<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
<!-- Document definition -->
<!DOCTYPE MEME[
<!ELEMENT MEME (
  training_set,
  model, 
  motifs, 
  scanned_sites_summary?
)>
<!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>
<!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="4.11.3" release="Fri Feb 19 13:23:06 2016 -0800">
<training_set datafile="common/crp0.s" length="18">
<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="ce1cg" length="105" weight="1.000000" />
<sequence id="sequence_1" name="ara" length="105" weight="1.000000" />
<sequence id="sequence_2" name="bglr1" length="105" weight="1.000000" />
<sequence id="sequence_3" name="crp" length="105" weight="1.000000" />
<sequence id="sequence_4" name="cya" length="105" weight="1.000000" />
<sequence id="sequence_5" name="deop2" length="105" weight="1.000000" />
<sequence id="sequence_6" name="gale" length="105" weight="1.000000" />
<sequence id="sequence_7" name="ilv" length="105" weight="1.000000" />
<sequence id="sequence_8" name="lac" length="105" weight="1.000000" />
<sequence id="sequence_9" name="male" length="105" weight="1.000000" />
<sequence id="sequence_10" name="malk" length="105" weight="1.000000" />
<sequence id="sequence_11" name="malt" length="105" weight="1.000000" />
<sequence id="sequence_12" name="ompa" length="105" weight="1.000000" />
<sequence id="sequence_13" name="tnaa" length="105" weight="1.000000" />
<sequence id="sequence_14" name="uxu1" length="105" weight="1.000000" />
<sequence id="sequence_15" name="pbr322" length="105" weight="1.000000" />
<sequence id="sequence_16" name="trn9cat" length="105" weight="1.000000" />
<sequence id="sequence_17" name="tdc" length="105" weight="1.000000" />
<letter_frequencies>
<alphabet_array>
<value letter_id="A">0.304</value>
<value letter_id="C">0.196</value>
<value letter_id="G">0.196</value>
<value letter_id="T">0.304</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme common/crp0.s -oc results/meme3 -mod tcm -dna -revcomp -nmotifs 2 -minw 8 -nostatus </command_line>
<host>Timothys-iMac.rd.unr.edu</host>
<type>tcm</type>
<nmotifs>2</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>50</maxsites>
<wnsites>0.8</wnsites>
<spmap>uni</spmap>
<spfuzz>0.5</spfuzz>
<prior>dirichlet</prior>
<beta>0.01</beta>
<maxiter>50</maxiter>
<distance>1e-05</distance>
<num_sequences>18</num_sequences>
<num_positions>1890</num_positions>
<seed>0</seed>
<ctfrac>-1</ctfrac>
<maxwords>-1</maxwords>
<strands>both</strands>
<priors_file></priors_file>
<reason_for_stopping>Stopped because requested number of motifs (2) found.</reason_for_stopping>
<background_frequencies source="dataset with add-one prior applied">
<alphabet_array>
<value letter_id="A">0.304</value>
<value letter_id="C">0.196</value>
<value letter_id="G">0.196</value>
<value letter_id="T">0.304</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="WWWATKTGAHCNABNTCACA" alt="MEME-1" width="20" sites="18" ic="16.6" re="15.9" llr="198" e_value="4.8e-004" bayes_threshold="6.5452" elapsed_time="0.495632">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">55</value>
<value letter_id="C">-82</value>
<value letter_id="G">-1081</value>
<value letter_id="T">55</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">72</value>
<value letter_id="C">-1081</value>
<value letter_id="G">-82</value>
<value letter_id="T">35</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">13</value>
<value letter_id="C">-1081</value>
<value letter_id="G">-1081</value>
<value letter_id="T">113</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">72</value>
<value letter_id="C">-23</value>
<value letter_id="G">-23</value>
<value letter_id="T">-87</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-245</value>
<value letter_id="C">50</value>
<value letter_id="G">-182</value>
<value letter_id="T">101</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-245</value>
<value letter_id="C">-182</value>
<value letter_id="G">150</value>
<value letter_id="T">13</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1081</value>
<value letter_id="C">18</value>
<value letter_id="G">-1081</value>
<value letter_id="T">135</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-45</value>
<value letter_id="C">-1081</value>
<value letter_id="G">177</value>
<value letter_id="T">-145</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">113</value>
<value letter_id="C">50</value>
<value letter_id="G">-1081</value>
<value letter_id="T">-245</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">35</value>
<value letter_id="C">18</value>
<value letter_id="G">-23</value>
<value letter_id="T">-45</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-245</value>
<value letter_id="C">188</value>
<value letter_id="G">-23</value>
<value letter_id="T">-245</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-13</value>
<value letter_id="C">18</value>
<value letter_id="G">77</value>
<value letter_id="T">-87</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">125</value>
<value letter_id="C">-1081</value>
<value letter_id="G">-23</value>
<value letter_id="T">-145</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-145</value>
<value letter_id="C">50</value>
<value letter_id="G">18</value>
<value letter_id="T">35</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-13</value>
<value letter_id="C">-23</value>
<value letter_id="G">50</value>
<value letter_id="T">-13</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1081</value>
<value letter_id="C">-23</value>
<value letter_id="G">-1081</value>
<value letter_id="T">145</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-245</value>
<value letter_id="C">227</value>
<value letter_id="G">-1081</value>
<value letter_id="T">-1081</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">155</value>
<value letter_id="C">-1081</value>
<value letter_id="G">-182</value>
<value letter_id="T">-245</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1081</value>
<value letter_id="C">235</value>
<value letter_id="G">-1081</value>
<value letter_id="T">-1081</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">163</value>
<value letter_id="C">-1081</value>
<value letter_id="G">-182</value>
<value letter_id="T">-1081</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.444444</value>
<value letter_id="C">0.111111</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.444444</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.500000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.111111</value>
