<STREME version="5.4.0" release="Mon Aug 16 16:18:19 2021 -0700">
  <model>
    <command_line>streme -p common/Puf3p.s -oc results/streme7 -objfun de -order 1 -nmotifs 2 -rna -pvt 1e-10 -hofract 0.2 -verbosity 1</command_line>
    <train_positives count="989" positions="98900" maxlen="100" file="common/Puf3p.s"/>
    <train_negatives count="989" positions="98900" from="shuffled"/>
    <test_positives count="247" positions="24700"/>
    <test_negatives count="247" positions="24700"/>
    <alphabet name="RNA" like="rna">
      <letter id="A" symbol="A" name="Adenine" colour="CC0000"/>
      <letter id="C" symbol="C" name="Cytosine" colour="0000CC"/>
      <letter id="G" symbol="G" name="Guanine" colour="FFB300"/>
      <letter id="U" symbol="U" aliases="T" name="Uracil" colour="008000"/>
      <letter id="N" symbol="N" aliases="X." equals="ACGU" name="Any base"/>
      <letter id="V" symbol="V" equals="ACG" name="Not U"/>
      <letter id="H" symbol="H" equals="ACU" name="Not G"/>
      <letter id="D" symbol="D" equals="AGU" name="Not C"/>
      <letter id="B" symbol="B" equals="CGU" 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="AU" name="Weak"/>
      <letter id="S" symbol="S" equals="CG" name="Strong"/>
      <letter id="Y" symbol="Y" equals="CU" name="Pyrimidine"/>
      <letter id="K" symbol="K" equals="GU" name="Keto"/>
    </alphabet>
    <strands>none</strands>
    <sequence_db A="0.333" C="0.171" G="0.145" U="0.352"/>
    <background_frequencies source="--negatives--" order="1">
      <alphabet_array>
        <value letter_id="A">0.333</value>
        <value letter_id="C">0.171</value>
        <value letter_id="G">0.145</value>
        <value letter_id="U">0.352</value>
      </alphabet_array>
    </background_frequencies>
    <stop thresh_type="pvalue" thresh="1e-10"/>
    <objfun>Differential Enrichment</objfun>
    <test>Fisher Exact Test</test>
    <minw>8</minw>
    <maxw>15</maxw>
    <kmer>2</kmer>
    <hofract>0.2</hofract>
    <neval>25</neval>
    <nref>4</nref>
    <niter>20</niter>
    <patience>3</patience>
    <seed>0</seed>
    <useer>no</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-HUGUAWAUAH" alt="STREME-1" width="10" initial_width="10" seed="CUGUAAAUAA" score_threshold="8.13516" train_pos_count="288" train_neg_count="36" train_log_pvalue="-57.886" train_pvalue="1.3e-058" train_dtc="-1.0" train_bernoulli="-1" test_pos_count="63" test_neg_count="11" test_log_pvalue="-10.957" test_pvalue="1.1e-011" test_log_evalue="-10.355" test_evalue="4.4e-011" test_dtc="-1.0" test_bernoulli="-1" is_palindromic="n/a" elapsed_time="1.1" total_sites="288" site_distr=" 3 1 0 0 0 1 1 0 0 0 1 6 1 2 0 4 0 2 2 1 1 0 0 0 2 2 2 1 2 2 2 2 1 3 1 6 7 13 9 9 8 7 12 7 17 20 19 11 12 6 10 7 4 4 0 4 3 4 3 1 1 5 2 1 0 1 3 4 2 2 2 0 2 0 1 0 0 1 0 1 0 2 2 0 3 0 0 1 0 2" max_sites="3" site_hist=" 0 266 21 1">
      <pos A="0.226978" C="0.366888" G="0.0641897" U="0.341945"/>
      <pos A="0.000204963" C="0.000105255" G="0.00436258" U="0.995327"/>
      <pos A="0.000204963" C="0.000105255" G="0.999473" U="0.00021698"/>
      <pos A="0.000204963" C="0.000105255" G="8.91091e-05" U="0.999601"/>
      <pos A="0.916624" C="0.018968" G="0.0257206" U="0.0386876"/>
      <pos A="0.533429" C="0.149071" G="0.0257268" U="0.291773"/>
      <pos A="0.999589" C="0.000105255" G="8.91091e-05" U="0.00021698"/>
      <pos A="0.0110623" C="0.000105255" G="8.91091e-05" U="0.988743"/>
      <pos A="0.999589" C="0.000105255" G="8.91091e-05" U="0.00021698"/>
      <pos A="0.354054" C="0.185514" G="0.108245" U="0.352187"/>
    </motif>
    <motif id="2-UAUAUAUAUAU" alt="STREME-2" width="11" initial_width="11" seed="UUUAUAUAUAU" score_threshold="8.88949" train_pos_count="165" train_neg_count="21" train_log_pvalue="-30.993" train_pvalue="1.0e-031" train_dtc="-1.0" train_bernoulli="-1" test_pos_count="29" test_neg_count="9" test_log_pvalue="-3.2686" test_pvalue="5.4e-004" test_log_evalue="-2.66654" test_evalue="2.2e-003" test_dtc="-1.0" test_bernoulli="-1" is_palindromic="n/a" elapsed_time="2.0" total_sites="165" site_distr=" 1 1 0 1 1 1 1 1 1 1 0 0 1 1 0 0 1 0 0 0 0 0 1 0 1 0 1 1 0 0 3 2 2 4 2 1 3 6 4 3 3 5 2 1 2 1 6 5 2 4 4 5 3 6 4 5 1 2 1 3 1 0 2 0 1 1 1 0 1 1 0 0 1 2 0 0 0 0 0 1 1 0 0 1 1 2 0 1 4" max_sites="14" site_hist=" 0 90 23 16 16 2 4 4 4 1 1 2 1 0 1">
