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annotate test-data/index.html @ 3:5784e268efca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
author bgruening
date Sun, 09 Aug 2020 10:15:12 -0400
parents 593bb8f5488b
children e78e25d3b4bd
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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2 <!doctype html>
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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3 <html lang="en">
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4 <head>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5 <meta charset="utf-8" />
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6 <title>input_tempfile - 1 region(s) - antiSMASH results</title>
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7 <style>img {width: 20px; height: 20px;}</style>
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8 <link rel="stylesheet" type="text/css" href="css/bacteria.css">
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9 <meta property="og:title" content="input_tempfile - 1 record(s) - 1 region(s)" />
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10 <meta property="og:description" content="">
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11 <meta property="og:image" content="https://antismash.secondarymetabolites.org/images/bacteria_logo.png" />
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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12 <meta property="og:image:alt" content="antiSMASH logo" />
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13 <meta property="og:image:width" content="600" />
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14 <meta property="og:image:height" content="600" />
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15 <meta property="og:url" content="https://antismash.secondarymetabolites.org/upload/input_tempfile/index.html" />
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16 <meta property="og:type" content="website" />
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17 <meta name="twitter:card" content="summary" />
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18 <meta name="twitter:site" content="@antismash_dev" />
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19 </head>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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21 <body>
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22 <div id="header">
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23 <nav>
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24 <div class="main-link">
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25 <div>
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26 <a href="https://antismash.secondarymetabolites.org/">
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27 <img src="images/bacteria_antismash_logo.svg" alt="antiSMASH logo" style="width:40px;height:unset;">
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28 </a>
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29 </div>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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30 <div>
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31 <a href="https://antismash.secondarymetabolites.org/">
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32 antiSMASH version 5.1.2
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33 </a>
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34 </div>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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35 </div>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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36 <div class="custom-description"></div>
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37 <div class="ancillary-links">
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38 <div class="ancillary-link dropdown-menu" id="download-dropdown"><a href="#" id="download-dropdown-link"><img src="images/download.svg" alt="download"> &nbsp; Download</a>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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39 <ul class="dropdown-options">
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41 <li><a href="input_tempfile.zip">Download all results</a></li>
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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43 <li><a href="input_tempfile.gbk">Download GenBank summary file</a></li>
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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45 </ul>
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46 </div>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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47 <div class="ancillary-link"><a href="https://antismash.secondarymetabolites.org/#!/about"><img src="images/about.svg" alt="about"> &nbsp; About</a></div>
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48 <div class="ancillary-link"><a href="https://docs.antismash.secondarymetabolites.org/"><img src="images/help.svg" alt="help"> &nbsp; Help</a></div>
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49 <div class="ancillary-link"><a href="https://antismash.secondarymetabolites.org/#!/contact"><img src="images/contact.svg" alt="contact"> &nbsp; Contact</a></div>
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50 </div>
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51 </nav>
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52 <div id="buttons">
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53 <span id="region-type">Select genomic region:</span>
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54 <div id="regionbuttons">
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55 <div class="arrow-left" id="prev-region"></div>
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56 <div class="regbutton" style="min-width: inherit;"><a href="#">Overview</a></div>
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57 <div style="display: flex; flex-wrap: wrap">
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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62 <div class="regbutton T1PKS r1c1">
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63 <a href="#r1c1">1.1</a>
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64 </div>
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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1
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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67 </div>
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68 <div id="last-regbutton"><div class="arrow-right" id="next-region"></div></div>
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69 </div>
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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70 </div>
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71 </div>
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593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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73 <!-- overview page -->
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75 <div class="page" id="overview">
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78 <h3>Identified secondary metabolite regions using strictness &#39;relaxed&#39;<span id="truncated"></span></h3>
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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80 <div class="overview-layout">
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81 <div id="record-tables">
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82 <div id="single-record-tables">
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83 <div class="record-overview-header">
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84 <strong>ARBH01000003.1</strong>
1
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85 </div>
3
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86 <div class="record-overview-details">
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87 <svg id="record-minimap-1" class="record-overview-svg" height="1" width="1"></svg>
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88 <table class="region-table">
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89 <thead>
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90 <tr>
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91 <th>Region</th>
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92 <th>Type</th>
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93 <th>From</th>
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94 <th>To</th>
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95 <th colspan="2">Most similar known cluster</th>
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96 <th>Similarity</th>
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97 </tr>
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98 </thead>
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99 <tbody>
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100 <tr class="linked-row odd" data-anchor="#r1c1">
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101
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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102
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103 <td class="regbutton T1PKS r1c1">
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104 <a href="#r1c1">Region&nbsp1</a>
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105 </td>
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106 <td>
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107
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108 <a class="external-link" href="https://docs.antismash.secondarymetabolites.org/glossary/#t1pks" target="_blank">T1PKS</a>
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109 </td>
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110 <td class="digits">1</td>
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111 <td class="digits table-split-left">3,500</td>
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112
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113 <td colspan="3"></td>
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114
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115 </tr>
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116
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117 </tbody>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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118 </table>
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119 </div>
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120 </div>
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121
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122
