<?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="5.4.0" release="Tue Mar 9 17:38:20 2021 -0800">
<training_set primary_sequences="common/Klf1-200.fa" primary_count="200" primary_positions="100000" 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">0.256</value>
<value letter_id="C">0.244</value>
<value letter_id="G">0.244</value>
<value letter_id="T">0.256</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme common/Klf1-200.fa -oc results/meme38 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun cd -maxw 30 -searchsize 40000 -norand -nostatus -mpi </command_line>
<host>Timothys-Mac-Mini.local</host>
<type>zoops</type>
<nmotifs>2</nmotifs>
<evalue_threshold>inf</evalue_threshold>
<object_function>Central Enrichment: p-value of mean distance</object_function>
<spfun>Mean distance of best site from sequence center</spfun>
<min_width>8</min_width>
<max_width>30</max_width>
<substring>yes</substring>
<minsites>2</minsites>
<maxsites>200</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>100000</num_positions>
<seed>0</seed>
<hsfrac>0.5</hsfrac>
<searchsize>40000</searchsize>
<maxsize>0</maxsize>
<norand>yes</norand>
<strands>both</strands>
<brief>0</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">0.256</value>
<value letter_id="C">0.244</value>
<value letter_id="G">0.244</value>
<value letter_id="T">0.256</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="GCCACACCCWKCYNNBH" alt="MEME-1" width="17" sites="148" ic="12.6" re="12.8" llr="1308" p_value="5.1e-004" e_value="5.1e-004" bayes_threshold="9.4654" elapsed_time="3.374185">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">5</value>
<value letter_id="C">-117</value>
<value letter_id="G">125</value>
<value letter_id="T">-241</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-41</value>
<value letter_id="C">136</value>
<value letter_id="G">-88</value>
<value letter_id="T">-241</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-241</value>
<value letter_id="C">185</value>
<value letter_id="G">-1302</value>
<value letter_id="T">-183</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">161</value>
<value letter_id="C">-34</value>
<value letter_id="G">-433</value>
<value letter_id="T">-441</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-441</value>
<value letter_id="C">198</value>
<value letter_id="G">-433</value>
<value letter_id="T">-441</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">142</value>
<value letter_id="C">-433</value>
<value letter_id="G">-17</value>
<value letter_id="T">-160</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-441</value>
<value letter_id="C">202</value>
<value letter_id="G">-1302</value>
<value letter_id="T">-1302</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-183</value>
<value letter_id="C">187</value>
<value letter_id="G">-433</value>
<value letter_id="T">-341</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-341</value>
<value letter_id="C">197</value>
<value letter_id="G">-1302</value>
<value letter_id="T">-341</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">99</value>
<value letter_id="C">-170</value>
<value letter_id="G">-636</value>
<value letter_id="T">69</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-105</value>
<value letter_id="C">-72</value>
<value letter_id="G">67</value>
<value letter_id="T">41</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-68</value>
<value letter_id="C">110</value>
<value letter_id="G">-98</value>
<value letter_id="T">-39</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-68</value>
<value letter_id="C">14</value>
<value letter_id="G">-148</value>
<value letter_id="T">92</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-28</value>
<value letter_id="C">15</value>
<value letter_id="G">-5</value>
<value letter_id="T">14</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-20</value>
<value letter_id="C">54</value>
<value letter_id="G">-21</value>
<value letter_id="T">-28</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-128</value>
<value letter_id="C">78</value>
<value letter_id="G">-19</value>
<value letter_id="T">3</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-3</value>
<value letter_id="C">10</value>
<value letter_id="G">-159</value>
<value letter_id="T">67</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.265060</value>
<value letter_id="C">0.108434</value>
<value letter_id="G">0.578313</value>
<value letter_id="T">0.048193</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.192771</value>
<value letter_id="C">0.626506</value>
<value letter_id="G">0.132530</value>
<value letter_id="T">0.048193</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.048193</value>
<value letter_id="C">0.879518</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.072289</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.783133</value>
<value letter_id="C">0.192771</value>
<value letter_id="G">0.012048</value>
<value letter_id="T">0.012048</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.012048</value>
<value letter_id="C">0.963855</value>
<value letter_id="G">0.012048</value>
<value letter_id="T">0.012048</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.686747</value>
<value letter_id="C">0.012048</value>
<value letter_id="G">0.216867</value>
<value letter_id="T">0.084337</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.012048</value>
<value letter_id="C">0.987952</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.072289</value>
<value letter_id="C">0.891566</value>
<value letter_id="G">0.012048</value>
