<STREME version="5.4.0" release="Mon Aug 16 16:18:19 2021 -0700">
  <model>
    <command_line>streme -p common/Klf1-200-100.fa -oc results/streme3 -objfun de -order 1 -nmotifs 2 -dna -neval 20 -useer -hofract 0.2 -verbosity 1</command_line>
    <train_positives count="136" positions="13600" maxlen="100" file="common/Klf1-200-100.fa"/>
    <train_negatives count="136" positions="13600" from="shuffled"/>
    <test_positives count="33" positions="3300"/>
    <test_negatives count="33" positions="3300"/>
    <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>
    <strands>both</strands>
    <sequence_db A="0.248" C="0.252" G="0.252" T="0.248"/>
    <background_frequencies source="--negatives--" order="1">
      <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>
    <stop nmotifs="2"/>
    <objfun>Differential Enrichment</objfun>
    <test>Fisher Exact Test</test>
    <minw>8</minw>
    <maxw>15</maxw>
    <kmer>2</kmer>
    <hofract>0.2</hofract>
    <neval>20</neval>
    <nref>4</nref>
    <niter>20</niter>
    <patience>3</patience>
    <seed>0</seed>
    <useer>yes</useer>
    <minscore>0</minscore>
    <ignore_depth>5</ignore_depth>
    <nsubsets>1</nsubsets>
    <min_pal_ratio>0.85</min_pal_ratio>
    <max_pal_ed>5</max_pal_ed>
    <cand>no</cand>
    <experimental>no</experimental>
    <totallength>0</totallength>
    <align>center</align>
    <host>Timothys-Mac-Mini.local</host>
  </model>
  <motifs>
    <motif id="1-RGCCACACCC" alt="STREME-1" width="10" initial_width="10" seed="GGCCACACCC" score_threshold="10.6317" train_pos_count="41" train_neg_count="1" train_log_pvalue="-12.4881" train_pvalue="3.2e-013" train_dtc="-1.0" train_bernoulli="-1" test_pos_count="13" test_neg_count="0" test_log_pvalue="-4.55239" test_pvalue="2.8e-005" test_log_evalue="-4.25136" test_evalue="5.6e-005" test_dtc="-1.0" test_bernoulli="-1" is_palindromic="no" elapsed_time="0.3" total_sites="41" site_distr=" 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 1 1 2 0 1 0 1 0 1 0 1 0 0 1 0 0 0 0 2 2 0 0 1 1 0 1 1 0 0 0 0 0 2 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0 1 1" max_sites="2" site_hist=" 0 37 4">
      <pos A="0.412563" C="0.108903" G="0.369584" T="0.10895"/>
      <pos A="0.304214" C="0.00078448" G="0.629391" T="0.0656108"/>
      <pos A="0.152406" C="0.737974" G="0.0872329" T="0.0223866"/>
      <pos A="0.0872229" C="0.911218" G="0.00078448" T="0.000774503"/>
      <pos A="0.738311" C="0.238518" G="0.0223966" T="0.000774503"/>
      <pos A="0.000774503" C="0.997667" G="0.00078448" T="0.000774503"/>
      <pos A="0.759923" C="0.00078448" G="0.173681" T="0.0656108"/>
      <pos A="0.000774503" C="0.997667" G="0.00078448" T="0.000774503"/>
      <pos A="0.000774503" C="0.997667" G="0.00078448" T="0.000774503"/>
      <pos A="0.000774503" C="0.997667" G="0.00078448" T="0.000774503"/>
    </motif>
    <motif id="2-CTTATCTBCTC" alt="STREME-2" width="11" initial_width="9" seed="CTTATCTCCTC" score_threshold="10.1372" train_pos_count="26" train_neg_count="0" train_log_pvalue="-8.4004" train_pvalue="4.0e-009" train_dtc="-1.0" train_bernoulli="-1" test_pos_count="2" test_neg_count="0" test_log_pvalue="-0.608793" test_pvalue="2.5e-001" test_log_evalue="-0.307763" test_evalue="4.9e-001" test_dtc="-1.0" test_bernoulli="-1" is_palindromic="no" elapsed_time="0.6" total_sites="26" site_distr=" 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 0 1 0 0 2 0 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 1 1 2 0 0 0 0 2 0 1 0 0 0 0 1 0" max_sites="1" site_hist=" 0 26">
      <pos A="0.0381604" C="0.811821" G="0.148698" T="0.00132023"/>
      <pos A="0.00132023" C="0.148698" G="0.0750176" T="0.774964"/>
      <pos A="0.00132023" C="0.0750176" G="0.0381774" T="0.885485"/>
      <pos A="0.996005" C="0.00133723" G="0.00133723" T="0.00132023"/>
      <pos A="0.00132023" C="0.00133723" G="0.00133723" T="0.996005"/>
      <pos A="0.0750006" C="0.885502" G="0.0381774" T="0.00132023"/>
      <pos A="0.296042" C="0.0381774" G="0.00133723" T="0.664444"/>
      <pos A="0.0381604" C="0.406579" G="0.296059" T="0.259202"/>
      <pos A="0.111841" C="0.701301" G="0.0750176" T="0.111841"/>
      <pos A="0.111841" C="0.185538" G="0.0381774" T="0.664444"/>
      <pos A="0.00132023" C="0.738141" G="0.222378" T="0.0381604"/>
    </motif>
  </motifs>
  <reason_for_stopping>Stopped because maximum number of motifs (2) reached.</reason_for_stopping>
  <run_time cpu="0.60"/>
</STREME>
