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3
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1 <?xml version="1.0"?>
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2 <root>
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3 <metadata>
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4 <gencode>11</gencode>
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5 <genomes>
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6 <genome>test-data/merlin.fa</genome>
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7 </genomes>
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8 </metadata>
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9 <tracks>
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10 <track cat="Auto Coloured" format="gene_calls">
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11 <files>
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12 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
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13 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
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14 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
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15 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
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16 </files>
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17
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18 <options>
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19 <style>
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20 <className>feature</className>
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21 <description>feature</description>
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22 <label>name,id</label>
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23 <height>100px</height>
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24 </style>
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25 <gff>
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26 </gff>
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27 <scaling>
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28 <method>ignore</method>
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29 <scheme>
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30 <color>__auto__</color>
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31 </scheme>
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32 </scaling>
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33 </options>
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34 </track>
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35 <track cat="Ignore Scale" format="gene_calls">
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36 <files>
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37 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
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38 </files>
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39
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40 <options>
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41 <style>
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42 <className>feature</className>
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43 <description>feature</description>
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44 <label>name,id</label>
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45 <height>100px</height>
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46 </style>
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47 <gff>
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48 </gff>
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49 <scaling>
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50 <method>ignore</method>
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51 <scheme>
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52 <color>#ff00ff</color>
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53 </scheme>
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54 </scaling>
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55 </options>
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56 </track>
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57 <track cat="Scaled Colour" format="gene_calls">
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58 <files>
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59 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
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60 </files>
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61
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62 <options>
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63 <style>
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64 <className>feature</className>
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65 <description>feature</description>
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66 <label>name,id</label>
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67 <height>100px</height>
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68 </style>
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69 <gff>
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70 </gff>
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71 <scaling>
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72 <method>score</method>
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73 <algo>linear</algo>
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74 <scales>
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75 <type>__auto__</type>
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76 </scales>
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77 <scheme>
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78 <type>opacity</type>
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79 <color>__auto__</color>
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80 </scheme>
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81 </scaling>
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82 </options>
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83 </track>
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84 <track cat="Scaled Colour" format="gene_calls">
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85 <files>
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86 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
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87 </files>
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88
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89 <options>
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90 <style>
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91 <className>feature</className>
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92 <description>feature</description>
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93 <label>name,id</label>
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94 <height>100px</height>
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95 </style>
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96 <gff>
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97 </gff>
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98 <scaling>
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99 <method>score</method>
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100 <algo>linear</algo>
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101 <scales>
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102 <type>__auto__</type>
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103 </scales>
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104 <scheme>
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105 <type>opacity</type>
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106 <color>#0000ff</color>
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107 </scheme>
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108 </scaling>
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109 </options>
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110 </track>
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111 <track cat="Scaled Colour" format="gene_calls">
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112 <files>
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113 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
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114 </files>
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115
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116 <options>
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117 <style>
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118 <className>feature</className>
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119 <description>feature</description>
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120 <label>name,id</label>
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121 <height>100px</height>
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122 </style>
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123 <gff>
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124 </gff>
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125 <scaling>
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126 <method>score</method>
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127 <algo>linear</algo>
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128 <scales>
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129 <type>manual</type>
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130 <min>0</min>
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131 <max>1000</max>
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132 </scales>
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133 <scheme>
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134 <type>opacity</type>
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135 <color>__auto__</color>
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136 </scheme>
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137 </scaling>
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138 </options>
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139 </track>
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140 <track cat="Scaled Colour" format="gene_calls">
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141 <files>
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142 <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
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143 </files>
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144
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145 <options>
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146 <style>
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147 <className>feature</className>
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148 <description>feature</description>
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149 <label>name,id</label>
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150 <height>100px</height>
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151 </style>
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152 <gff>
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153 </gff>
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154 <scaling>
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155 <method>score</method>
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156 <algo>linear</algo>
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157 <scales>
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158 <type>manual</type>
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159 <min>0</min>
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160 <max>1000</max>
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161 </scales>
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162 <scheme>
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163 <type>opacity</type>
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164 <color>#ff0000</color>
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165 </scheme>
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166 </scaling>
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167 </options>
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168 </track>
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169
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170
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171 <track cat="Realistic" format="gene_calls">
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172 <files>
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173 <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
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174 </files>
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175
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176 <options>
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177 <style>
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178 <className>feature</className>
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179 <description>feature</description>
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180 <label>name,id</label>
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181 <height>100px</height>
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182 </style>
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183 <gff>
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184 </gff>
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185 <scaling>
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186 <method>ignore</method>
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187 <scheme>
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188 <color>__auto__</color>
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189 </scheme>
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190 </scaling>
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191 </options>
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192 </track>
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193 <track cat="Realistic" format="gene_calls">
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194 <files>
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195 <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
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196 </files>
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197
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198 <options>
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199 <style>
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200 <className>feature</className>
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201 <description>feature</description>
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202 <label>name,id</label>
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203 <height>100px</height>
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204 </style>
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205 <gff>
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206 <match>cDNA_match</match>
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207 </gff>
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208 <scaling>
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209 <method>ignore</method>
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210 <scheme>
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211 <type>opacity</type>
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212 <color>__auto__</color>
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213 </scheme>
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214 </scaling>
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215 </options>
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216 </track>
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217 </tracks>
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218 </root>
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