<?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="5.3.2" release="Fri Feb 5 17:50:07 2021 -0800">
<training_set primary_sequences="common/Klf1-200-100.fa" primary_count="169" primary_positions="16900" control_sequences="Primary sequences shuffled preserving 2-mers" control_count="169" control_positions="16900">
<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">0.248</value>
<value letter_id="C">0.252</value>
<value letter_id="G">0.252</value>
<value letter_id="T">0.248</value>
</alphabet_array>
</letter_frequencies>
</training_set>
<model>
<command_line>meme common/Klf1-200-100.fa -oc results/meme35 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi </command_line>
<host>Timothys-Mac-Mini.local</host>
<type>zoops</type>
<nmotifs>2</nmotifs>
<evalue_threshold>inf</evalue_threshold>
<object_function>Selective mHG</object_function>
<spfun>log likelihood ratio (LLR)</spfun>
<min_width>12</min_width>
<max_width>12</max_width>
<substring>yes</substring>
<minsites>2</minsites>
<maxsites>169</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>16900</num_positions>
<seed>0</seed>
<hsfrac>0.6</hsfrac>
<searchsize>16900</searchsize>
<maxsize>0</maxsize>
<norand>no</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">0.248</value>
<value letter_id="C">0.252</value>
<value letter_id="G">0.252</value>
<value letter_id="T">0.248</value>
</alphabet_array>
</background_frequencies>
</model>
<motifs>
<motif id="motif_1" name="CWGGGTGTGGYY" alt="MEME-1" width="12" sites="42" ic="15.6" re="15.6" llr="454" p_value="3.0e-008" e_value="3.0e-008" bayes_threshold="8.30462" elapsed_time="0.343329">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-80</value>
<value letter_id="C">118</value>
<value letter_id="G">-82</value>
<value letter_id="T">-80</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">70</value>
<value letter_id="C">-1204</value>
<value letter_id="G">-340</value>
<value letter_id="T">120</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1204</value>
<value letter_id="C">-1204</value>
<value letter_id="G">199</value>
<value letter_id="T">-1204</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1204</value>
<value letter_id="C">-1204</value>
<value letter_id="G">196</value>
<value letter_id="T">-338</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1204</value>
<value letter_id="C">-1204</value>
<value letter_id="G">199</value>
<value letter_id="T">-1204</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-238</value>
<value letter_id="C">-108</value>
<value letter_id="G">-1204</value>
<value letter_id="T">175</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1204</value>
<value letter_id="C">-1204</value>
<value letter_id="G">199</value>
<value letter_id="T">-1204</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1204</value>
<value letter_id="C">-1204</value>
<value letter_id="G">-108</value>
<value letter_id="T">183</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1204</value>
<value letter_id="C">-1204</value>
<value letter_id="G">199</value>
<value letter_id="T">-1204</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-180</value>
<value letter_id="C">-182</value>
<value letter_id="G">155</value>
<value letter_id="T">-106</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-338</value>
<value letter_id="C">135</value>
<value letter_id="G">-1204</value>
<value letter_id="T">42</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-58</value>
<value letter_id="C">41</value>
<value letter_id="G">-140</value>
<value letter_id="T">70</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.142857</value>
<value letter_id="C">0.571429</value>
<value letter_id="G">0.142857</value>
<value letter_id="T">0.142857</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.404762</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.023810</value>
<value letter_id="T">0.571429</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">0.976190</value>
<value letter_id="T">0.023810</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">0.047619</value>
<value letter_id="C">0.119048</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.833333</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">0.119048</value>
<value letter_id="T">0.880952</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">0.071429</value>
<value letter_id="C">0.071429</value>
<value letter_id="G">0.738095</value>
<value letter_id="T">0.119048</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.023810</value>
<value letter_id="C">0.642857</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.333333</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.166667</value>
<value letter_id="C">0.333333</value>
<value letter_id="G">0.095238</value>
<value letter_id="T">0.404762</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
C[TA]GGGTGTGG[CT][TC]
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
<motif id="motif_2" name="CTCCYTCTSCCY" alt="MEME-2" width="12" sites="33" ic="12.0" re="11.9" llr="273" p_value="4.1e-001" e_value="4.1e-001" bayes_threshold="8.39895" elapsed_time="0.650540">
<scores>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">-203</value>
<value letter_id="C">159</value>
<value letter_id="G">-205</value>
<value letter_id="T">-103</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-4</value>
<value letter_id="C">-1169</value>
<value letter_id="G">-305</value>
<value letter_id="T">155</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1169</value>
<value letter_id="C">159</value>
<value letter_id="G">-25</value>
<value letter_id="T">-303</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-23</value>
<value letter_id="C">159</value>
<value letter_id="G">-1169</value>
<value letter_id="T">-303</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-303</value>
<value letter_id="C">127</value>
<value letter_id="G">-1169</value>
<value letter_id="T">55</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-45</value>
<value letter_id="C">-47</value>
<value letter_id="G">-305</value>
<value letter_id="T">129</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-303</value>
<value letter_id="C">165</value>
<value letter_id="G">-205</value>
<value letter_id="T">-103</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1169</value>
<value letter_id="C">-1169</value>
<value letter_id="G">-1169</value>
<value letter_id="T">201</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1169</value>
<value letter_id="C">75</value>
<value letter_id="G">85</value>
<value letter_id="T">-103</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1169</value>
<value letter_id="C">165</value>
<value letter_id="G">-147</value>
<value letter_id="T">-103</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-203</value>
<value letter_id="C">147</value>
<value letter_id="G">-1169</value>
<value letter_id="T">-4</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">-1169</value>
<value letter_id="C">41</value>
<value letter_id="G">-1169</value>
<value letter_id="T">142</value>
</alphabet_array>
</alphabet_matrix>
</scores>
<probabilities>
<alphabet_matrix>
<alphabet_array>
<value letter_id="A">0.060606</value>
<value letter_id="C">0.757576</value>
<value letter_id="G">0.060606</value>
<value letter_id="T">0.121212</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.242424</value>
<value letter_id="C">0.000000</value>
<value letter_id="G">0.030303</value>
<value letter_id="T">0.727273</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.757576</value>
<value letter_id="G">0.212121</value>
<value letter_id="T">0.030303</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.212121</value>
<value letter_id="C">0.757576</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.030303</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.030303</value>
<value letter_id="C">0.606061</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.363636</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.181818</value>
<value letter_id="C">0.181818</value>
<value letter_id="G">0.030303</value>
<value letter_id="T">0.606061</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.030303</value>
<value letter_id="C">0.787879</value>
<value letter_id="G">0.060606</value>
<value letter_id="T">0.121212</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">0.000000</value>
<value letter_id="C">0.424242</value>
<value letter_id="G">0.454545</value>
<value letter_id="T">0.121212</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.787879</value>
<value letter_id="G">0.090909</value>
<value letter_id="T">0.121212</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.060606</value>
<value letter_id="C">0.696970</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.242424</value>
</alphabet_array>
<alphabet_array>
<value letter_id="A">0.000000</value>
<value letter_id="C">0.333333</value>
<value letter_id="G">0.000000</value>
<value letter_id="T">0.666667</value>
</alphabet_array>
</alphabet_matrix>
</probabilities>
<regular_expression>
C[TA][CG][CA][CT]TCT[GC]C[CT][TC]
</regular_expression>
<contributing_sites>
</contributing_sites>
</motif>
</motifs>
</MEME>
