<STREME version="5.4.0" release="Mon Aug 16 16:18:19 2021 -0700">
  <model>
    <command_line>streme -p common/lipocalin.s -oc results/streme6 -objfun de -order 1 -nmotifs 2 -protein -maxw 20 -hofract 0.2 -verbosity 1</command_line>
    <train_positives count="5" positions="903" maxlen="189" file="common/lipocalin.s"/>
    <train_negatives count="5" positions="903" from="shuffled"/>
    <test_positives count="0" positions="0"/>
    <test_negatives count="0" positions="0"/>
    <alphabet name="Protein" like="protein">
      <letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
      <letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
      <letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
      <letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
      <letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
      <letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
      <letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
      <letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
      <letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
      <letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
      <letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
      <letter id="N" symbol="N" name="Asparagine" colour="008000"/>
      <letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
      <letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
      <letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
      <letter id="S" symbol="S" name="Serine" colour="008000"/>
      <letter id="T" symbol="T" name="Threonine" colour="008000"/>
      <letter id="V" symbol="V" name="Valine" colour="0000CC"/>
      <letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
      <letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
      <letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
      <letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
      <letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
      <letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
    </alphabet>
    <strands>none</strands>
    <sequence_db A="0.072" C="0.0288" D="0.0687" E="0.0775" F="0.0432" G="0.0576" H="0.0255" I="0.0476" K="0.0864" L="0.0875" M="0.0177" N="0.0532" P="0.0321" Q="0.0288" R="0.031" S="0.0587" T="0.0476" V="0.0698" W="0.0166" Y="0.0498"/>
    <background_frequencies source="--negatives--" order="1">
      <alphabet_array>
        <value letter_id="A">0.072</value>
        <value letter_id="C">0.0288</value>
        <value letter_id="D">0.0686</value>
        <value letter_id="E">0.0775</value>
        <value letter_id="F">0.0432</value>
        <value letter_id="G">0.0576</value>
        <value letter_id="H">0.0255</value>
        <value letter_id="I">0.0476</value>
        <value letter_id="K">0.0863</value>
        <value letter_id="L">0.0874</value>
        <value letter_id="M">0.0177</value>
        <value letter_id="N">0.0532</value>
        <value letter_id="P">0.0321</value>
        <value letter_id="Q">0.0288</value>
        <value letter_id="R">0.031</value>
        <value letter_id="S">0.0587</value>
        <value letter_id="T">0.0476</value>
        <value letter_id="V">0.0698</value>
        <value letter_id="W">0.0167</value>
        <value letter_id="Y">0.0498</value>
      </alphabet_array>
    </background_frequencies>
    <stop nmotifs="2"/>
    <objfun>Differential Enrichment</objfun>
    <test>Fisher Exact Test</test>
    <minw>8</minw>
    <maxw>20</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>
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    <motif id="2-YPEGDLEIL" alt="STREME-2" width="9" initial_width="4" seed="TPEGDLEIL" score_threshold="1.01389" train_pos_count="3" train_neg_count="0" train_log_pvalue="-1.07918" train_pvalue="8.3e-002" train_dtc="-1.0" train_bernoulli="-1" test_pos_count="0" test_neg_count="0" test_log_pvalue="0" test_pvalue="1.0e+000" test_log_evalue="0.30103" test_evalue="2.0e+000" test_dtc="-1.0" test_bernoulli="-1" is_palindromic="n/a" elapsed_time="0.1" total_sites="3" site_distr=" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0" max_sites="2" site_hist=" 0 2 1">
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  </motifs>
  <reason_for_stopping>Stopped because maximum number of motifs (2) reached.</reason_for_stopping>
  <run_time cpu="0.06"/>
</STREME>
