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1 <!DOCTYPE html>
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2 <html lang="en">
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3 <head>
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4 <meta charset="utf-8">
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5 <meta http-equiv="X-UA-Compatible" content="IE=edge">
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6 <meta name="viewport" content="width=device-width, initial-scale=1">
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7 <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags -->
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8 <meta name="description" content="">
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9 <meta name="author" content="">
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10 <title>Phage QC on AY216660.2 - 76</title>
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11 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
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12 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css">
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13
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14 <style type="text/css">
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15 /*
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16 * Base structure
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17 */
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18
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19 /* Move down content because we have a fixed navbar that is 50px tall */
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20 body {
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21 padding-top: 50px;
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22 }
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23
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24 h3:before {
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25 display: block;
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26 content: " ";
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27 margin-top: -50px;
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28 height: 50px;
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29 visibility: hidden;
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30 }
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31
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32 /*
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33 * Global add-ons
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34 */
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35
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36 .sub-header {
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37 padding-bottom: 10px;
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38 border-bottom: 1px solid #eee;
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39 }
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40
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41 /*
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42 * Top navigation
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43 * Hide default border to remove 1px line.
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44 */
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45 .navbar-fixed-top {
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46 border: 0;
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47 }
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48
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49 /*
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50 * Sidebar
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51 */
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52
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53 /* Hide for mobile, show later */
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54 .sidebar {
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55 display: none;
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56 }
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57 @media (min-width: 768px) {
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58 .sidebar {
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59 position: fixed;
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60 top: 51px;
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61 bottom: 0;
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62 left: 0;
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63 z-index: 1000;
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64 display: block;
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65 padding: 20px;
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66 overflow-x: hidden;
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67 overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
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68 background-color: #f5f5f5;
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69 border-right: 1px solid #eee;
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70 }
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71 }
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72
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73 /* Sidebar navigation */
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74 .nav-sidebar {
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75 margin-right: -21px; /* 20px padding + 1px border */
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76 margin-bottom: 20px;
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77 margin-left: -20px;
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78 }
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79 .nav-sidebar > li > a {
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80 padding-right: 20px;
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81 padding-left: 20px;
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82 }
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83 .nav-sidebar > .active > a,
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84 .nav-sidebar > .active > a:hover,
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85 .nav-sidebar > .active > a:focus {
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86 color: #fff;
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87 background-color: #428bca;
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88 }
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89
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90
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91 /*
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92 * Main content
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93 */
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94
