<STREME version="5.4.1" release="Sat Aug 21 19:23:23 2021 -0700">
  <model>
    <command_line>streme --verbosity 1 --oc /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/streme_out -dna --p /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/seqs-centered --minw 6 --maxw 15 --order 2</command_line>
    <train_positives count="9051" positions="905100" maxlen="100" file="/scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/seqs-centered"/>
    <train_negatives count="9051" positions="905100" from="shuffled"/>
    <test_positives count="1005" positions="100500"/>
    <test_negatives count="1005" positions="100500"/>
    <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="0.195" C="0.305" G="0.305" T="0.195"/>
    <background_frequencies source="--negatives--" order="2">
      <alphabet_array>
        <value letter_id="A">0.195</value>
        <value letter_id="C">0.305</value>
        <value letter_id="G">0.305</value>
        <value letter_id="T">0.195</value>
      </alphabet_array>
    </background_frequencies>
    <stop thresh_type="pvalue" thresh="0.05"/>
    <objfun>Differential Enrichment</objfun>
    <test>Fisher Exact Test</test>
    <minw>6</minw>
    <maxw>15</maxw>
    <kmer>3</kmer>
    <hofract>0.1</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>fv-az119-924</host>
  </model>
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</STREME>