<value letter_id="T">0.024096</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.024096</value>
<value letter_id="C">0.951807</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.024096</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.509112</value>
<value letter_id="C">0.075225</value>
<value letter_id="G">0.002936</value>
<value letter_id="T">0.412726</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.123570</value>
<value letter_id="C">0.147515</value>
<value letter_id="G">0.388478</value>
<value letter_id="T">0.340437</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.159714</value>
<value letter_id="C">0.521009</value>
<value letter_id="G">0.123418</value>
<value letter_id="T">0.195859</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.159714</value>
<value letter_id="C">0.267997</value>
<value letter_id="G">0.087274</value>
<value letter_id="T">0.485016</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.210995</value>
<value letter_id="C">0.270933</value>
<value letter_id="G">0.234788</value>
<value letter_id="T">0.283284</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.223043</value>
<value letter_id="C">0.355270</value>
<value letter_id="G">0.210692</value>
<value letter_id="T">0.210995</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.105649</value>
<value letter_id="C">0.418447</value>
<value letter_id="G">0.213628</value>
<value letter_id="T">0.262276</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.250227</value>
<value letter_id="C">0.261821</value>
<value letter_id="G">0.081098</value>
<value letter_id="T">0.406854</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[GA]CCAC[AG]CCC[AT][GT]C[TC][TCGA][CATG][CTG][TCA]
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
<motif id="motif_2" name="SAAWCCMCAYY" alt="MEME-2" width="11" sites="40" ic="12.6" re="12.6" llr="350" p_value="2.9e-001" e_value="3.4e-001" bayes_threshold="11.9323" elapsed_time="6.505885">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-463</value>
<value letter_id="C">122</value>
<value letter_id="G">75</value>
<value letter_id="T">-463</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">192</value>
<value letter_id="C">-463</value>
<value letter_id="G">-463</value>
<value letter_id="T">-463</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">173</value>
<value letter_id="C">-144</value>
<value letter_id="G">-229</value>
<value letter_id="T">-463</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">53</value>
<value letter_id="C">-52</value>
<value letter_id="G">-463</value>
<value letter_id="T">81</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-268</value>
<value letter_id="C">192</value>
<value letter_id="G">-1129</value>
<value letter_id="T">-268</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-268</value>
<value letter_id="C">198</value>
<value letter_id="G">-1129</value>
<value letter_id="T">-1129</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">90</value>
<value letter_id="C">98</value>
<value letter_id="G">-1129</value>
<value letter_id="T">-268</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1129</value>
<value letter_id="C">198</value>
<value letter_id="G">-260</value>
<value letter_id="T">-1129</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">190</value>
<value letter_id="C">-260</value>
<value letter_id="G">-1129</value>
<value letter_id="T">-1129</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-235</value>
<value letter_id="C">25</value>
<value letter_id="G">-144</value>
<value letter_id="T">115</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-150</value>
<value letter_id="C">75</value>
<value letter_id="G">-91</value>
<value letter_id="T">53</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.010252</value>
<value letter_id="C">0.569748</value>
<value letter_id="G">0.409748</value>
<value letter_id="T">0.010252</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.970252</value>
<value letter_id="C">0.009748</value>
<value letter_id="G">0.009748</value>
<value letter_id="T">0.010252</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.850252</value>
<value letter_id="C">0.089748</value>
<value letter_id="G">0.049748</value>
<value letter_id="T">0.010252</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.370252</value>
<value letter_id="C">0.169748</value>
<value letter_id="G">0.009748</value>
<value letter_id="T">0.450252</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.040000</value>
<value letter_id="C">0.920000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.040000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.040000</value>
<value letter_id="C">0.960000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.480000</value>
<value letter_id="C">0.480000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.040000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.960000</value>
<value letter_id="G">0.040000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.960000</value>
<value letter_id="C">0.040000</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.000000</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.050252</value>
<value letter_id="C">0.289748</value>
<value letter_id="G">0.089748</value>
<value letter_id="T">0.570252</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.090252</value>
<value letter_id="C">0.409748</value>
<value letter_id="G">0.129748</value>
<value letter_id="T">0.370252</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
[CG]AA[TA]CC[AC]CA[TC][CT]
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
</motifs>
</MEME>
