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1 # bowtie2_indices.loc.sample
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
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3 # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
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4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
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5 # First create these data files and save them in your own data directory structure.
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6 # Then, create a bowtie_indices.loc file to use those indexes with tools.
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7 # Copy this file, save it with the same name (minus the .sample),
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8 # follow the format examples, and store the result in this directory.
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9 # The file should include an one line entry for each index set.
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10 # The path points to the "basename" for the set, not a specific file.
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11 # It has four text columns seperated by TABS.
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12 #
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13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
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14 #
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15 # So, for example, if you had hg18 indexes stored in:
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16 #
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17 # /depot/data2/galaxy/hg19/bowtie2/
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18 #
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19 # containing hg19 genome and hg19.*.bt2 files, such as:
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20 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
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21 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
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22 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
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23 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
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24 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
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25 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
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26 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
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27 #
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28 # then the bowtie2_indices.loc entry could look like this:
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29 #
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30 Acacia auriculiformis Acacia auriculiformis Acacia auriculiformis
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31 Acacia mangium Acacia mangium Acacia mangium
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32 Acyrthosiphon pisum Acyrthosiphon pisum Acyrthosiphon pisum
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33 Aedes aegypti Aedes aegypti Aedes aegypti
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34 Aegilops tauschii Aegilops tauschii Aegilops tauschii
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35 Alligator mississippiensis Alligator mississippiensis Alligator mississippiensis
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36 Amborella trichopoda Amborella trichopoda Amborella trichopoda
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37 Amphimedon queenslandica Amphimedon queenslandica Amphimedon queenslandica
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38 Anas platyrhynchos Anas platyrhynchos Anas platyrhynchos
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39 Anolis carolinensis Anolis carolinensis Anolis carolinensis
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40 Anopheles gambiae Anopheles gambiae Anopheles gambiae
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41 Apis mellifera Apis mellifera Apis mellifera
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42 Aquilegia caerulea Aquilegia caerulea Aquilegia caerulea
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43 Arabidopsis lyrata Arabidopsis lyrata Arabidopsis lyrata
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44 Arabidopsis thaliana Arabidopsis thaliana Arabidopsis thaliana
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45 Arachis hypogaea Arachis hypogaea Arachis hypogaea
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46 Artibeus jamaicensis Artibeus jamaicensis Artibeus jamaicensis
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47 Ascaris suum Ascaris suum Ascaris suum
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48 Asparagus officinalis Asparagus officinalis Asparagus officinalis
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49 Astatotilapia burtoni Astatotilapia burtoni Astatotilapia burtoni
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50 Ateles geoffroyi Ateles geoffroyi Ateles geoffroyi
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51 Avicennia marina Avicennia marina Avicennia marina
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52 BK polyomavirus BK polyomavirus BK polyomavirus
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53 Bactrocera dorsalis Bactrocera dorsalis Bactrocera dorsalis
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54 Bandicoot papillomatosis Bandicoot papillomatosis Bandicoot papillomatosis
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55 Biston betularia Biston betularia Biston betularia
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56 Bombyx mori Bombyx mori Bombyx mori
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57 Bos taurus Bos taurus Bos taurus
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58 Bovine foamy Bovine foamy Bovine foamy
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59 Bovine herpesvirus Bovine herpesvirus Bovine herpesvirus
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60 Bovine leukemia Bovine leukemia Bovine leukemia
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61 Brachypodium distachyon Brachypodium distachyon Brachypodium distachyon
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62 Branchiostoma belcheri Branchiostoma belcheri Branchiostoma belcheri
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63 Branchiostoma floridae Branchiostoma floridae Branchiostoma floridae
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64 Brassica napus Brassica napus Brassica napus
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65 Brassica oleracea Brassica oleracea Brassica oleracea
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66 Brassica rapa Brassica rapa Brassica rapa
