<?xml version="1.0" encoding="utf-8"?>
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  <notes>
    <stats ortholog_groups="170" inparalogs="548"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Chloroflexus aurantiacus " NCBITaxId="324602">
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    <notes>
      <additionalInformation abbreviation="C.aurantiacus" link="http://www.uniprot.org/taxonomy/324602"/>
    </notes>
  </species>
  <species name="Giardia intestinalis " NCBITaxId="184922">
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    <notes>
      <additionalInformation abbreviation="G.intestinalis" link="http://www.uniprot.org/taxonomy/184922"/>
    </notes>
  </species>
  <scores>
    <scoreDef id="bit" desc="BLAST score in bits of seed orthologs"/>
    <scoreDef id="inparalog" desc="Inparalog similarity relative to seed ortholog similarity"/>
    <scoreDef id="bootstrap" desc="Reliability of seed orthologs"/>
  </scores>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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        <score id="bootstrap" value="1"/>
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      <geneRef id="4">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
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    <orthologGroup id="3">
      <score id="bit" value="696"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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      <geneRef id="6">
        <score id="inparalog" value="0.13"/>
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      <geneRef id="7">
        <score id="inparalog" value="0.093"/>
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      <geneRef id="8">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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    <orthologGroup id="4">
      <score id="bit" value="574"/>
      <geneRef id="9">
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        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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      <score id="bit" value="532"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
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      <score id="bit" value="523"/>
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        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="0.99"/>
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        <score id="inparalog" value="0.162"/>
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