Mercurial > repos > iuc > meme_dreme

diff test-data/meme_output_test2.xml @ 2:3e5c80594237 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:04:55 -0500
parents cb8a2242bf03
children f33d77dcacce
line wrap: on
line diff
--- a/test-data/meme_output_test2.xml	Thu May 17 14:11:27 2018 -0400
+++ b/test-data/meme_output_test2.xml	Wed Dec 11 18:04:55 2019 -0500
@@ -10,975 +10,73 @@
 <!ATTLIST MEME 
   version CDATA #REQUIRED
   release CDATA #REQUIRED
->
 <!-- Training-set elements -->
 <!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)>
-<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED>
+<!ATTLIST training_set primary_sequences CDATA #REQUIRED primary_count CDATA #REQUIRED primary_positions CDATA #REQUIRED
+  control_sequences CDATA "" control_count CDATA "" control_positions CDATA "">
 <!ELEMENT alphabet (letter*)>
 <!ATTLIST alphabet name CDATA #REQUIRED>
-<!ELEMENT ambigs (letter*)>
-<!ELEMENT letter EMPTY>
-<!ATTLIST letter id ID #REQUIRED>
-<!ATTLIST letter symbol CDATA #REQUIRED>
-<!ATTLIST letter equals CDATA #IMPLIED>
-<!ATTLIST letter aliases CDATA #IMPLIED>
-<!ATTLIST letter complement CDATA #IMPLIED>
-<!ATTLIST letter name CDATA #IMPLIED>
-<!ATTLIST letter colour CDATA #IMPLIED>
-<!ELEMENT sequence EMPTY>
-<!ATTLIST sequence id ID #REQUIRED
-                   name CDATA #REQUIRED
-                   length CDATA #REQUIRED
-                   weight CDATA #REQUIRED
->
 <!ELEMENT letter_frequencies (alphabet_array)>
-
 <!-- Model elements -->
 <!ELEMENT model (
   command_line,
   host,
   type,
   nmotifs,
-  evalue_threshold,
-  object_function,
-  spfun,
-  min_width,
-  max_width,
-  wg,
-  ws,
-  endgaps,
-  minsites,
-  maxsites,
-  wnsites,
-  spmap,
-  spfuzz,
-  prior,
-  beta,
-  maxiter,
-  distance,
-  num_sequences,
-  num_positions,
-  seed,
-  hsfrac,
-  maxwords,
-  maxsize,
-  csites,
-  strands,
-  priors_file,
-  reason_for_stopping,
-  back_order,
-  background_frequencies
 )>
 <!ELEMENT command_line (#PCDATA)*>
-<!ELEMENT host (#PCDATA)*>
-<!ELEMENT type (#PCDATA)*>
-<!ELEMENT nmotifs (#PCDATA)*>
-<!ELEMENT evalue_threshold (#PCDATA)*>
-<!ELEMENT object_function (#PCDATA)*>
-<!ELEMENT spfun (#PCDATA)*>
-<!ELEMENT min_width (#PCDATA)*>
-<!ELEMENT max_width (#PCDATA)*>
-<!ELEMENT wg (#PCDATA)*>
-<!ELEMENT ws (#PCDATA)*>
-<!ELEMENT endgaps (#PCDATA)*>
-<!ELEMENT minsites (#PCDATA)*>
-<!ELEMENT maxsites (#PCDATA)*>
-<!ELEMENT wnsites (#PCDATA)*>
-<!ELEMENT spmap (#PCDATA)*>
-<!ELEMENT spfuzz (#PCDATA)*>
-<!ELEMENT prior (#PCDATA)*>
-<!ELEMENT beta (#PCDATA)*>
-<!ELEMENT maxiter (#PCDATA)*>
-<!ELEMENT distance (#PCDATA)*>
-<!ELEMENT num_sequences (#PCDATA)*>
-<!ELEMENT num_positions (#PCDATA)*>
-<!ELEMENT seed (#PCDATA)*>
-<!ELEMENT hsfrac (#PCDATA)*>
-<!ELEMENT maxwords (#PCDATA)*>
-<!ELEMENT maxsites (#PCDATA)*>
-<!ELEMENT csites (#PCDATA)*>
-<!ELEMENT strands (#PCDATA)*>
-<!ELEMENT priors_file (#PCDATA)*>
-<!ELEMENT reason_for_stopping (#PCDATA)*>
-<!ELEMENT back_order (#PCDATA)*>
-<!ELEMENT background_frequencies (alphabet_array)>
-<!ATTLIST background_frequencies source CDATA #REQUIRED>
-
-<!-- Motif elements -->
 <!ELEMENT motifs (motif*)>
 <!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)>
-<!ATTLIST motif id ID #REQUIRED
-                name CDATA #REQUIRED
-                alt CDATA ""
-                width CDATA #REQUIRED
-                sites CDATA #REQUIRED
-                llr CDATA #REQUIRED
-                ic CDATA #REQUIRED
-                re CDATA #REQUIRED
-                bayes_threshold CDATA #REQUIRED
-                e_value CDATA #REQUIRED
-                elapsed_time CDATA #REQUIRED
-                url CDATA ""
->
-<!ELEMENT scores (alphabet_matrix)>
-<!ELEMENT probabilities (alphabet_matrix)>
-<!ELEMENT regular_expression (#PCDATA)*>
-
-<!-- Contributing site elements -->
-<!-- Contributing sites are motif occurences found during the motif discovery phase -->
-<!ELEMENT contributing_sites (contributing_site*)>
-<!ELEMENT contributing_site (left_flank, site, right_flank)>
-<!ATTLIST contributing_site sequence_id IDREF #REQUIRED
-                          position CDATA #REQUIRED
-                          strand (plus|minus|none) 'none'
-                          pvalue CDATA #REQUIRED
->
 <!-- The left_flank contains the sequence for 10 bases to the left of the motif start -->
 <!ELEMENT left_flank (#PCDATA)>
 <!-- The site contains the sequence for the motif instance -->
 <!ELEMENT site (letter_ref*)>
 <!-- The right_flank contains the sequence for 10 bases to the right of the motif end -->