<value letter_id="T">0.388889</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.666667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.500000</value>
<value letter_id="C">0.166667</value>
<value letter_id="G">0.166667</value>
<value letter_id="T">0.166667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.055556</value>
<value letter_id="C">0.277778</value>
<value letter_id="G">0.055556</value>
<value letter_id="T">0.611111</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.055556</value>
<value letter_id="C">0.055556</value>
<value letter_id="G">0.555556</value>
<value letter_id="T">0.333333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.222222</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.777778</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.222222</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="T">0.111111</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.666667</value>
<value letter_id="C">0.277778</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.055556</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.388889</value>
<value letter_id="C">0.222222</value>
<value letter_id="G">0.166667</value>
<value letter_id="T">0.222222</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.055556</value>
<value letter_id="C">0.722222</value>
<value letter_id="G">0.166667</value>
<value letter_id="T">0.055556</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.277778</value>
<value letter_id="C">0.222222</value>
<value letter_id="G">0.333333</value>
<value letter_id="T">0.166667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.722222</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.166667</value>
<value letter_id="T">0.111111</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.111111</value>
<value letter_id="C">0.277778</value>
<value letter_id="G">0.222222</value>
<value letter_id="T">0.388889</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.277778</value>
<value letter_id="C">0.166667</value>
<value letter_id="G">0.277778</value>
<value letter_id="T">0.277778</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.166667</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.833333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.055556</value>
<value letter_id="C">0.944444</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.888889</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.055556</value>
<value letter_id="T">0.055556</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.944444</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.055556</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[AT][AT][TA]A[TC][GT][TC][GA][AC][ACT]C[GAC]A[TCG][AGT]TCACA
</regular_expression>
<contributing_sites>
<contributing_site sequence_id="sequence_1" position="53" strand="plus" pvalue="4.15e-08" >
<left_flank>GTCCACATTG</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>CTTTGCTATG</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_5" position="5" strand="plus" pvalue="5.85e-07" >
<left_flank>AGTGA</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>TTACAGTGAT</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_3" position="61" strand="plus" pvalue="7.31e-07" >
<left_flank>ATGTACTGCA</left_flank>
<site>
<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="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>TTACCGTGCA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_0" position="19" strand="minus" pvalue="9.08e-07" >
<left_flank>CACCACGCGC</left_flank>
<site>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>AAAACCAGCA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_0" position="59" strand="plus" pvalue="1.38e-06" >
<left_flank>TGAAAGACTG</left_flank>
<site>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<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="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>AAAATGGAAG</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_11" position="43" strand="minus" pvalue="1.69e-06" >
<left_flank>TTTATGTGTC</left_flank>
<site>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>ATTCCAAATC</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_15" position="55" strand="minus" pvalue="1.86e-06" >
<left_flank>TCTCCTTACG</left_flank>
<site>
<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="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<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="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="A"/>
</site>
<right_flank>CCGCATATGG</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_12" position="46" strand="plus" pvalue="1.86e-06" >
<left_flank>TTTTTTTTCA</left_flank>
<site>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<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="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>CTTGTAAGTT</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_4" position="52" strand="minus" pvalue="2.72e-06" >
<left_flank>AAAATGGTCT</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<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="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<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>CCTTGCTGAT</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_14" position="19" strand="minus" pvalue="2.98e-06" >
<left_flank>CCGAATTCTA</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<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="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>ACAATTTCAC</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_9" position="12" strand="plus" pvalue="3.27e-06" >
<left_flank>ATTACCGCCA</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<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"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>CAAAGCGACG</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_8" position="11" strand="minus" pvalue="4.65e-06" >
<left_flank>TGGGGTGCCT</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<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="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<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="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>TTAATTGCGT</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_7" position="37" strand="plus" pvalue="5.52e-06" >
<left_flank>AATTCAGTAC</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<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="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>ATTTTCCCTT</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_2" position="78" strand="minus" pvalue="6.01e-06" >
