<?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/AT4G25470_peak_sequences.fasta" primary_count="4073" primary_positions="772517" 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">0.3</value>
<value letter_id="C">0.2</value>
<value letter_id="G">0.2</value>
<value letter_id="T">0.3</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme seqs/AT4G25470_peak_sequences.fasta -dna -oc out/AT4G25470 -nostatus -time 300 -mod zoops -nmotifs 2 -minw 6 -maxw 50 -objfun classic -revcomp -markov_order 0 -mpi </command_line>
<host>fv-az290-979</host>
<type>zoops</type>
<nmotifs>2</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>50</max_width>
<wg>11</wg>
<ws>1</ws>
<endgaps>yes</endgaps>
<substring>yes</substring>
<minsites>2</minsites>
<maxsites>4073</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>772517</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 requested number of motifs (2) found.</reason_for_stopping>
<background_frequencies source="--sequences--" order="0">
<alphabet_array>
<value letter_id="A">0.302</value>
<value letter_id="C">0.198</value>
<value letter_id="G">0.198</value>
<value letter_id="T">0.302</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="YYRCCGACAWH" alt="MEME-1" width="11" sites="4031" ic="11.9" re="12.7" llr="35546" p_value="2.3e-1919" e_value="1.9e-643" bayes_threshold="9.65177" elapsed_time="81.606353">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-97</value>
<value letter_id="C">50</value>
<value letter_id="G">-95</value>
<value letter_id="T">62</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-125</value>
<value letter_id="C">92</value>
<value letter_id="G">-29</value>
<value letter_id="T">16</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">72</value>
<value letter_id="C">-618</value>
<value letter_id="G">133</value>
<value letter_id="T">-725</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1862</value>
<value letter_id="C">229</value>
<value letter_id="G">-1862</value>
<value letter_id="T">-311</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1025</value>
<value letter_id="C">234</value>
<value letter_id="G">-1862</value>
<value letter_id="T">-1862</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1862</value>
<value letter_id="C">-1862</value>
<value letter_id="G">234</value>
<value letter_id="T">-1862</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">172</value>
<value letter_id="C">-1862</value>
<value letter_id="G">-1862</value>
<value letter_id="T">-793</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1025</value>
<value letter_id="C">234</value>
<value letter_id="G">-1862</value>
<value letter_id="T">-1862</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">98</value>
<value letter_id="C">-85</value>
<value letter_id="G">-36</value>
<value letter_id="T">-110</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-14</value>
<value letter_id="C">-68</value>
<value letter_id="G">-161</value>
<value letter_id="T">83</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">26</value>
<value letter_id="C">38</value>
<value letter_id="G">-16</value>
<value letter_id="T">-57</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.153808</value>
<value letter_id="C">0.279831</value>
<value letter_id="G">0.102456</value>
<value letter_id="T">0.463905</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.126768</value>
<value letter_id="C">0.373853</value>
<value letter_id="G">0.162243</value>
<value letter_id="T">0.337137</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.498387</value>
<value letter_id="C">0.002729</value>
<value letter_id="G">0.496899</value>
<value letter_id="T">0.001985</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.965021</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.034979</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000248</value>
<value letter_id="C">0.999752</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">0.998760</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.001240</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000248</value>
<value letter_id="C">0.999752</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.594642</value>
<value letter_id="C">0.109650</value>
<value letter_id="G">0.154552</value>
<value letter_id="T">0.141156</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.274374</value>
<value letter_id="C">0.123046</value>
<value letter_id="G">0.064748</value>
<value letter_id="T">0.537832</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.361697</value>
<value letter_id="C">0.256760</value>
<value letter_id="G">0.177623</value>
<value letter_id="T">0.203920</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[TC][CT][AG]CCGACA[TA][ACT]
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
<motif id="motif_2" name="HTYTTYTTCTTYTTYTTYYTY" alt="MEME-2" width="21" sites="855" ic="16.3" re="15.2" llr="9006" p_value="2.2e-561" e_value="1.5e-071" bayes_threshold="11.8761" elapsed_time="153.314146">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-51</value>
<value letter_id="C">75</value>
<value letter_id="G">-80</value>
<value letter_id="T">18</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-269</value>
<value letter_id="C">12</value>
<value letter_id="G">-259</value>
<value letter_id="T">122</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-107</value>
<value letter_id="C">134</value>
<value letter_id="G">-249</value>
<value letter_id="T">8</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-100</value>
<value letter_id="C">-85</value>
<value letter_id="G">-35</value>
<value letter_id="T">95</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-229</value>
<value letter_id="C">26</value>
<value letter_id="G">-179</value>
<value letter_id="T">109</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-801</value>
<value letter_id="C">134</value>
<value letter_id="G">-1638</value>
<value letter_id="T">72</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-154</value>