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95 .main {
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96 padding: 20px;
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97 }
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98 @media (min-width: 768px) {
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99 .main {
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100 padding-right: 40px;
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101 padding-left: 40px;
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102 }
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103 }
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104 .main .page-header {
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105 margin-top: 0;
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106 }
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107
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108
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109 /*
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110 * Placeholder dashboard ideas
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111 */
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112
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113 .placeholders {
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114 margin-bottom: 30px;
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115 text-align: center;
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116 }
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117 .placeholders h4 {
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118 margin-bottom: 0;
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119 }
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120 .placeholder {
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121 margin-bottom: 20px;
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122 }
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123 .placeholder img {
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124 display: inline-block;
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125 border-radius: 50%;
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126 }
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127
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128 td.moron {
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129 font-size: 150%;
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130 padding: 0px;
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131 color: gray;
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132 }
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133 .strand_emph {
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134 text-decoration: underline;
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135 color: black;
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136 }
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137
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138 </style>
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139 <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries -->
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140 <!--[if lt IE 9]>
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141 <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
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142 <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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143 <![endif]-->
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144 </head>
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145 <body>
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146
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147 <nav class="navbar navbar-inverse navbar-fixed-top">
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148 <div class="container-fluid">
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149 <div class="navbar-header">
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150 <a class="navbar-brand" href="#">Phage QC on AY216660.2</a>
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151 </div>
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152 </div>
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153 </nav>
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154
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155 <div class="container-fluid">
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156 <div class="row">
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157 <div class="col-sm-3 col-md-2 sidebar">
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158 <ul class="nav nav-sidebar">
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159 <li><a href="#main"><b>Overview</b></a></li>
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160 <li><a href="#bad_gene_starts"><b>Bad Gene Starts</b></a></li>
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161 <li><a href="#missing_rbs"><small>Missing RBS</small></a></li>
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162 <li><a href="#weird_starts"><small>Unusual Start Codons</small></a></li>
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163 <li><a href="#excessive_gaps"><small>Excessive Gaps</small></a></li>
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164 <li><a href="#excessive_overlap"><small>Excessive Overlaps</small></a></li>
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165 <!--<li><a href="#coding_density"><small>Coding Density</small></a></li>-->
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166 <li><a href="#antisense"><b>Antisense Genes</b></a></li>
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167 <li><a href="#morons"><small>Possible Morons</small></a></li>
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168 <li><a href="#annotations"><b>Annotation Issues</b></a></li>
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169 <li><a href="#missing_product"><small>Missing Product Tags</small></a></li>
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170 </ul>
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171 </div>
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172 <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main" id="main">
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173 <div class="jumbotron">
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174 <div class="row">
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175 <div class="col-sm-7">
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176 <h1>Phage AY216660.2</h1>
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177 <!--<h2>Score: 76/100</h2>-->
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178 </div>
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179 <!--<div class="col-sm-5">