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67 Brugia malayi Brugia malayi Brugia malayi
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68 Bruguiera cylindrica Bruguiera cylindrica Bruguiera cylindrica
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69 Bruguiera gymnorhiza Bruguiera gymnorhiza Bruguiera gymnorhiza
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70 Caenorhabditis brenneri Caenorhabditis brenneri Caenorhabditis brenneri
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71 Caenorhabditis briggsae Caenorhabditis briggsae Caenorhabditis briggsae
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72 Caenorhabditis elegans Caenorhabditis elegans Caenorhabditis elegans
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73 Caenorhabditis remanei Caenorhabditis remanei Caenorhabditis remanei
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74 Callithrix jacchus Callithrix jacchus Callithrix jacchus
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75 Camelina sativa Camelina sativa Camelina sativa
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76 Canis familiaris Canis familiaris Canis familiaris
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77 Capitella teleta Capitella teleta Capitella teleta
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78 Capra hircus Capra hircus Capra hircus
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79 Carica papaya Carica papaya Carica papaya
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80 Cavia porcellus Cavia porcellus Cavia porcellus
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81 Cerebratulus lacteus Cerebratulus lacteus Cerebratulus lacteus
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82 Chlamydomonas reinhardtii Chlamydomonas reinhardtii Chlamydomonas reinhardtii
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83 Chrysemys picta Chrysemys picta Chrysemys picta
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84 Ciona intestinalis Ciona intestinalis Ciona intestinalis
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85 Ciona savignyi Ciona savignyi Ciona savignyi
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86 Citrus clementina Citrus clementina Citrus clementina
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87 Citrus reticulata Citrus reticulata Citrus reticulata
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88 Citrus sinensis Citrus sinensis Citrus sinensis
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89 Citrus trifoliata Citrus trifoliata Citrus trifoliata
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90 Columba livia Columba livia Columba livia
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91 Cricetulus griseus Cricetulus griseus Cricetulus griseus
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92 Cucumis melo Cucumis melo Cucumis melo
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93 Cucumis sativus Cucumis sativus Cucumis sativus
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94 Culex quinquefasciatus Culex quinquefasciatus Culex quinquefasciatus
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95 Cunninghamia lanceolata Cunninghamia lanceolata Cunninghamia lanceolata
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96 Cynara cardunculus Cynara cardunculus Cynara cardunculus
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97 Cyprinus carpio Cyprinus carpio Cyprinus carpio
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98 Danio rerio Danio rerio Danio rerio
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99 Daphnia pulex Daphnia pulex Daphnia pulex
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100 Dasypus novemcinctus Dasypus novemcinctus Dasypus novemcinctus
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101 Daubentonia madagascariensis Daubentonia madagascariensis Daubentonia madagascariensis
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102 Dictyostelium discoideum Dictyostelium discoideum Dictyostelium discoideum
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103 Digitalis purpurea Digitalis purpurea Digitalis purpurea
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104 Dinoponera quadriceps Dinoponera quadriceps Dinoponera quadriceps
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105 Drosophila ananassae Drosophila ananassae Drosophila ananassae
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106 Drosophila erecta Drosophila erecta Drosophila erecta
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107 Drosophila grimshawi Drosophila grimshawi Drosophila grimshawi
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108 Drosophila melanogaster Drosophila melanogaster Drosophila melanogaster
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109 Drosophila mojavensis Drosophila mojavensis Drosophila mojavensis
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110 Drosophila persimilis Drosophila persimilis Drosophila persimilis
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111 Drosophila pseudoobscura Drosophila pseudoobscura Drosophila pseudoobscura
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112 Drosophila sechellia Drosophila sechellia Drosophila sechellia
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113 Drosophila simulans Drosophila simulans Drosophila simulans
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114 Drosophila virilis Drosophila virilis Drosophila virilis
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115 Drosophila willistoni Drosophila willistoni Drosophila willistoni
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116 Drosophila yakuba Drosophila yakuba Drosophila yakuba
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117 Duck enteritis Duck enteritis Duck enteritis
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118 Echinococcus granulosus Echinococcus granulosus Echinococcus granulosus
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119 Echinococcus multilocularis Echinococcus multilocularis Echinococcus multilocularis
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120 Ectocarpus siliculosus Ectocarpus siliculosus Ectocarpus siliculosus
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121 Elaeis guineensis Elaeis guineensis Elaeis guineensis
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122 Electrophorus electricus Electrophorus electricus Electrophorus electricus
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123 Epstein Barr Epstein Barr Epstein Barr
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124 Eptesicus fuscus Eptesicus fuscus Eptesicus fuscus
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125 Equus caballus Equus caballus Equus caballus
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126 Eugenia uniflora Eugenia uniflora Eugenia uniflora
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127 Fasciola hepatica Fasciola hepatica Fasciola hepatica