<value letter_id="C">33</value>
<value letter_id="G">-129</value>
<value letter_id="T">91</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-237</value>
<value letter_id="C">-1638</value>
<value letter_id="G">-440</value>
<value letter_id="T">163</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1638</value>
<value letter_id="C">167</value>
<value letter_id="G">-165</value>
<value letter_id="T">1</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-171</value>
<value letter_id="C">-82</value>
<value letter_id="G">-191</value>
<value letter_id="T">130</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1638</value>
<value letter_id="C">50</value>
<value letter_id="G">-85</value>
<value letter_id="T">101</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-240</value>
<value letter_id="C">119</value>
<value letter_id="G">-1638</value>
<value letter_id="T">70</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-190</value>
<value letter_id="C">39</value>
<value letter_id="G">-170</value>
<value letter_id="T">99</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-343</value>
<value letter_id="C">-394</value>
<value letter_id="G">-1638</value>
<value letter_id="T">167</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-369</value>
<value letter_id="C">156</value>
<value letter_id="G">-1638</value>
<value letter_id="T">38</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-362</value>
<value letter_id="C">-7</value>
<value letter_id="G">-142</value>
<value letter_id="T">124</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1638</value>
<value letter_id="C">23</value>
<value letter_id="G">-185</value>
<value letter_id="T">124</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1638</value>
<value letter_id="C">123</value>
<value letter_id="G">-282</value>
<value letter_id="T">75</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1638</value>
<value letter_id="C">63</value>
<value letter_id="G">-72</value>
<value letter_id="T">93</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-293</value>
<value letter_id="C">-25</value>
<value letter_id="G">-740</value>
<value letter_id="T">139</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-543</value>
<value letter_id="C">144</value>
<value letter_id="G">-54</value>
<value letter_id="T">8</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.211696</value>
<value letter_id="C">0.333333</value>
<value letter_id="G">0.113450</value>
<value letter_id="T">0.341520</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.046784</value>
<value letter_id="C">0.215205</value>
<value letter_id="G">0.032749</value>
<value letter_id="T">0.705263</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.143860</value>
<value letter_id="C">0.501754</value>
<value letter_id="G">0.035088</value>
<value letter_id="T">0.319298</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.150877</value>
<value letter_id="C">0.109942</value>
<value letter_id="G">0.155556</value>
<value letter_id="T">0.583626</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.061988</value>
<value letter_id="C">0.237427</value>
<value letter_id="G">0.057310</value>
<value letter_id="T">0.643275</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.001170</value>
<value letter_id="C">0.501754</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.497076</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.104094</value>
<value letter_id="C">0.249123</value>
<value letter_id="G">0.080702</value>
<value letter_id="T">0.566082</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.058480</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.009357</value>
<value letter_id="T">0.932164</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.631579</value>
<value letter_id="G">0.063158</value>
<value letter_id="T">0.305263</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.092398</value>
<value letter_id="C">0.112281</value>
<value letter_id="G">0.052632</value>
<value letter_id="T">0.742690</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.280702</value>
<value letter_id="G">0.109942</value>
<value letter_id="T">0.609357</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.057310</value>
<value letter_id="C">0.450292</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.492398</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.080702</value>
<value letter_id="C">0.259649</value>
<value letter_id="G">0.060819</value>
<value letter_id="T">0.598830</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.028070</value>
<value letter_id="C">0.012865</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.959064</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.023392</value>
<value letter_id="C">0.582456</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.394152</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.024561</value>
<value letter_id="C">0.188304</value>
<value letter_id="G">0.073684</value>
<value letter_id="T">0.713450</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.231579</value>
<value letter_id="G">0.054971</value>
<value letter_id="T">0.713450</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.463158</value>
<value letter_id="G">0.028070</value>
<value letter_id="T">0.508772</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.305263</value>
<value letter_id="G">0.120468</value>
<value letter_id="T">0.574269</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.039766</value>
<value letter_id="C">0.166082</value>
<value letter_id="G">0.001170</value>
<value letter_id="T">0.792982</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.007018</value>
<value letter_id="C">0.538012</value>
<value letter_id="G">0.135673</value>
<value letter_id="T">0.319298</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[TCA][TC][CT]T[TC][CT][TC]T[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[CT]
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
</motifs>
</MEME>