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180 <table class="table table-striped">
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181 <thead>
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182 <tr>
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183 <th>Section</th>
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184 <th>Score</th>
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185 </tr>
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186 </thead>
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187 <tbody>
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188 <tr><td>Missing RBS</td><td>0%</td></tr>
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189 <tr><td>Excessive Gaps</td><td>76%</td></tr>
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190 <tr><td>Excessive Overlap</td><td>76%</td></tr>
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191 <tr><td>Coding Density Score</td><td>99%</td></tr>
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192 <tr><td>Possible Morons</td><td>98%</td></tr>
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193 <tr><td>Missing Product Tags</td><td>100%</td></tr>
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194 </tbody>
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195 </table>
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196 </div>-->
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197 </div>
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198 </div>
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199
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200 <h2 class="sub-header" id="bad_gene_starts">Gene Starts</h2>
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201 <h3 id="missing_rbs">Genes missing RBS <small>0 / 79</small></h3>
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202 <p>The following genes have issues with their RBS.</p>
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203 <p>
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204 Since you have not annotated any possible RBSs, this does not count off from your overall score.
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205 </p>
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206 <div class="table-responsive">
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207 <table class="table table-striped">
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208 <thead>
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209 <tr>
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210 <th>Feature Type</th>
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211 <th>ID</th>
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212 <th>Location</th>
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213 <th>Error</th>
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214 <th>Upstream (-15 .. -5)</th>
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215 </tr>
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216 </thead>
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217 <tbody>
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218 <tr>
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219 <td>gene</td>
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220 <td>CPT-T1_001.gene</td>
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221 <td>40..576 [1]</td>
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222 <td>No RBS annotated, None found</td>
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223 <td><span style="font-family:monospace">taaatgttaa</span></td>
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224 </tr>
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225 <tr>
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226 <td>gene</td>
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227 <td>CPT-T1_002.gene</td>
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228 <td>589..2184 [1]</td>
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229 <td>Unannotated but valid RBS</td>
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230 <td><span style="font-family:monospace">taacttt AGG </span></td>
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231 </tr>
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232 <tr>
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233 <td>gene</td>
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234 <td>CPT-T1_003.gene</td>
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235 <td>2230..3522 [1]</td>
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236 <td>No RBS annotated, None found</td>
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237 <td><span style="font-family:monospace">acggcccttt</span></td>
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238 </tr>
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239 <tr>
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240 <td>gene</td>
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241 <td>CPT-T1_004.gene</td>
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242 <td>3496..4273 [1]</td>
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243 <td>Unannotated but valid RBS</td>
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244 <td><span style="font-family:monospace">cc GGAG ccgg</span></td>
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245 </tr>
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246 <tr>
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247 <td>gene</td>
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248 <td>CPT-T1_005.gene</td>
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249 <td>4264..5388 [1]</td>
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250 <td>No RBS annotated, None found</td>
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251 <td><span style="font-family:monospace">tccagacttt</span></td>
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252 </tr>
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253 <tr>
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254 <td>gene</td>
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255 <td>CPT-T1_006.gene</td>
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256 <td>5389..5876 [1]</td>
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257 <td>No RBS annotated, None found</td>
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258 <td><span style="font-family:monospace">agcaaagtaa</span></td>
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259 </tr>
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260 <tr>
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261 <td>gene</td>
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262 <td>CPT-T1_007.gene</td>
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263 <td>5926..6705 [1]</td>