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128 Festuca arundinacea Festuca arundinacea Festuca arundinacea
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129 Fragaria vesca Fragaria vesca Fragaria vesca
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130 Fugu rubripes Fugu rubripes Fugu rubripes
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131 Gadus morhua Gadus morhua Gadus morhua
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132 Gallus gallus Gallus gallus Gallus gallus
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133 Glottidia pyramidata Glottidia pyramidata Glottidia pyramidata
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134 Glycine max Glycine max Glycine max
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135 Glycine soja Glycine soja Glycine soja
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136 Gorilla gorilla Gorilla gorilla Gorilla gorilla
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137 Gossypium arboreum Gossypium arboreum Gossypium arboreum
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138 Gossypium herbaceum Gossypium herbaceum Gossypium herbaceum
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139 Gossypium hirsutum Gossypium hirsutum Gossypium hirsutum
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140 Gossypium raimondii Gossypium raimondii Gossypium raimondii
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141 Gyrodactylus salaris Gyrodactylus salaris Gyrodactylus salaris
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142 Haemonchus contortus Haemonchus contortus Haemonchus contortus
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143 Haliotis rufescens Haliotis rufescens Haliotis rufescens
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144 Helianthus annuus Helianthus annuus Helianthus annuus
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145 Helianthus argophyllus Helianthus argophyllus Helianthus argophyllus
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146 Helianthus ciliaris Helianthus ciliaris Helianthus ciliaris
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147 Helianthus exilis Helianthus exilis Helianthus exilis
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148 Helianthus paradoxus Helianthus paradoxus Helianthus paradoxus
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149 Helianthus petiolaris Helianthus petiolaris Helianthus petiolaris
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150 Helianthus tuberosus Helianthus tuberosus Helianthus tuberosus
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151 Heliconius melpomene Heliconius melpomene Heliconius melpomene
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152 Heligmosomoides polygyrus Heligmosomoides polygyrus Heligmosomoides polygyrus
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153 Herpes B Herpes B Herpes B
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154 Herpes Simplex Herpes Simplex Herpes Simplex
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155 Herpesvirus of Herpesvirus of Herpesvirus of
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156 Herpesvirus saimiri Herpesvirus saimiri Herpesvirus saimiri
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157 Hevea brasiliensis Hevea brasiliensis Hevea brasiliensis
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158 Hippoglossus hippoglossus Hippoglossus hippoglossus Hippoglossus hippoglossus
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159 Homo sapiens Homo sapiens Homo sapiens
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160 Hordeum vulgare Hordeum vulgare Hordeum vulgare
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161 Human cytomegalovirus Human cytomegalovirus Human cytomegalovirus
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162 Human herpesvirus Human herpesvirus Human herpesvirus
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163 Human immunodeficiency Human immunodeficiency Human immunodeficiency
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164 Hydra magnipapillata Hydra magnipapillata Hydra magnipapillata
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165 Ictalurus punctatus Ictalurus punctatus Ictalurus punctatus
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166 Infectious laryngotracheitis Infectious laryngotracheitis Infectious laryngotracheitis
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167 Ixodes scapularis Ixodes scapularis Ixodes scapularis
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168 JC polyomavirus JC polyomavirus JC polyomavirus
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169 Kaposi sarcoma-associated Kaposi sarcoma-associated Kaposi sarcoma-associated
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170 Lagothrix lagotricha Lagothrix lagotricha Lagothrix lagotricha
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171 Lemur catta Lemur catta Lemur catta
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172 Leucosolenia complicata Leucosolenia complicata Leucosolenia complicata
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173 Linum usitatissimum Linum usitatissimum Linum usitatissimum
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174 Locusta migratoria Locusta migratoria Locusta migratoria
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175 Lottia gigantea Lottia gigantea Lottia gigantea
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176 Lotus japonicus Lotus japonicus Lotus japonicus
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177 Lytechinus variegatus Lytechinus variegatus Lytechinus variegatus
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178 Macaca mulatta Macaca mulatta Macaca mulatta
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179 Macaca nemestrina Macaca nemestrina Macaca nemestrina
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180 Macropus eugenii Macropus eugenii Macropus eugenii
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181 Malus domestica Malus domestica Malus domestica
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182 Manduca sexta Manduca sexta Manduca sexta
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183 Manihot esculenta Manihot esculenta Manihot esculenta
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184 Mareks disease Mareks disease Mareks disease
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185 Marsupenaeus japonicus Marsupenaeus japonicus Marsupenaeus japonicus
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186 Medicago truncatula Medicago truncatula Medicago truncatula
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187 Melibe leonina Melibe leonina Melibe leonina
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188 Merkel cell Merkel cell Merkel cell
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189 Mesocestoides corti Mesocestoides corti Mesocestoides corti
