<?xml version="1.0" encoding="utf-8"?>
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  <notes>
    <stats ortholog_groups="5336" inparalogs="11266"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Ajellomyces capsulata " NCBITaxId="447093">
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    <notes>
      <additionalInformation abbreviation="A.capsulata" link="http://www.uniprot.org/taxonomy/447093"/>
    </notes>
  </species>
  <species name="Nectria haematococca " NCBITaxId="660122">
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        <gene id="11009" protId="H6D5E4" geneId="atp8"/>
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        <gene id="11088" protId="C7ZA88" geneId="NECHADRAFT_82013"/>
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        <gene id="11090" protId="C7Z0E1" geneId="NECHADRAFT_79860"/>
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        <gene id="11092" protId="C7YKV0" geneId="NECHADRAFT_58773"/>
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        <gene id="11097" protId="C7YN94" geneId="NECHADRAFT_99764"/>
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        <gene id="11117" protId="C7Z6I1" geneId="NECHADRAFT_76111"/>
        <gene id="11118" protId="C7ZK29" geneId="NECHADRAFT_52455"/>
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        <gene id="11122" protId="C7YLD5" geneId="NECHADRAFT_35425"/>
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        <gene id="11207" protId="C7YYB1" geneId="NECHADRAFT_106302"/>
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        <gene id="11222" protId="C7YMX7" geneId="NECHADRAFT_78033"/>
        <gene id="11224" protId="C7YJG2" geneId="NECHADRAFT_75667"/>
        <gene id="11226" protId="C7ZDY8" geneId="NECHADRAFT_88256"/>
        <gene id="11227" protId="C7ZC25" geneId="NECHADRAFT_55214"/>
        <gene id="11229" protId="C7YWS6" geneId="NECHADRAFT_82768"/>
        <gene id="11231" protId="C7Z5L9" geneId="NECHADRAFT_76912"/>
        <gene id="11233" protId="C7ZA75" geneId="NECHADRAFT_82001"/>
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        <gene id="11237" protId="C7YPI4" geneId="NECHADRAFT_78765"/>
        <gene id="11239" protId="C7Z4I7" geneId="NECHADRAFT_76536"/>
        <gene id="11241" protId="C7Z4J3" geneId="NECHADRAFT_99266"/>
        <gene id="11243" protId="C7ZMN1" geneId="NECHADRAFT_52740"/>
        <gene id="11246" protId="C7YNC3" geneId="NECHADRAFT_78179"/>
        <gene id="11248" protId="C7YHY8" geneId="NECHADRAFT_75134"/>
        <gene id="11250" protId="C7YXL3" geneId="NECHADRAFT_82569"/>
        <gene id="11252" protId="C7Z354" geneId="NECHADRAFT_87832"/>
        <gene id="11254" protId="C7YPY2" geneId="NECHADRAFT_78914"/>
        <gene id="11256" protId="C7ZM15" geneId="NECHADRAFT_78551"/>
        <gene id="11258" protId="C7Z1B2" geneId="NECHADRAFT_123342"/>
        <gene id="11265" protId="C7ZR46" geneId="NECHADRAFT_16010"/>
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      </genes>
    </database>
    <notes>
      <additionalInformation abbreviation="N.haematococca" link="http://www.uniprot.org/taxonomy/660122"/>
    </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>
  <groups>
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      <geneRef id="1">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="2">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="2">
      <score id="bit" value="4448"/>
      <geneRef id="3">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="4">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="3">
      <score id="bit" value="4285"/>
      <geneRef id="5">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
      <geneRef id="6">
        <score id="inparalog" value="1"/>
        <score id="bootstrap" value="1"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="4">
      <score id="bit" value="3588"/>
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