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264 <td>No RBS annotated, None found</td>
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265 <td><span style="font-family:monospace">tagtcctttt</span></td>
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266 </tr>
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267 <tr>
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268 <td>gene</td>
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269 <td>CPT-T1_008.gene</td>
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270 <td>6784..7755 [1]</td>
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271 <td>No RBS annotated, None found</td>
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272 <td><span style="font-family:monospace">ttttttatta</span></td>
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273 </tr>
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274 <tr>
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275 <td>gene</td>
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276 <td>CPT-T1_009.gene</td>
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277 <td>7794..8093 [1]</td>
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278 <td>No RBS annotated, None found</td>
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279 <td><span style="font-family:monospace">gtcccttttt</span></td>
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280 </tr>
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281 <tr>
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282 <td>gene</td>
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283 <td>CPT-T1_010.gene</td>
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284 <td>8127..8548 [1]</td>
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285 <td>No RBS annotated, None found</td>
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286 <td><span style="font-family:monospace">agcgcctttt</span></td>
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287 </tr>
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288 <tr>
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289 <td>gene</td>
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290 <td>CPT-T1_011.gene</td>
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291 <td>8534..8919 [1]</td>
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292 <td>Unannotated but valid RBS</td>
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293 <td><span style="font-family:monospace">atgac AGGA c</span></td>
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294 </tr>
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295 <tr>
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296 <td>gene</td>
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297 <td>CPT-T1_012.gene</td>
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298 <td>8897..9355 [1]</td>
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299 <td>No RBS annotated, None found</td>
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300 <td><span style="font-family:monospace">atcgtccagt</span></td>
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301 </tr>
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302 <tr>
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303 <td>gene</td>
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304 <td>CPT-T1_013.gene</td>
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305 <td>9332..9743 [1]</td>
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306 <td>No RBS annotated, None found</td>
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307 <td><span style="font-family:monospace">gcaatcaagc</span></td>
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308 </tr>
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309 <tr>
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310 <td>gene</td>
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311 <td>CPT-T1_014.gene</td>
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312 <td>9733..10414 [1]</td>
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313 <td>Unannotated but valid RBS</td>
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314 <td><span style="font-family:monospace">tac GAG taga</span></td>
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315 </tr>
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316 <tr>
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317 <td>gene</td>
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318 <td>CPT-T1_015.gene</td>
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319 <td>10516..10845 [1]</td>
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320 <td>No RBS annotated, None found</td>
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321 <td><span style="font-family:monospace">tgctatcaac</span></td>
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322 </tr>
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323 <tr>
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324 <td>gene</td>
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325 <td>CPT-T1_016.gene</td>
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326 <td>10516..11162 [1]</td>
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327 <td>No RBS annotated, None found</td>
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328 <td><span style="font-family:monospace">tgctatcaac</span></td>
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329 </tr>
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330 <tr>
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331 <td>gene</td>
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332 <td>CPT-T1_017.gene</td>
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333 <td>11192..14076 [1]</td>
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334 <td>No RBS annotated, None found</td>
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335 <td><span style="font-family:monospace">gttttttcgt</span></td>
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336 </tr>
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337 <tr>
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338 <td>gene</td>
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339 <td>CPT-T1_018.gene</td>
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340 <td>14067..14432 [1]</td>
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341 <td>Unannotated but valid RBS</td>
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342 <td><span style="font-family:monospace">cattc AGGA a</span></td>
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343 </tr>
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344 <tr>
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345 <td>gene</td>
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346 <td>CPT-T1_019.gene</td>
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347 <td>14500..15294 [1]</td>
