Mercurial > repos > iuc > meme_meme
annotate test-data/meme_output_test2.xml @ 15:9dd5373f6a5a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
author | iuc |
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date | Wed, 18 Nov 2020 19:41:27 +0000 |
parents | 3f0dd362b755 |
children | 19237efe98d1 |
rev | line source |
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13
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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1 <?xml version='1.0' encoding='UTF-8' standalone='yes'?> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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2 <!-- Document definition --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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3 <!DOCTYPE MEME[ |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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4 <!ELEMENT MEME ( |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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5 training_set, |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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6 model, |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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7 motifs, |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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8 scanned_sites_summary? |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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9 )> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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10 <!ATTLIST MEME |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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11 version CDATA #REQUIRED |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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12 release CDATA #REQUIRED |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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13 <!-- Training-set elements --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
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14 <!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)> |
14
3f0dd362b755
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents:
13
diff
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15 <!ATTLIST training_set primary_sequences CDATA #REQUIRED primary_count CDATA #REQUIRED primary_positions CDATA #REQUIRED |
3f0dd362b755
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents:
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16 control_sequences CDATA "" control_count CDATA "" control_positions CDATA ""> |
13
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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17 <!ELEMENT alphabet (letter*)> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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18 <!ATTLIST alphabet name CDATA #REQUIRED> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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19 <!ELEMENT letter_frequencies (alphabet_array)> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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20 <!-- Model elements --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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21 <!ELEMENT model ( |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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22 command_line, |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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23 host, |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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24 type, |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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25 nmotifs, |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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26 )> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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27 <!ELEMENT command_line (#PCDATA)*> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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28 <!ELEMENT motifs (motif*)> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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29 <!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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30 <!-- The left_flank contains the sequence for 10 bases to the left of the motif start --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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31 <!ELEMENT left_flank (#PCDATA)> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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32 <!-- The site contains the sequence for the motif instance --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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33 <!ELEMENT site (letter_ref*)> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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34 <!-- The right_flank contains the sequence for 10 bases to the right of the motif end --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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35 <!ELEMENT right_flank (#PCDATA)> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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36 <!-- Scanned site elements --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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37 <!-- Scanned sites are motif occurences found during the sequence scan phase --> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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38 <!ELEMENT scanned_sites_summary (scanned_sites*)> |
14
3f0dd362b755
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
parents:
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39 <training_set primary_sequences="Galaxy_FASTA_Input" primary_count="30" primary_positions="1500" control_sequences="--none--" control_count="0" control_positions="0"> |
13
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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40 <alphabet name="DNA" like="dna"> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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41 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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42 <sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" /> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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43 <value letter_id="G">0.257</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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44 <value letter_id="T">0.217</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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45 </alphabet_array> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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46 <model> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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47 <type>zoops</type> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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48 <scores> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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49 <alphabet_matrix> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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50 <alphabet_array> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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51 <value letter_id="A">-14</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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52 <value letter_id="A">3</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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53 <value letter_id="A">-1155</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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54 <value letter_id="A">156</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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changeset
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55 <value letter_id="A">-1155</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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56 <value letter_id="A">172</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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57 <value letter_id="A">125</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
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58 <value letter_id="A">167</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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59 <value letter_id="A">144</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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60 <value letter_id="A">0.266667</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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61 <value letter_id="A">0.300000</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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62 <value letter_id="A">0.800000</value> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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63 <contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" > |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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64 <left_flank>AAGGCCAGGA</left_flank> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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65 <letter_ref letter_id="G"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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66 <right_flank>GCCTGAGAGC</right_flank> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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67 <contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" > |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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68 <letter_ref letter_id="A"/> |
14
3f0dd362b755
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
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69 <contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" > |
3f0dd362b755
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
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70 <right_flank>AGCCCTGTAC</right_flank> |
3f0dd362b755
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
iuc
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71 <contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" > |
13
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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72 <left_flank>CGTGGTCGCG</left_flank> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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73 <right_flank>GC</right_flank> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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74 <contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" > |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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75 <left_flank>GCTGCCGGTG</left_flank> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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76 <right_flank>GCCCTGGCG</right_flank> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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77 <contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" > |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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78 <scanned_sites_summary p_thresh="0.0001"> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
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79 <scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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80 <scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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81 <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites> |
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff
changeset
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82 </MEME> |