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123 </div>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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124
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125 </div>
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126 </div>
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127
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128
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129
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130
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131
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132
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133
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134 <div class="page" id='r1c1' style="display: none;">
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135 <div class="region-grid">
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136 <div class = "content">
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137 <div class ="description-container">
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138 <div class="heading"> ARBH01000003.1 - Region 1 - T1PKS <div class="help-container"> <div class="help-icon" data-id="region_svg-help-4"></div> <span class="help-tooltip" id="region_svg-help-4">Shows the layout of the region, marking coding sequences and areas of interest. Clicking a gene will select it and show any relevant details. Clicking an area feature (e.g. a candidate cluster) will select all coding sequences within that area. Double clicking an area feature will zoom to that area. Multiple genes and area features can be selected by clicking them while holding the Ctrl key.<br>More detailed help is available <a class='external-link' href='https://docs.antismash.secondarymetabolites.org/understanding_output/#the-antismash-5-region-concept' target='_blank'>here</a>.</span></div></div>
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139 <div class="region-download">
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140 <a href = ARBH01000003.1.region001.gbk>Download region GenBank file</a>
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141 </div>
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142 <div class = 'description-text'>
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143 Location: 1 - 3,500 nt. (total: 3,500 nt)
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144
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145 <a class="cluster-rules-header" id="r1c1-rules-header" href="#r1c1">Show pHMM detection rules used</a>
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146
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147
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148 <div class="contig-edge-warning">Region on contig edge.</div>
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149
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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150 </div>
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151
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152 <div class="cluster-rules" id="r1c1-rules">T1PKS: cds(PKS_AT and (PKS_KS or ene_KS or mod_KS or hyb_KS or itr_KS or tra_KS))</div>
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153
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154 <div class="region-svg-container">
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155 <div id='r1c1-svg'>
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156 </div>
1
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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157 </div>
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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158 </div>
3
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159 <div class="legend">
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160 <h4>Legend:</h4>
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161 <div class="legend-items">
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162 <div class="button-like legend-selector" data-id="legend-type-biosynthetic">
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163 <div class="legend-field legend-type-biosynthetic"></div>
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164 <div class="legend-label">core biosynthetic genes</div>
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165 </div>
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166 <div class="button-like legend-selector" data-id="legend-type-biosynthetic-additional">
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167 <div class="legend-field legend-type-biosynthetic-additional"></div>
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168 <div class="legend-label">additional biosynthetic genes</div>
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169 </div>
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170 <div class="button-like legend-selector" data-id="legend-type-transport">
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171 <div class="legend-field legend-type-transport"></div>
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172 <div class="legend-label">transport-related genes</div>
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173 </div>
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174 <div class="button-like legend-selector" data-id="legend-type-regulatory">
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175 <div class="legend-field legend-type-regulatory"></div>
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176 <div class="legend-label">regulatory genes</div>
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177 </div>
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178 <div class="button-like legend-selector" data-id="legend-type-other">
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179 <div class="legend-field legend-type-other"></div>
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180 <div class="legend-label">other genes</div>
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181 </div>
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182 <div style="margin-right: 2em;"></div>
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183 <div class="button-like legend-selector" data-id="legend-resistance">
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184 <div class="legend-symbol">
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185 <svg viewbox="0 0 8 8">
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186 <rect x=0 y=2 height=4 width=8 class="svgene-resistance"></rect>
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187 </svg>
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188 </div>
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189 <div class="legend-label">resistance</div>
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190 </div>
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191
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192 <div class="button-like legend-selector" data-id="legend-tta-codon">
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193 <div class="legend-symbol">
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194 <svg viewbox="0 0 6 6">
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195 <polyline class="svgene-tta-codon" points="3,0 0,6 6,6 3,0"></rect>
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196 </svg>
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197 </div>
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198 <div class="legend-label">TTA codons</div>
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199 </div>
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200
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201
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202
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203 </div>
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204 </div>
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205 <div class="zoom-buttons">
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206 <div class="button-like zoom-button zoom-reset"><img src="images/expand-arrows-alt-solid.svg" alt="reset zoom">reset view</div>
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207 <div class="button-like zoom-button zoom-in"><img src="images/search-solid.svg" alt="zoom">zoom to selection</div>
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208 </div>
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209 </div>
1
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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210
3
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211 <div class="focus-panel">
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212 <div class="heading">
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213 <span>Gene details</span>
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214 <div class="help-container"> <div class="help-icon" data-id="focus-panel-help-5"></div> <span class="help-tooltip" id="focus-panel-help-5">Shows details of the most recently selected gene, including names, products, location, and other annotations.</span></div>
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215 </div>
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216 <div class="focus-panel-content focus-panel-content-r1c1">
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217 <div style="text-align: center; margin-top: 30%;">
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218 Select a gene to view the details available for it
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219 </div>
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220 </div>
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221 </div>
1
593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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222
3
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223
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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224 <div class="body-details">
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225 <div class="body-details-headers">
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226
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227
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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228 <div class="body-details-header r1c1-nrps_pks" data-name="r1c1-nrps_pks">
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229 NRPS/PKS domains
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230 </div>
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231
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232
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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233
