000 |
4 |
; Kr_FlyReg_FBgn0001325 versus positions_7nt_m1; m=2/2; ncol2=15; w=10; offset=-3; strand=D; shift=0; score= 4; rrrAAAGGGTTAArd
; cor=0.950; Ncor=0.634; logoDP=5.608; NIcor=0.630; NsEucl=0.931; SSD=0.965; NSW=0.952; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.000; match_rank=4
a | 325 287 388 918 991 801 0 0 0 1 1 821 814 317 252
c | 201 244 235 0 1 5 0 0 0 0 0 0 49 162 228
g | 288 256 319 72 12 200 1008 1008 1008 10 0 187 73 370 271
t | 194 221 66 18 4 2 0 0 0 997 1007 0 72 159 257
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