      <pos A="0.000331733" C="0.128073" G="0.000144223" U="0.871451"/>
      <pos A="0.749206" C="0.000170355" G="0.0209118" U="0.229712"/>
      <pos A="0.0395419" C="0.188715" G="0.000144223" U="0.771599"/>
      <pos A="0.950395" C="0.0491097" G="0.000144223" U="0.000351182"/>
      <pos A="0.000331733" C="0.000170355" G="0.000144223" U="0.999354"/>
      <pos A="0.865978" C="0.000170355" G="0.133501" U="0.000351182"/>
      <pos A="0.000331733" C="0.136012" G="0.05834" U="0.805316"/>
      <pos A="0.885737" C="0.0278318" G="0.08608" U="0.000351182"/>
      <pos A="0.000331733" C="0.000170355" G="0.0139825" U="0.985515"/>
      <pos A="0.881715" C="0.000170355" G="0.000144223" U="0.117971"/>
      <pos A="0.0344978" C="0.176454" G="0.00707349" U="0.781975"/>
    </motif>
    <motif id="3-GAAGAAGC" alt="STREME-3" width="8" initial_width="7" seed="GAAGAAGC" score_threshold="8.51728" train_pos_count="111" train_neg_count="29" train_log_pvalue="-12.8707" train_pvalue="1.3e-013" train_dtc="-1.0" train_bernoulli="-1" test_pos_count="29" test_neg_count="11" test_log_pvalue="-2.64678" test_pvalue="2.3e-003" test_log_evalue="-2.04472" test_evalue="9.0e-003" test_dtc="-1.0" test_bernoulli="-1" is_palindromic="n/a" elapsed_time="3.8" total_sites="111" site_distr=" 3 0 2 1 4 1 5 2 2 3 1 0 2 3 4 0 1 1 1 3 3 1 1 2 1 1 1 0 3 0 0 0 1 1 0 0 0 1 0 0 2 0 1 1 0 0 0 0 0 1 0 1 0 1 0 0 3 1 0 1 3 0 1 1 1 2 2 1 1 0 1 2 2 1 3 0 2 1 1 1 1 0 2 2 0 2 0 2 0 3 1 3" max_sites="4" site_hist=" 0 98 12 0 1">
      <pos A="0.0557077" C="0.0556574" G="0.788239" U="0.100396"/>
      <pos A="0.856823" C="0.00580968" G="0.0768032" U="0.0605646"/>
      <pos A="0.806709" C="0.111034" G="0.000230989" U="0.0820259"/>
      <pos A="0.000531307" C="0.0224202" G="0.976486" U="0.000562457"/>
      <pos A="0.689319" C="0.0778169" G="0.221228" U="0.0116361"/>
      <pos A="0.735886" C="0.0501125" G="0.115585" U="0.0984163"/>
      <pos A="0.0254173" C="0.00486614" G="0.969154" U="0.000562457"/>
      <pos A="0.199438" C="0.560508" G="0.105508" U="0.134546"/>
    </motif>
    <motif id="4-UUUUCUUYYUC" alt="STREME-4" width="11" initial_width="7" seed="UUUUCUUUUUC" score_threshold="9.12266" train_pos_count="135" train_neg_count="32" train_log_pvalue="-17.0967" train_pvalue="8.0e-018" train_dtc="-1.0" train_bernoulli="-1" test_pos_count="25" test_neg_count="11" test_log_pvalue="-1.93447" test_pvalue="1.2e-002" test_log_evalue="-1.33241" test_evalue="4.7e-002" test_dtc="-1.0" test_bernoulli="-1" is_palindromic="n/a" elapsed_time="2.9" total_sites="135" site_distr=" 2 0 2 3 2 1 3 5 2 3 2 1 0 1 3 1 2 1 1 2 0 1 0 1 2 2 1 0 2 3 2 1 0 1 0 2 2 4 2 2 0 1 5 4 1 0 1 1 2 3 3 3 0 1 1 1 0 0 1 2 1 0 2 1 2 1 2 0 0 1 1 0 1 2 2 3 1 3 1 1 3 0 0 2 0 3 1 1 2" max_sites="16" site_hist=" 0 109 20 4 1 0 0 0 0 0 0 0 0 0 0 0 1">
      <pos A="0.0853433" C="0.190242" G="0.000147741" U="0.724267"/>
      <pos A="0.000339825" C="0.190816" G="0.000147741" U="0.808697"/>
      <pos A="0.000339825" C="0.0991547" G="0.0922236" U="0.808282"/>
      <pos A="0.000339825" C="0.0497538" G="0.000147741" U="0.949759"/>
      <pos A="0.000339825" C="0.984969" G="0.000147741" U="0.0145434"/>
      <pos A="0.000339825" C="0.104025" G="0.0922288" U="0.803406"/>
      <pos A="0.00742258" C="0.0314486" G="0.13473" U="0.826398"/>
      <pos A="0.000339825" C="0.421288" G="0.000147741" U="0.578224"/>
      <pos A="0.000339825" C="0.295062" G="0.187237" U="0.517361"/>
      <pos A="0.0570045" C="0.264659" G="0.144746" U="0.53359"/>
      <pos A="0.0382911" C="0.659164" G="0.0284788" U="0.274066"/>
    </motif>
  </motifs>
  <reason_for_stopping>Stopped because 3 consecutive motifs exceeded the p-value threshold (1e-10).</reason_for_stopping>
  <run_time cpu="3.90"/>
</STREME>