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234
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235
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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236 <div class="body-details-header r1c1-knownclusterblast" data-name="r1c1-knownclusterblast">
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237 KnownClusterBlast
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238 </div>
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239
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240 <div class="body-details-header r1c1-subclusterblast" data-name="r1c1-subclusterblast">
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241 SubClusterBlast
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242 </div>
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243
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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244
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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245 </div>
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246
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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247
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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248 <div class="body-details-section r1c1-nrps_pks">
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249 <div class="details">
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250 <div class="heading">
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251 <span>Detailed domain annotation</span>
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252 <div class="help-container"> <div class="help-icon" data-id="nrps-domain-help-1"></div> <span class="help-tooltip" id="nrps-domain-help-1">Shows <a href='https://docs.antismash.secondarymetabolites.org/glossary/#nrps' target='_blank'>NRPS</a>- and <a href='https://docs.antismash.secondarymetabolites.org/glossary/#pks' target='_blank'>PKS</a>-related domains for each feature that contains them. Click on each domain for more information about the domain's location, consensus monomer prediction, and other details.<br>A glossary is available <a href='https://docs.antismash.secondarymetabolites.org/modules/nrps_pks_domains/' target='_blank'>here</a>.</span></div>
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253 </div>
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254 <div class="nrps-pks-domain-buttons">
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255 <div class="domains-selected-only switch-container"><span class="switch-desc">Selected features only</span> <label class="switch"> <input class="domains-selected-only" type="checkbox"> <span class="slider"></span> </label></div>
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256 <div class="show-module-domains switch-container"><span class="switch-desc">Show module domains</span> <label class="switch"> <input class="show-module-domains" type="checkbox"> <span class="slider"></span> </label></div>
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257 </div>
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258 <div class="details-svg" id="r1c1-details-svg"></div>
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259 </div>
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260 </div>
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261
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264
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265
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266 <div class="body-details-section r1c1-knownclusterblast">
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267 <div class = "knownclusterblast">
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268 <div class="heading">
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269 <span>Similar known gene clusters</span>
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270 <div class="help-container"> <div class="help-icon" data-id="cb-known-help-2"></div> <span class="help-tooltip" id="cb-known-help-2">Shows clusters from the MiBIG database that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.<br>Click on reference genes to show details of similarities to genes within the current region.<br>Click on an accession to open that entry in the MiBIG database.</span></div>
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271 </div>
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272
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273 <div>
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274 <p>No matches found.</p>
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275 </div>
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276
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277 </div>
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278 </div>
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279
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280 <div class="body-details-section r1c1-subclusterblast">
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281 <div class = "subclusterblast">
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282 <div class="heading">
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283 <span>Similar subclusters</span>
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284 <div class="help-container"> <div class="help-icon" data-id="cb-sub-help-3"></div> <span class="help-tooltip" id="cb-sub-help-3">Shows sub-cluster units that are similar to the current region. Genes marked with the same colour are interrelated. White genes have no relationship.<br>Click on reference genes to show details of similarities to genes within the current region.</span></div>
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285 </div>
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286
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287 <div>
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288 <p>No matches found.</p>
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289 </div>
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290
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291 </div>
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292 </div>
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293
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294
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295 </div>
1
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296
3
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297 <div class="sidepanel">
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298 <div class="sidepanel-details-headers">
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299
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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303
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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305
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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306 </div>
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307
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308
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311
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312
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313
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314 </div>
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315
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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316 </div>
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317
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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318 </div>
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319
1
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320
3
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321 <footer class="footer">
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322 <div class="container">
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323 <div>
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324 <img src="images/bacteria_antismash_logo.svg" style="height:90px;width:unset;">
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325 </div>
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326 <div class="cite-me">
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327 If you have found antiSMASH useful, please <a href="https://antismash.secondarymetabolites.org/#!/about">cite us</a>.
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328 </div>
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329 <div>
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330 <img src="images/bacteria_antismash_icon.svg" style="height:100px;width:unset;">
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331 </div>
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332 </div>
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333 </footer>
1
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334
3
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335 <script src="js/jquery.js"></script>
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336 <script src="js/antismash.js"></script>
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337 <script src="regions.js"></script>
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338 <script>
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339 $(document).ready(function() {
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340 viewer["start"](all_regions, details_data, recordData);
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341 })
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342 </script>
1
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343
3
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344 <svg xmlns="http://www.w3.org/2000/svg" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink">
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345 <defs>
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346 <filter id="inset-shadow">
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347 <feOffset dx="-2" dy="-2"></feOffset>
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348 <feGaussianBlur result="offset-blur" stdDeviation="2"></feGaussianBlur>
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349 <feComposite operator="out" in="SourceGraphic" in2="offset-blur" result="inverse"></feComposite>
5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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5784e268efca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
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593bb8f5488b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
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360 </html>