<?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 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_positions,
  seed,
  hsfrac,
  searchsize,
  maxsize,
  norand,
  csites,
  strands,
  brief,
  psp_file,
  priors_file,
  reason_for_stopping,
  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_positions (#PCDATA)*>
<!ELEMENT seed (#PCDATA)*>
<!ELEMENT hsfrac (#PCDATA)*>
<!ELEMENT searchsize (#PCDATA)*>
<!ELEMENT maxsize (#PCDATA)*>
<!ELEMENT norand (#PCDATA)*>
<!ELEMENT csites (#PCDATA)*>
<!ELEMENT strands (#PCDATA)*>
<!ELEMENT brief (#PCDATA)*>
<!ELEMENT psp_file (#PCDATA)*>
<!ELEMENT priors_file (#PCDATA)*>
<!ELEMENT reason_for_stopping (#PCDATA)*>
<!ELEMENT background_frequencies (alphabet_array)>
<!ATTLIST background_frequencies source CDATA #REQUIRED
		   order 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
                ic CDATA #REQUIRED
                re CDATA #REQUIRED
                llr CDATA #REQUIRED
                p_value CDATA #REQUIRED
                e_value CDATA #REQUIRED
                bayes_threshold 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="5.4.1" release="Sat Aug 21 19:23:23 2021 -0700">
<training_set primary_sequences="./seqs-centered" primary_count="3019" primary_positions="301900" 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>
<letter_frequencies>
<alphabet_array>
<value letter_id="A">0.189</value>
<value letter_id="C">0.311</value>
<value letter_id="G">0.311</value>
<value letter_id="T">0.189</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme ./seqs-centered -oc meme_out -mod zoops -nmotifs 50 -minw 6 -maxw 15 -bfile ./background -dna -searchsize 100000 -time 2919 -revcomp -nostatus </command_line>
<host>noble-meme.grid.gs.washington.edu</host>
<type>zoops</type>
<nmotifs>50</nmotifs>
<evalue_threshold>inf</evalue_threshold>
<object_function>E-value of product of p-values</object_function>
<spfun>E-value of product of p-values</spfun>
<min_width>6</min_width>
<max_width>15</max_width>
<wg>11</wg>
<ws>1</ws>
<endgaps>yes</endgaps>
<substring>yes</substring>
<minsites>2</minsites>
<maxsites>3019</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_positions>301900</num_positions>
<seed>0</seed>
<hsfrac>0</hsfrac>
<searchsize>100000</searchsize>
<maxsize>0</maxsize>
<norand>no</norand>
<csites>1000</csites>
<strands>both</strands>
<brief>1000</brief>
<psp_file></psp_file>
<priors_file></priors_file>
<reason_for_stopping>Stopped because MEME would probably exceed the allowed time (2919.00 secs) before finding the next motif.</reason_for_stopping>
<background_frequencies source="./background" order="2">
<alphabet_array>
<value letter_id="A">0.179</value>
<value letter_id="C">0.321</value>
<value letter_id="G">0.321</value>
<value letter_id="T">0.179</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="TCARTACATMAMAAA" alt="MEME-1" width="15" sites="30" ic="18.3" re="22.0" llr="458" p_value="4.3e-092" e_value="8.8e-010" bayes_threshold="14.7844" elapsed_time="430.841430">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-242</value>
<value letter_id="C">-1155</value>
<value letter_id="G">-1155</value>
<value letter_id="T">243</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-42</value>
<value letter_id="C">119</value>
<value letter_id="G">-1155</value>
<value letter_id="T">-42</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">233</value>
<value letter_id="C">-326</value>
<value letter_id="G">-1155</value>
<value letter_id="T">-142</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">90</value>
<value letter_id="C">-1155</value>
<value letter_id="G">105</value>
<value letter_id="T">-1155</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-242</value>
<value letter_id="C">-168</value>
<value letter_id="G">-1155</value>
<value letter_id="T">228</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">216</value>
<value letter_id="C">-227</value>
<value letter_id="G">-1155</value>
<value letter_id="T">-42</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-142</value>
<value letter_id="C">126</value>
<value letter_id="G">-127</value>
<value letter_id="T">-242</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">166</value>
<value letter_id="C">-95</value>
<value letter_id="G">-1155</value>
<value letter_id="T">58</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">248</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">90</value>
<value letter_id="C">73</value>
<value letter_id="G">-1155</value>
<value letter_id="T">-42</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">228</value>
<value letter_id="C">-1155</value>
<value letter_id="G">-326</value>
<value letter_id="T">-84</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">90</value>
<value letter_id="C">105</value>
<value letter_id="G">-1155</value>
<value letter_id="T">-1155</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">216</value>
<value letter_id="C">-1155</value>
<value letter_id="G">-1155</value>
<value letter_id="T">16</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">248</value>
<value letter_id="C">-1155</value>
<value letter_id="G">-1155</value>
<value letter_id="T">-1155</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">203</value>
<value letter_id="C">-326</value>
<value letter_id="G">-68</value>
<value letter_id="T">-242</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.033333</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.966667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.133333</value>
<value letter_id="C">0.733333</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.133333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.900000</value>
<value letter_id="C">0.033333</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.066667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.666667</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.033333</value>
<value letter_id="C">0.100000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.866667</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.800000</value>
<value letter_id="C">0.066667</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.133333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.066667</value>
<value letter_id="C">0.766667</value>
<value letter_id="G">0.133333</value>
<value letter_id="T">0.033333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.566667</value>
