Mercurial > repos > iuc > meme_fimo

annotate test-data/dreme_output_test1.xml @ 15:0c5239d1aa65 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:05:35 -0500
parents 4eb02864e5df
children c5209f38700d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
0c5239d1aa65 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents: 13
diff changeset
1 <dreme version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
13
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
2 <model>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
3 <negatives name="shuffled positive sequences" count="1000" from="shuffled"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
4 <alphabet name="RNA" like="rna">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
5 <letter id="A" symbol="A" name="Adenine" colour="CC0000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
6 <letter id="C" symbol="C" name="Cytosine" colour="0000CC"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
7 <letter id="G" symbol="G" name="Guanine" colour="FFB300"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
8 <letter id="U" symbol="U" aliases="T" name="Uracil" colour="008000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
9 <letter id="N" symbol="N" aliases="X." equals="ACGU" name="Any base"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
10 <letter id="V" symbol="V" equals="ACG" name="Not U"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
11 <letter id="H" symbol="H" equals="ACU" name="Not G"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
12 <letter id="D" symbol="D" equals="AGU" name="Not C"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
13 <letter id="B" symbol="B" equals="CGU" name="Not A"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
14 <letter id="M" symbol="M" equals="AC" name="Amino"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
15 <letter id="R" symbol="R" equals="AG" name="Purine"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
16 <letter id="W" symbol="W" equals="AU" name="Weak"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
17 <letter id="S" symbol="S" equals="CG" name="Strong"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
18 <letter id="Y" symbol="Y" equals="CU" name="Pyrimidine"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
19 <letter id="K" symbol="K" equals="GU" name="Keto"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
20 </alphabet>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
21 <strands>none</strands>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
22 <background A="0.221" C="0.245" G="0.221" U="0.312" from="dataset"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
23 <stop evalue="0.05"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
24 <ngen>100</ngen>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
25 <add_pv_thresh>0.01</add_pv_thresh>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
26 <seed>1</seed>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
27 </model>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
28 <motifs>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
29 <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="1.2e-013" unerased_evalue="1.2e-013">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
30 <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
31 <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
32 <pos A="0.000000" C="0.294118" G="0.000000" U="0.705882"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
33 <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
34 <pos A="0.000000" C="1.000000" G="0.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
35 <pos A="0.000000" C="0.474946" G="0.000000" U="0.525054"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
36 <match seq="UUUUCC" p="147" n="75" pvalue="1.8e-007" evalue="8.1e-003"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
37 <match seq="UUUUCU" p="155" n="94" pvalue="2.2e-005" evalue="1.0e+000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
38 <match seq="UUCUCU" p="94" n="51" pvalue="1.3e-004" evalue="6.1e+000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
39 <match seq="UUCUCC" p="75" n="42" pvalue="1.1e-003" evalue="5.0e+001"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
40 </motif>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
41 <motif id="m02" alt="DREME-2" seq="YAGG" length="4" nsites="793" p="600" n="416" pvalue="1.1e-016" evalue="5.1e-012" unerased_evalue="2.4e-012">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
42 <pos A="0.000000" C="0.692308" G="0.000000" U="0.307692"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
43 <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
44 <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
45 <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
46 <match seq="CAGG" p="441" n="304" pvalue="1.5e-010" evalue="6.6e-006"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
47 <match seq="UAGG" p="232" n="165" pvalue="1.1e-004" evalue="4.7e+000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
48 </motif>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
49 <motif id="m03" alt="DREME-3" seq="GAAGAW" length="6" nsites="89" p="81" n="22" pvalue="8.2e-010" evalue="3.4e-005" unerased_evalue="3.5e-004">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
50 <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
51 <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
52 <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
53 <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
54 <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
55 <pos A="0.494382" C="0.000000" G="0.000000" U="0.505618"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
56 <match seq="GAAGAU" p="45" n="7" pvalue="2.4e-008" evalue="9.9e-004"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
57 <match seq="GAAGAA" p="40" n="16" pvalue="7.9e-004" evalue="3.3e+001"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
58 </motif>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
59 <motif id="m04" alt="DREME-4" seq="SMUGGA" length="6" nsites="119" p="110" n="47" pvalue="9.1e-008" evalue="3.7e-003" unerased_evalue="2.6e-005">
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
60 <pos A="0.000000" C="0.529412" G="0.470588" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
61 <pos A="0.428571" C="0.571429" G="0.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
62 <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
63 <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
64 <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
65 <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
66 <match seq="GAUGGA" p="22" n="6" pvalue="1.7e-003" evalue="7.1e+001"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
67 <match seq="GCUGGA" p="33" n="14" pvalue="3.6e-003" evalue="1.5e+002"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
68 <match seq="CCUGGA" p="32" n="15" pvalue="8.6e-003" evalue="3.5e+002"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
69 <match seq="CAUGGA" p="29" n="13" pvalue="9.1e-003" evalue="3.7e+002"/>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
70 </motif>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
71 </motifs>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
72 </dreme>