<left_flank>ATTGATA</left_flank>
<site>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>GTTATTAACT</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_13" position="73" strand="minus" pvalue="6.52e-06" >
<left_flank>TGAAATTGTT</left_flank>
<site>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>ATCGTTCGGG</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_8" position="75" strand="minus" pvalue="6.52e-06" >
<left_flank>GTGAAATTGT</left_flank>
<site>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>CAACATACGA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_10" position="63" strand="minus" pvalue="1.23e-05" >
<left_flank>ATCGCCACGA</left_flank>
<site>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>AAATTCCTTA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_6" position="40" strand="plus" pvalue="1.53e-05" >
<left_flank>AACGATTCCA</left_flank>
<site>
<letter_ref letter_id="C"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="A"/>
<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="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="A"/>
</site>
<right_flank>CTTTTCGCAT</right_flank>
</contributing_site>
</contributing_sites>
</motif>
<motif id="motif_2" name="CGGYGGGG" alt="MEME-2" width="8" sites="2" ic="15.0" re="17.5" llr="24" e_value="1.6e+004" bayes_threshold="9.783" elapsed_time="0.830177">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">235</value>
<value letter_id="G">-765</value>
<value letter_id="T">-765</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">-765</value>
<value letter_id="G">235</value>
<value letter_id="T">-765</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">-765</value>
<value letter_id="G">235</value>
<value letter_id="T">-765</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">135</value>
<value letter_id="G">-765</value>
<value letter_id="T">71</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">-765</value>
<value letter_id="G">235</value>
<value letter_id="T">-765</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">-765</value>
<value letter_id="G">235</value>
<value letter_id="T">-765</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">-765</value>
<value letter_id="G">235</value>
<value letter_id="T">-765</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-765</value>
<value letter_id="C">-765</value>
<value letter_id="G">235</value>
<value letter_id="T">-765</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">1.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.500000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.500000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">1.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
CGG[CT]GGGG
</regular_expression>
<contributing_sites>
<contributing_site sequence_id="sequence_7" position="4" strand="plus" pvalue="2.18e-06" >
<left_flank>GCTC</left_flank>
<site>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>TTTTTTGTTA</right_flank>
</contributing_site>
<contributing_site sequence_id="sequence_9" position="40" strand="plus" pvalue="5.56e-06" >
<left_flank>CACAAAGCGA</left_flank>
<site>
<letter_ref letter_id="C"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="T"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
<letter_ref letter_id="G"/>
</site>
<right_flank>CGTAGGGGCA</right_flank>
</contributing_site>
</contributing_sites>
</motif>
</motifs>
<scanned_sites_summary p_thresh="0.0001">
<scanned_sites sequence_id="sequence_0" pvalue="9.14e-04" num_sites="2"><scanned_site motif_id="motif_1" strand="minus" position="19" pvalue="9.08e-07"/>
<scanned_site motif_id="motif_1" strand="plus" position="59" pvalue="1.38e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_1" pvalue="7.87e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="53" pvalue="4.15e-08"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_2" pvalue="7.92e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="minus" position="78" pvalue="6.01e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_3" pvalue="1.08e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="61" pvalue="7.31e-07"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_4" pvalue="3.50e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="minus" position="52" pvalue="2.72e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_5" pvalue="6.14e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="5" pvalue="5.85e-07"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_6" pvalue="1.82e-02" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="40" pvalue="1.53e-05"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_7" pvalue="6.37e-06" num_sites="2"><scanned_site motif_id="motif_2" strand="plus" position="4" pvalue="2.18e-06"/>
<scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="5.52e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_8" pvalue="3.95e-03" num_sites="2"><scanned_site motif_id="motif_1" strand="minus" position="11" pvalue="4.65e-06"/>
<scanned_site motif_id="motif_1" strand="minus" position="75" pvalue="6.52e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_9" pvalue="9.36e-06" num_sites="2"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.27e-06"/>
<scanned_site motif_id="motif_2" strand="plus" position="40" pvalue="5.56e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_10" pvalue="3.60e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="minus" position="63" pvalue="1.23e-05"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_11" pvalue="2.29e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="minus" position="43" pvalue="1.69e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_12" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="46" pvalue="1.86e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_13" pvalue="3.58e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="minus" position="73" pvalue="6.52e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_14" pvalue="2.66e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="minus" position="19" pvalue="2.98e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_15" pvalue="1.17e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="minus" position="55" pvalue="1.86e-06"/>
</scanned_sites>
<scanned_sites sequence_id="sequence_16" pvalue="9.86e-01" num_sites="0"></scanned_sites>
<scanned_sites sequence_id="sequence_17" pvalue="1.63e-01" num_sites="0"></scanned_sites>
</scanned_sites_summary>
</MEME>