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190 Metriaclima zebra Metriaclima zebra Metriaclima zebra
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191 Microcebus murinus Microcebus murinus Microcebus murinus
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192 Monodelphis domestica Monodelphis domestica Monodelphis domestica
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193 Mouse cytomegalovirus Mouse cytomegalovirus Mouse cytomegalovirus
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194 Mouse gammaherpesvirus Mouse gammaherpesvirus Mouse gammaherpesvirus
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195 Mus musculus Mus musculus Mus musculus
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196 Nasonia giraulti Nasonia giraulti Nasonia giraulti
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197 Nasonia longicornis Nasonia longicornis Nasonia longicornis
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198 Nasonia vitripennis Nasonia vitripennis Nasonia vitripennis
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199 Nematostella vectensis Nematostella vectensis Nematostella vectensis
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200 Neolamprologus brichardi Neolamprologus brichardi Neolamprologus brichardi
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201 Nicotiana tabacum Nicotiana tabacum Nicotiana tabacum
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202 Nomascus leucogenys Nomascus leucogenys Nomascus leucogenys
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203 Oikopleura dioica Oikopleura dioica Oikopleura dioica
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204 Ophiophagus hannah Ophiophagus hannah Ophiophagus hannah
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205 Oreochromis niloticus Oreochromis niloticus Oreochromis niloticus
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206 Ornithorhynchus anatinus Ornithorhynchus anatinus Ornithorhynchus anatinus
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207 Oryctolagus cuniculus Oryctolagus cuniculus Oryctolagus cuniculus
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208 Oryza sativa Oryza sativa Oryza sativa
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209 Oryzias latipes Oryzias latipes Oryzias latipes
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210 Otolemur garnettii Otolemur garnettii Otolemur garnettii
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211 Ovis aries Ovis aries Ovis aries
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212 Paeonia lactiflora Paeonia lactiflora Paeonia lactiflora
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213 Pan paniscus Pan paniscus Pan paniscus
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214 Pan troglodytes Pan troglodytes Pan troglodytes
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215 Panagrellus redivivus Panagrellus redivivus Panagrellus redivivus
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216 Panax ginseng Panax ginseng Panax ginseng
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217 Papio hamadryas Papio hamadryas Papio hamadryas
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218 Paralichthys olivaceus Paralichthys olivaceus Paralichthys olivaceus
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219 Parasteatoda tepidariorum Parasteatoda tepidariorum Parasteatoda tepidariorum
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220 Patiria miniata Patiria miniata Patiria miniata
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221 Petromyzon marinus Petromyzon marinus Petromyzon marinus
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222 Phaeodactylum tricornutum Phaeodactylum tricornutum Phaeodactylum tricornutum
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223 Phaseolus vulgaris Phaseolus vulgaris Phaseolus vulgaris
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224 Physcomitrella patens Physcomitrella patens Physcomitrella patens
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225 Phytophthora infestans Phytophthora infestans Phytophthora infestans
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226 Phytophthora ramorum Phytophthora ramorum Phytophthora ramorum
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227 Phytophthora sojae Phytophthora sojae Phytophthora sojae
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228 Picea abies Picea abies Picea abies
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229 Pinus densata Pinus densata Pinus densata
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230 Pinus taeda Pinus taeda Pinus taeda
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231 Plutella xylostella Plutella xylostella Plutella xylostella
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232 Polistes canadensis Polistes canadensis Polistes canadensis
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233 Pongo pygmaeus Pongo pygmaeus Pongo pygmaeus
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234 Populus euphratica Populus euphratica Populus euphratica
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235 Populus trichocarpa Populus trichocarpa Populus trichocarpa
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236 Pristionchus pacificus Pristionchus pacificus Pristionchus pacificus
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237 Prunus persica Prunus persica Prunus persica
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238 Pseudorabies virus Pseudorabies virus Pseudorabies virus
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239 Pteropus alecto Pteropus alecto Pteropus alecto
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240 Pundamilia nyererei Pundamilia nyererei Pundamilia nyererei
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241 Pygathrix bieti Pygathrix bieti Pygathrix bieti
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242 Python bivittatus Python bivittatus Python bivittatus
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243 Raccoon polyomavirus Raccoon polyomavirus Raccoon polyomavirus
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244 Rattus norvegicus Rattus norvegicus Rattus norvegicus
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245 Rehmannia glutinosa Rehmannia glutinosa Rehmannia glutinosa
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246 Rhesus lymphocryptovirus Rhesus lymphocryptovirus Rhesus lymphocryptovirus
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247 Rhesus monkey Rhesus monkey Rhesus monkey
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248 Rhipicephalus microplus Rhipicephalus microplus Rhipicephalus microplus
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249 Ricinus communis Ricinus communis Ricinus communis
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250 Saccharum officinarum Saccharum officinarum Saccharum officinarum
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251 Saccharum sp. Saccharum sp. Saccharum sp.
