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  <notes>
    <stats ortholog_groups="2336" inparalogs="6099"/>
    <parameters scoreCutoff="40" confidenceCutoff="0.05" overlapCutoff="0.5" mergingCutoff="0.5" matrix="BLOSUM62"/>
  </notes>
  <species name="Ciona intestinalis " NCBITaxId="7719">
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    <notes>
      <additionalInformation abbreviation="C.intestinalis" link="http://www.uniprot.org/taxonomy/7719"/>
    </notes>
  </species>
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        <gene id="1923" protId="H3G7H3" geneId="gwEuk.60.99.1"/>
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        <gene id="1929" protId="H3GMN5" geneId="uncharacterized_H3GMN5"/>
        <gene id="1931" protId="H3GS12" geneId="uncharacterized_H3GS12"/>
        <gene id="1933" protId="H3GW23" geneId="uncharacterized_H3GW23"/>
        <gene id="1935" protId="H3GY38" geneId="uncharacterized_H3GY38"/>
        <gene id="1937" protId="H3G737" geneId="gwEuk.45.90.1"/>
        <gene id="1939" protId="H3HCW2" geneId="uncharacterized_H3HCW2"/>
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        <gene id="1944" protId="H3GG39" geneId="uncharacterized_H3GG39"/>
        <gene id="1945" protId="H3GQ58" geneId="uncharacterized_H3GQ58"/>
        <gene id="1947" protId="H3GA23" geneId="uncharacterized_H3GA23"/>
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        <gene id="1952" protId="H3G8T9" geneId="uncharacterized_H3G8T9"/>
        <gene id="1954" protId="H3GR18" geneId="uncharacterized_H3GR18"/>
        <gene id="1956" protId="H3GVQ8" geneId="uncharacterized_H3GVQ8"/>
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        <gene id="1960" protId="H3G6A1" geneId="gwEuk.23.223.1"/>
        <gene id="1962" protId="H3G9V3" geneId="uncharacterized_H3G9V3"/>
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        <gene id="1964" protId="H3GB90" geneId="fgenesh1_pm.C_scaffold_2098000001"/>
        <gene id="1965" protId="H3G661" geneId="gwEuk.2169.13.1"/>
        <gene id="1966" protId="H3GB95" geneId="fgenesh1_pm.C_scaffold_2169000003"/>
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        <gene id="1971" protId="H3HAB9" geneId="fgenesh1_pg.C_scaffold_2755000001"/>
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        <gene id="1976" protId="H3GD20" geneId="uncharacterized_H3GD20"/>
        <gene id="1978" protId="H3GAM0" geneId="uncharacterized_H3GAM0"/>
        <gene id="1980" protId="H3GBK0" geneId="uncharacterized_H3GBK0"/>
        <gene id="1982" protId="H3GH31" geneId="uncharacterized_H3GH31"/>
        <gene id="1984" protId="H3HCM2" geneId="uncharacterized_H3HCM2"/>
        <gene id="1990" protId="H3GMG3" geneId="uncharacterized_H3GMG3"/>
        <gene id="1991" protId="H3H8Y3" geneId="fgenesh1_pg.C_scaffold_1777000001"/>
        <gene id="1992" protId="H3GU40" geneId="uncharacterized_H3GU40"/>
        <gene id="1993" protId="H3H503" geneId="uncharacterized_H3H503"/>
        <gene id="1994" protId="H3H5G0" geneId="uncharacterized_H3H5G0"/>
        <gene id="1995" protId="H3GU41" geneId="uncharacterized_H3GU41"/>
        <gene id="1996" protId="H3GQ89" geneId="uncharacterized_H3GQ89"/>
        <gene id="1998" protId="H3G5V3" geneId="gwEuk.19.11.1"/>
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        <gene id="2002" protId="H3GC34" geneId="uncharacterized_H3GC34"/>
        <gene id="2004" protId="H3G9F5" geneId="uncharacterized_H3G9F5"/>
        <gene id="2006" protId="H3GE00" geneId="uncharacterized_H3GE00"/>
        <gene id="2008" protId="H3GYD8" geneId="uncharacterized_H3GYD8"/>
        <gene id="2010" protId="H3GER6" geneId="uncharacterized_H3GER6"/>
        <gene id="2012" protId="H3G980" geneId="uncharacterized_H3G980"/>
        <gene id="2014" protId="H3HB33" geneId="uncharacterized_H3HB33"/>
        <gene id="2018" protId="H3H673" geneId="uncharacterized_H3H673"/>
        <gene id="2019" protId="H3H803" geneId="fgenesh1_pg.C_scaffold_1364000001"/>
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        <gene id="2024" protId="H3GA45" geneId="uncharacterized_H3GA45"/>
        <gene id="2026" protId="H3G5V4" geneId="gwEuk.19.27.1"/>
        <gene id="2028" protId="H3GS71" geneId="uncharacterized_H3GS71"/>
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        <gene id="2032" protId="H3GM85" geneId="uncharacterized_H3GM85"/>
        <gene id="2035" protId="H3H4R1" geneId="uncharacterized_H3H4R1"/>
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        <gene id="2039" protId="H3GWM1" geneId="uncharacterized_H3GWM1"/>
        <gene id="2041" protId="H3HDG0" geneId="uncharacterized_H3HDG0"/>
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        <gene id="3320" protId="H3H6T6" geneId="uncharacterized_H3H6T6"/>
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        <gene id="3324" protId="H3GUW8" geneId="uncharacterized_H3GUW8"/>
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        <gene id="3330" protId="H3H5A8" geneId="uncharacterized_H3H5A8"/>
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        <gene id="3334" protId="H3GS50" geneId="uncharacterized_H3GS50"/>
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        <gene id="3337" protId="H3G8Z1" geneId="uncharacterized_H3G8Z1"/>
        <gene id="3338" protId="H3G9E6" geneId="uncharacterized_H3G9E6"/>
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        <gene id="3341" protId="H3GB20" geneId="uncharacterized_H3GB20"/>
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        <gene id="6087" protId="H3H9N3" geneId="fgenesh1_pg.C_scaffold_2195000001"/>
        <gene id="6088" protId="H3H9T0" geneId="fgenesh1_pg.C_scaffold_2279000001"/>
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    <notes>
      <additionalInformation abbreviation="P.ramorum" link="http://www.uniprot.org/taxonomy/164328"/>
    </notes>
  </species>
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    <scoreDef id="bootstrap" desc="Reliability of seed orthologs"/>
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