 <!ELEMENT right_flank (#PCDATA)>
-
 <!-- Scanned site elements -->
 <!-- Scanned sites are motif occurences found during the sequence scan phase -->
 <!ELEMENT scanned_sites_summary (scanned_sites*)>
-<!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED>
-<!ELEMENT scanned_sites (scanned_site*)>
-<!ATTLIST scanned_sites sequence_id IDREF #REQUIRED
-                        pvalue CDATA #REQUIRED
-                        num_sites CDATA #REQUIRED>
-<!ELEMENT scanned_site EMPTY>
-<!ATTLIST scanned_site  motif_id IDREF #REQUIRED
-                        strand (plus|minus|none) 'none'
-                        position CDATA #REQUIRED
-                        pvalue CDATA #REQUIRED>
-
-<!-- Utility elements -->
-<!-- A reference to a letter in the alphabet -->
-<!ELEMENT letter_ref EMPTY>
-<!ATTLIST letter_ref letter_id IDREF #REQUIRED>
-<!-- A alphabet-array contains one floating point value for each letter in an alphabet -->
-<!ELEMENT alphabet_array (value*)>
-<!ELEMENT value (#PCDATA)>
-<!ATTLIST value letter_id IDREF #REQUIRED>
-
-<!-- A alphabet_matrix contains one alphabet_array for each position in a motif -->
-<!ELEMENT alphabet_matrix (alphabet_array*)>
-
-]>
-<!-- Begin document body -->
-<MEME version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
-<training_set datafile="Galaxy_FASTA_Input" length="30">
+<training_set primary_sequences="Galaxy_FASTA_Input" primary_count="30" primary_positions="1500" control_sequences="--none--" control_count="0" control_positions="0">
 <alphabet name="DNA" like="dna">
 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
-<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
-<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
-<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
-<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
-<letter id="V" symbol="V" equals="ACG" name="Not T"/>
-<letter id="H" symbol="H" equals="ACT" name="Not G"/>
-<letter id="D" symbol="D" equals="AGT" name="Not C"/>
-<letter id="B" symbol="B" equals="CGT" name="Not A"/>
-<letter id="M" symbol="M" equals="AC" name="Amino"/>
-<letter id="R" symbol="R" equals="AG" name="Purine"/>
-<letter id="W" symbol="W" equals="AT" name="Weak"/>
-<letter id="S" symbol="S" equals="CG" name="Strong"/>
-<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
-<letter id="K" symbol="K" equals="GT" name="Keto"/>
-</alphabet>
 <sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" />
-<sequence id="sequence_1" name="chr21_26934381_26934431_+" length="50" weight="1.000000" />
-<sequence id="sequence_2" name="chr21_28217753_28217803_-" length="50" weight="1.000000" />
-<sequence id="sequence_3" name="chr21_31710037_31710087_-" length="50" weight="1.000000" />
-<sequence id="sequence_4" name="chr21_31744582_31744632_-" length="50" weight="1.000000" />
-<sequence id="sequence_5" name="chr21_31768316_31768366_+" length="50" weight="1.000000" />
-<sequence id="sequence_6" name="chr21_31914206_31914256_-" length="50" weight="1.000000" />
-<sequence id="sequence_7" name="chr21_31933633_31933683_-" length="50" weight="1.000000" />
-<sequence id="sequence_8" name="chr21_31962741_31962791_-" length="50" weight="1.000000" />
-<sequence id="sequence_9" name="chr21_31964683_31964733_+" length="50" weight="1.000000" />
-<sequence id="sequence_10" name="chr21_31973364_31973414_+" length="50" weight="1.000000" />
-<sequence id="sequence_11" name="chr21_31992870_31992920_+" length="50" weight="1.000000" />
-<sequence id="sequence_12" name="chr21_32185595_32185645_-" length="50" weight="1.000000" />
-<sequence id="sequence_13" name="chr21_32202076_32202126_-" length="50" weight="1.000000" />
-<sequence id="sequence_14" name="chr21_32253899_32253949_-" length="50" weight="1.000000" />
-<sequence id="sequence_15" name="chr21_32410820_32410870_-" length="50" weight="1.000000" />
-<sequence id="sequence_16" name="chr21_36411748_36411798_-" length="50" weight="1.000000" />
-<sequence id="sequence_17" name="chr21_37838750_37838800_-" length="50" weight="1.000000" />
-<sequence id="sequence_18" name="chr21_45705687_45705737_+" length="50" weight="1.000000" />
-<sequence id="sequence_19" name="chr21_45971413_45971463_-" length="50" weight="1.000000" />
-<sequence id="sequence_20" name="chr21_45978668_45978718_-" length="50" weight="1.000000" />
-<sequence id="sequence_21" name="chr21_45993530_45993580_+" length="50" weight="1.000000" />
-<sequence id="sequence_22" name="chr21_46020421_46020471_+" length="50" weight="1.000000" />
-<sequence id="sequence_23" name="chr21_46031920_46031970_+" length="50" weight="1.000000" />