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252 Saccoglossus kowalevskii Saccoglossus kowalevskii Saccoglossus kowalevskii
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253 Saguinus labiatus Saguinus labiatus Saguinus labiatus
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254 Saimiri boliviensis Saimiri boliviensis Saimiri boliviensis
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255 Salicornia europaea Salicornia europaea Salicornia europaea
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256 Salmo salar Salmo salar Salmo salar
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257 Salvia miltiorrhiza Salvia miltiorrhiza Salvia miltiorrhiza
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258 Salvia sclarea Salvia sclarea Salvia sclarea
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259 Sarcophilus harrisii Sarcophilus harrisii Sarcophilus harrisii
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260 Schistosoma japonicum Schistosoma japonicum Schistosoma japonicum
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261 Schistosoma mansoni Schistosoma mansoni Schistosoma mansoni
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262 Schmidtea mediterranea Schmidtea mediterranea Schmidtea mediterranea
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263 Selaginella moellendorffii Selaginella moellendorffii Selaginella moellendorffii
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264 Simian foamy Simian foamy Simian foamy
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265 Simian virus Simian virus Simian virus
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266 Solanum lycopersicum Solanum lycopersicum Solanum lycopersicum
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267 Solanum tuberosum Solanum tuberosum Solanum tuberosum
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268 Sorghum bicolor Sorghum bicolor Sorghum bicolor
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269 Spodoptera frugiperda Spodoptera frugiperda Spodoptera frugiperda
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270 Strigamia maritima Strigamia maritima Strigamia maritima
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271 Strongylocentrotus purpuratus Strongylocentrotus purpuratus Strongylocentrotus purpuratus
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272 Strongyloides ratti Strongyloides ratti Strongyloides ratti
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273 Sus scrofa Sus scrofa Sus scrofa
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274 Sycon ciliatum Sycon ciliatum Sycon ciliatum
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275 Symbiodinium microadriaticum Symbiodinium microadriaticum Symbiodinium microadriaticum
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276 Symphalangus syndactylus Symphalangus syndactylus Symphalangus syndactylus
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277 Taeniopygia guttata Taeniopygia guttata Taeniopygia guttata
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278 Terebratulina retusa Terebratulina retusa Terebratulina retusa
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279 Tetranychus urticae Tetranychus urticae Tetranychus urticae
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280 Tetraodon nigroviridis Tetraodon nigroviridis Tetraodon nigroviridis
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281 Theobroma cacao Theobroma cacao Theobroma cacao
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282 Torque teno Torque teno Torque teno
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283 Tribolium castaneum Tribolium castaneum Tribolium castaneum
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284 Triops cancriformis Triops cancriformis Triops cancriformis
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285 Triticum aestivum Triticum aestivum Triticum aestivum
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286 Triticum turgidum Triticum turgidum Triticum turgidum
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287 Tupaia chinensis Tupaia chinensis Tupaia chinensis
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288 Vigna unguiculata Vigna unguiculata Vigna unguiculata
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289 Vitis vinifera Vitis vinifera Vitis vinifera
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290 Vriesea carinata Vriesea carinata Vriesea carinata
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291 Xenopus laevis Xenopus laevis Xenopus laevis
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292 Xenopus tropicalis Xenopus tropicalis Xenopus tropicalis
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293 Xenoturbella bocki Xenoturbella bocki Xenoturbella bocki
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294 Zea mays Zea mays Zea mays
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295 #
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296 #More examples:
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297 #
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298 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
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299 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
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300 #
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