<value letter_id="C">0.166667</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.266667</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">0.333333</value>
<value letter_id="C">0.533333</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.133333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.866667</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.033333</value>
<value letter_id="T">0.100000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.333333</value>
<value letter_id="C">0.666667</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">0.000000</value>
<value letter_id="T">0.200000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">1.000000</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.733333</value>
<value letter_id="C">0.033333</value>
<value letter_id="G">0.200000</value>
<value letter_id="T">0.033333</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
TCA[GA]TAC[AT]T[CA]A[CA][AT]A[AG]
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
<motif id="motif_2" name="KCGTCGSTCAT" alt="MEME-2" width="11" sites="367" ic="12.6" re="13.2" llr="3353" p_value="2.9e-506" e_value="2.7e-028" bayes_threshold="11.6216" elapsed_time="788.802696">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-79</value>
<value letter_id="C">-1516</value>
<value letter_id="G">5</value>
<value letter_id="T">166</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-258</value>
<value letter_id="C">76</value>
<value letter_id="G">-88</value>
<value letter_id="T">50</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-75</value>
<value letter_id="C">-21</value>
<value letter_id="G">94</value>
<value letter_id="T">-1516</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1516</value>
<value letter_id="C">-1516</value>
<value letter_id="G">-37</value>
<value letter_id="T">207</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1516</value>
<value letter_id="C">122</value>
<value letter_id="G">-488</value>
<value letter_id="T">42</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1</value>
<value letter_id="C">-279</value>
<value letter_id="G">101</value>
<value letter_id="T">-45</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-323</value>
<value letter_id="C">75</value>
<value letter_id="G">33</value>
<value letter_id="T">-223</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1516</value>
<value letter_id="C">-230</value>
<value letter_id="G">-1516</value>
<value letter_id="T">239</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1516</value>
<value letter_id="C">152</value>
<value letter_id="G">-202</value>
<value letter_id="T">-1516</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">248</value>
<value letter_id="C">-1516</value>
<value letter_id="G">-1516</value>
<value letter_id="T">-1516</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1516</value>
<value letter_id="C">-1516</value>
<value letter_id="G">-1516</value>
<value letter_id="T">248</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.103542</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.332425</value>
<value letter_id="T">0.564033</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.029973</value>
<value letter_id="C">0.542234</value>
<value letter_id="G">0.174387</value>
<value letter_id="T">0.253406</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.106267</value>
<value letter_id="C">0.277929</value>
<value letter_id="G">0.615804</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">0.247956</value>
<value letter_id="T">0.752044</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.749319</value>
<value letter_id="G">0.010899</value>
<value letter_id="T">0.239782</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.177112</value>
<value letter_id="C">0.046322</value>
<value letter_id="G">0.645777</value>
<value letter_id="T">0.130790</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.019074</value>
<value letter_id="C">0.539510</value>
<value letter_id="G">0.403270</value>
<value letter_id="T">0.038147</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.065395</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.934605</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.920981</value>
<value letter_id="G">0.079019</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">1.000000</value>
<value letter_id="C">0.000000</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">0.000000</value>
<value letter_id="T">1.000000</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[TG][CT][GC][TG][CT]G[CG]TCAT
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
<motif id="motif_3" name="WAAKVSTTDT" alt="MEME-3" width="10" sites="121" ic="11.9" re="14.6" llr="1225" p_value="1.1e-214" e_value="1.3e-002" bayes_threshold="13.3782" elapsed_time="1137.324825">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">152</value>
<value letter_id="C">-1356</value>
<value letter_id="G">-1356</value>
<value letter_id="T">145</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">248</value>
<value letter_id="C">-1356</value>
<value letter_id="G">-1356</value>
<value letter_id="T">-1356</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">248</value>
<value letter_id="C">-1356</value>
<value letter_id="G">-1356</value>
<value letter_id="T">-1356</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1356</value>
<value letter_id="C">-58</value>
<value letter_id="G">47</value>
<value letter_id="T">92</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">61</value>
<value letter_id="C">-24</value>
<value letter_id="G">1</value>
<value letter_id="T">-44</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-27</value>
<value letter_id="C">-7</value>
<value letter_id="G">63</value>
<value letter_id="T">-185</value>
</alphabet_array>
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</contributing_sites>
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AGA[GC]TA[AT]AGAAC[TG]TA
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</contributing_sites>
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<regular_expression>
GCCTGTTAGTTGAGA
</regular_expression>
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</contributing_sites>
</motif>
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<regular_expression>
CTTAGCTCAG[AC]CTGG
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
</motifs>
</MEME>