-<sequence id="sequence_24" name="chr21_46046964_46047014_+" length="50" weight="1.000000" />
-<sequence id="sequence_25" name="chr21_46057197_46057247_+" length="50" weight="1.000000" />
-<sequence id="sequence_26" name="chr21_46086869_46086919_-" length="50" weight="1.000000" />
-<sequence id="sequence_27" name="chr21_46102103_46102153_-" length="50" weight="1.000000" />
-<sequence id="sequence_28" name="chr21_47517957_47518007_+" length="50" weight="1.000000" />
-<sequence id="sequence_29" name="chr21_47575506_47575556_-" length="50" weight="1.000000" />
-<letter_frequencies>
-<alphabet_array>
-<value letter_id="A">0.294</value>
-<value letter_id="C">0.231</value>
 <value letter_id="G">0.257</value>
 <value letter_id="T">0.217</value>
 </alphabet_array>
-</letter_frequencies>
-</training_set>
 <model>
-<command_line>meme meme_input_1.fasta -o meme_test2_out -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib prior30.plib -spmap uni -spfuzz 0.5 </command_line>
-<host>ThinkPad-T450s</host>
 <type>zoops</type>
-<nmotifs>1</nmotifs>
-<evalue_threshold>inf</evalue_threshold>
-<object_function>E-value of product of p-values</object_function>
-<use_llr>0</use_llr>
-<min_width>8</min_width>
-<max_width>50</max_width>
-<wg>11</wg>
-<ws>1</ws>
-<endgaps>yes</endgaps>
-<substring>yes</substring>
-<minsites>2</minsites>
-<maxsites>30</maxsites>
-<wnsites>0.8</wnsites>
-<spmap>uni</spmap>
-<spfuzz>0.5</spfuzz>
-<prior>dirichlet</prior>
-<beta>0.01</beta>
-<maxiter>50</maxiter>
-<distance>0.001</distance>
-<num_sequences>30</num_sequences>
-<num_positions>1500</num_positions>
-<seed>0</seed>
-<ctfrac>-1</ctfrac>
-<maxwords>-1</maxwords>
-<strands>forward</strands>
-<priors_file>prior30.plib</priors_file>
-<reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping>
-<background_frequencies source="dataset with add-one prior applied">
-<alphabet_array>
-<value letter_id="A">0.294</value>
-<value letter_id="C">0.231</value>
-<value letter_id="G">0.257</value>
-<value letter_id="T">0.217</value>
-</alphabet_array>
-</background_frequencies>
-</model>
-<motifs>
-<motif id="motif_1" name="GGSRTATAAAA" alt="MEME-1" width="11" sites="30" ic="13.0" re="12.2" llr="254" e_value="5.1e-040" bayes_threshold="5.2854" elapsed_time="0.376000">
 <scores>
 <alphabet_matrix>
 <alphabet_array>
 <value letter_id="A">-14</value>
-<value letter_id="C">-179</value>
-<value letter_id="G">114</value>
-<value letter_id="T">-112</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">3</value>
-<value letter_id="C">-1155</value>
-<value letter_id="G">137</value>
-<value letter_id="T">-270</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">-114</value>
-<value letter_id="C">20</value>
-<value letter_id="G">86</value>
-<value letter_id="T">-71</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">3</value>
-<value letter_id="C">-279</value>
-<value letter_id="G">122</value>
-<value letter_id="T">-170</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">-1155</value>
-<value letter_id="C">-1155</value>
-<value letter_id="G">-295</value>
-<value letter_id="T">215</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">156</value>
-<value letter_id="C">-179</value>
-<value letter_id="G">-1155</value>
-<value letter_id="T">-170</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">-1155</value>
-<value letter_id="C">-1155</value>
-<value letter_id="G">-1155</value>
-<value letter_id="T">220</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">172</value>
-<value letter_id="C">-279</value>
-<value letter_id="G">-1155</value>
-<value letter_id="T">-1155</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">125</value>
-<value letter_id="C">-1155</value>
-<value letter_id="G">-1155</value>
-<value letter_id="T">46</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">167</value>
-<value letter_id="C">-179</value>
-<value letter_id="G">-1155</value>
-<value letter_id="T">-1155</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">144</value>
-<value letter_id="C">-1155</value>
-<value letter_id="G">-63</value>
-<value letter_id="T">-270</value>
-</alphabet_array>
-</alphabet_matrix>
-</scores>
-<probabilities>
-<alphabet_matrix>
-<alphabet_array>
 <value letter_id="A">0.266667</value>
-<value letter_id="C">0.066667</value>
-<value letter_id="G">0.566667</value>
-<value letter_id="T">0.100000</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">0.300000</value>
-<value letter_id="C">0.000000</value>
-<value letter_id="G">0.666667</value>
