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_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.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_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_FlyFactorSurvey
One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 4 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_shift0 (positions_7nt_m1) |
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; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
; Alignment reference
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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| Kr_NAR_FBgn0001325_shift1 (Kr_NAR_FBgn0001325) |
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0.953 |
0.699 |
8.685 |
0.699 |
0.950 |
0.614 |
0.972 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m1 versus Kr_NAR_FBgn0001325; m=1/3; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1; -crAAaGGGTTa---
; cor=0.953; Ncor=0.699; logoDP=8.685; NIcor=0.699; NsEucl=0.950; SSD=0.614; NSW=0.972; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; 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_FlyReg_FBgn0001325) |
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0.950 |
0.634 |
5.608 |
0.630 |
0.931 |
0.965 |
0.952 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; positions_7nt_m1 versus Kr_FlyReg_FBgn0001325; m=2/3; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 2; ---AAmGGGTtaw--
; cor=0.950; Ncor=0.634; logoDP=5.608; NIcor=0.630; NsEucl=0.931; SSD=0.965; NSW=0.952; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; 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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| Ptx1_SOLEXA_FBgn0020912_rc_shift6 (Ptx1_SOLEXA_FBgn0020912_rc) |
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0.751 |
0.400 |
0.103 |
-0.128 |
0.868 |
2.230 |
0.861 |
3 |
3 |
3 |
3 |
3 |
3 |
3 |
3.000 |
3 |
; positions_7nt_m1 versus Ptx1_SOLEXA_FBgn0020912_rc; m=3/3; ncol2=8; w=8; offset=6; strand=R; shift=6; score= 3; ------GGATTArc-
; cor=0.751; Ncor=0.400; logoDP=0.103; NIcor=-0.128; NsEucl=0.868; SSD=2.230; NSW=0.861; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.000; match_rank=3
a | 0 0 0 0 0 0 23 1 355 0 0 348 186 65 0
c | 0 0 0 0 0 0 6 0 3 6 3 0 14 139 0
g | 0 0 0 0 0 0 329 361 4 4 0 11 110 87 0
t | 0 0 0 0 0 0 4 0 0 352 359 3 52 71 0
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