-<value letter_id="T">0.033333</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.133333</value>
-<value letter_id="C">0.266667</value>
-<value letter_id="G">0.466667</value>
-<value letter_id="T">0.133333</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.300000</value>
-<value letter_id="C">0.033333</value>
-<value letter_id="G">0.600000</value>
-<value letter_id="T">0.066667</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.000000</value>
-<value letter_id="C">0.000000</value>
-<value letter_id="G">0.033333</value>
-<value letter_id="T">0.966667</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.866667</value>
-<value letter_id="C">0.066667</value>
-<value letter_id="G">0.000000</value>
-<value letter_id="T">0.066667</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.000000</value>
-<value letter_id="C">0.000000</value>
-<value letter_id="G">0.000000</value>
-<value letter_id="T">1.000000</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.966667</value>
-<value letter_id="C">0.033333</value>
-<value letter_id="G">0.000000</value>
-<value letter_id="T">0.000000</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.700000</value>
-<value letter_id="C">0.000000</value>
-<value letter_id="G">0.000000</value>
-<value letter_id="T">0.300000</value>
-</alphabet_array>
-<alphabet_array>
-<value letter_id="A">0.933333</value>
-<value letter_id="C">0.066667</value>
-<value letter_id="G">0.000000</value>
-<value letter_id="T">0.000000</value>
-</alphabet_array>
-<alphabet_array>
 <value letter_id="A">0.800000</value>
-<value letter_id="C">0.000000</value>
-<value letter_id="G">0.166667</value>
-<value letter_id="T">0.033333</value>
-</alphabet_array>
-</alphabet_matrix>
-</probabilities>
-<regular_expression>
-[GA][GA][GC][GA]TATA[AT]AA
-</regular_expression>
-<contributing_sites>
 <contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" >
 <left_flank>AAGGCCAGGA</left_flank>
-<site>
 <letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
 <right_flank>GCCTGAGAGC</right_flank>
-</contributing_site>
 <contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" >
-<left_flank>ATACCCAGGG</left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>CCTCAGCAGC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >
-<left_flank>CCACCAGCTT</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>AGCCCTGTAC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >
-<left_flank>ACAGGCCCTG</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>GCC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_21" position="7" strand="plus" pvalue="4.86e-06" >
-<left_flank>CCAAGGA</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>GCCCCACAAA</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_19" position="9" strand="plus" pvalue="4.86e-06" >
-<left_flank>CAGGCCCTG</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>GCCCCAGCAG</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_9" position="13" strand="plus" pvalue="4.86e-06" >
-<left_flank>GATTCACTGA</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>GGCCCTCTGC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_28" position="32" strand="plus" pvalue="6.48e-06" >
-<left_flank>CCGGCGGGGC</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-</site>
-<right_flank>GGGGCGG</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_20" position="4" strand="plus" pvalue="6.48e-06" >
-<left_flank>CAGA</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
 <letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-</site>
-<right_flank>GTTCCGACCA</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_12" position="18" strand="plus" pvalue="6.48e-06" >
-<left_flank>CACCAGAGCT</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>AGAAGGTTCT</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_15" position="21" strand="plus" pvalue="1.38e-05" >
-<left_flank>AATCACTGAG</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>GTCCCAGGGA</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_11" position="16" strand="plus" pvalue="1.38e-05" >
-<left_flank>CACTATTGAA</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>TTTCATTTGC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_0" position="39" strand="plus" pvalue="1.41e-05" >
-<left_flank>CCTCGGGACG</left_flank>
-<site>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank></right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_6" position="15" strand="plus" pvalue="1.61e-05" >
-<left_flank>CCCACTACTT</left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>TCATTCTGAG</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_22" position="2" strand="plus" pvalue="1.95e-05" >
-<left_flank>GA</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>GCCAACATCC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_14" position="17" strand="plus" pvalue="1.95e-05" >
-<left_flank>CCCACCAGCA</left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>AAGCTCAGGA</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_18" position="37" strand="plus" pvalue="2.16e-05" >
+<contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" >
+<right_flank>AGCCCTGTAC</right_flank>
+<contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" >
 <left_flank>CGTGGTCGCG</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-</site>
 <right_flank>GC</right_flank>
-</contributing_site>
 <contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" >
 <left_flank>GCTGCCGGTG</left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-</site>
 <right_flank>GCCCTGGCG</right_flank>
-</contributing_site>
 <contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" >
-<left_flank>CAGGTCTAAG</left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>CTTGGAGTCC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_5" position="0" strand="plus" pvalue="3.67e-05" >
-<left_flank></left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>ATGGTCCTGT</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_1" position="27" strand="plus" pvalue="3.93e-05" >
-<left_flank>AGTCACAAGT</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>GGGTCGCACG</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_7" position="4" strand="plus" pvalue="5.65e-05" >
-<left_flank>TCAG</left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>ATGTTCCTGT</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_3" position="14" strand="plus" pvalue="6.24e-05" >
-<left_flank>CCCAGGTTTC</left_flank>
-<site>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>TCGCCGCACC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_16" position="22" strand="plus" pvalue="7.15e-05" >
-<left_flank>AGTTTCAGTT</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>attatataac</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_27" position="36" strand="plus" pvalue="1.39e-04" >
-<left_flank>TGCCTGGGTC</left_flank>
-<site>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-</site>
-<right_flank>GCT</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_26" position="37" strand="plus" pvalue="1.39e-04" >
-<left_flank>TGCCTGGGCC</left_flank>
-<site>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="G"/>
-</site>
-<right_flank>GC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_17" position="2" strand="plus" pvalue="4.81e-04" >
-<left_flank>ga</left_flank>
-<site>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>ggggcctcac</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_8" position="13" strand="plus" pvalue="8.57e-04" >
-<left_flank>TATAACTCAG</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>TAATTTGTAC</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_10" position="7" strand="plus" pvalue="1.47e-03" >
-<left_flank>aaactta</left_flank>
-<site>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="A"/>
-</site>
-<right_flank>acttaaaact</right_flank>
-</contributing_site>
-<contributing_site sequence_id="sequence_2" position="26" strand="plus" pvalue="2.64e-03" >
-<left_flank>GGTGGGGGTG</left_flank>
-<site>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="G"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="T"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="A"/>
-<letter_ref letter_id="C"/>
-<letter_ref letter_id="T"/>
-</site>
-<right_flank>GGTCCACTAT</right_flank>
-</contributing_site>
-</contributing_sites>
-</motif>
-</motifs>
 <scanned_sites_summary p_thresh="0.0001">
 <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"/>
-</scanned_sites>
 <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"/>
-</scanned_sites>
 <scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites>
-<scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.04e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites>
-<scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites>
-<scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites>
-<scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites>
-<scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites>
-<scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/>
-</scanned_sites>
-<scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/>
-</scanned_sites>
-</scanned_sites_summary>
 </MEME>