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348 <td>Unannotated but valid RBS</td>
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349 <td><span style="font-family:monospace">gttgc AGGT a</span></td>
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350 </tr>
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351 <tr>
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352 <td>gene</td>
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353 <td>CPT-T1_020.gene</td>
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354 <td>15279..16025 [1]</td>
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355 <td>No RBS annotated, None found</td>
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356 <td><span style="font-family:monospace">tgtcgcttca</span></td>
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357 </tr>
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358 <tr>
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359 <td>gene</td>
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360 <td>CPT-T1_021.gene</td>
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361 <td>16009..16621 [1]</td>
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362 <td>No RBS annotated, None found</td>
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363 <td><span style="font-family:monospace">taatcgttcg</span></td>
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364 </tr>
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365 <tr>
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366 <td>gene</td>
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367 <td>CPT-T1_022.gene</td>
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368 <td>16688..20217 [1]</td>
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369 <td>No RBS annotated, None found</td>
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370 <td><span style="font-family:monospace">ataaatagca</span></td>
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371 </tr>
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372 <tr>
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373 <td>gene</td>
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374 <td>CPT-T1_023.gene</td>
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375 <td>20251..20568 [1]</td>
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376 <td>No RBS annotated, None found</td>
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377 <td><span style="font-family:monospace">atgccctttt</span></td>
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378 </tr>
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379 <tr>
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380 <td>gene</td>
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381 <td>CPT-T1_024.gene</td>
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382 <td>20556..21257 [1]</td>
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383 <td>No RBS annotated, None found</td>
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384 <td><span style="font-family:monospace">cttaatagca</span></td>
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385 </tr>
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386 <tr>
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387 <td>gene</td>
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|
|
388 <td>CPT-T1_025.gene</td>
|
|
|
389 <td>21279..21518 [-1]</td>
|
|
|
390 <td>No RBS annotated, None found</td>
|
|
|
391 <td><span style="font-family:monospace">aatcacacta</span></td>
|
|
|
392 </tr>
|
|
|
393 <tr>
|
|
|
394 <td>gene</td>
|
|
|
395 <td>CPT-T1_026.gene</td>
|
|
|
396 <td>21755..21906 [1]</td>
|
|
|
397 <td>No RBS annotated, None found</td>
|
|
|
398 <td><span style="font-family:monospace">tgtatatcgt</span></td>
|
|
|
399 </tr>
|
|
|
400 <tr>
|
|
|
401 <td>gene</td>
|
|
|
402 <td>CPT-T1_027.gene</td>
|
|
|
403 <td>22020..23098 [1]</td>
|
|
|
404 <td>No RBS annotated, None found</td>
|
|
|
405 <td><span style="font-family:monospace">attcatcgta</span></td>
|
|
|
406 </tr>
|
|
|
407 <tr>
|
|
|
408 <td>gene</td>
|
|
|
409 <td>CPT-T1_028.gene</td>
|
|
|
410 <td>23129..23820 [1]</td>
|
|
|
411 <td>No RBS annotated, None found</td>
|
|
|
412 <td><span style="font-family:monospace">aaacaaataa</span></td>
|
|
|
413 </tr>
|
|
|
414 <tr>
|
|
|
415 <td>gene</td>
|
|
|
416 <td>CPT-T1_029.gene</td>
|
|
|
417 <td>23854..24289 [1]</td>
|
|
|
418 <td>No RBS annotated, None found</td>
|
|
|
419 <td><span style="font-family:monospace">tcgcccataa</span></td>
|
|
|
420 </tr>
|
|
|
421 <tr>
|
|
|
422 <td>gene</td>
|
|
|
423 <td>CPT-T1_030.gene</td>
|
|
|
424 <td>24351..26550 [-1]</td>
|
|
|
425 <td>No RBS annotated, None found</td>
|
|
|
426 <td><span style="font-family:monospace">cgtgctattt</span></td>
|
|
|
427 </tr>
|
|
|
428 <tr>
|
|
|
429 <td>gene</td>
|
|
|
430 <td>CPT-T1_031.gene</td>
|
|
|
431 <td>26447..26600 [-1]</td>
|
|
|
432 <td>No RBS annotated, None found</td>
|
|
|
433 <td><span style="font-family:monospace">tgcccattgc</span></td>
|
|
|
434 </tr>
|
|
|
435 <tr>
|
|
|
436 <td>gene</td>
|
|
|
437 <td>CPT-T1_032.gene</td>
|
|
|
438 <td>26638..27585 [-1]</td>
|
|
|
439 <td>No RBS annotated, None found</td>
|
|
|
440 <td><span style="font-family:monospace">cgcgtttttt</span></td>
|
|
|
441 </tr>
|
|
|
442 <tr>
|
|
|
443 <td>gene</td>
|
|
|
444 <td>CPT-T1_033.gene</td>
|
|
|
445 <td>27635..28098 [-1]</td>
|
|
|
446 <td>No RBS annotated, None found</td>
|
|
|
447 <td><span style="font-family:monospace">gcaaaaagtg</span></td>
|
|
|
448 </tr>
|
|
|
449 <tr>
|
|
|
450 <td>gene</td>
|
|
|
451 <td>CPT-T1_034.gene</td>
|
|
|
452 <td>28168..30199 [1]</td>
|
|
|
453 <td>No RBS annotated, None found</td>
|
|
|
454 <td><span style="font-family:monospace">gttacaacga</span></td>
|
|
|
455 </tr>
|
|
|
456 <tr>
|
|
|
457 <td>gene</td>
|
|
|
458 <td>CPT-T1_035.gene</td>
|
|
|
459 <td>30181..30612 [1]</td>
|
|
|
460 <td>No RBS annotated, None found</td>
|
|
|
461 <td><span style="font-family:monospace">caaagacttc</span></td>
|
|
|
462 </tr>
|
|
|
463 <tr>
|
|
|
464 <td>gene</td>
|
|
|
465 <td>CPT-T1_036.gene</td>
|
|
|
466 <td>30669..31393 [1]</td>
|
|
|
467 <td>No RBS annotated, None found</td>
|
|
|
468 <td><span style="font-family:monospace">atctcaccaa</span></td>
|
|
|
469 </tr>
|
|
|
470 <tr>
|
|
|
471 <td>gene</td>
|
|
|
472 <td>CPT-T1_037.gene</td>
|
|
|
473 <td>31377..31641 [1]</td>
|
|
|
474 <td>No RBS annotated, None found</td>
|
|
|
475 <td><span style="font-family:monospace">aaaacaaacg</span></td>
|
|
|
476 </tr>
|
|
|
477 <tr>
|
|
|
478 <td>gene</td>
|
|
|
479 <td>CPT-T1_038.gene</td>
|
|
|
480 <td>31695..31917 [1]</td>
|
|
|
481 <td>No RBS annotated, None found</td>
|
|
|
482 <td><span style="font-family:monospace">tcatagaaac</span></td>
|
|
|
483 </tr>
|
|
|
484 <tr>
|
|
|
485 <td>gene</td>
|
|
|
486 <td>CPT-T1_039.gene</td>
|
|
|
487 <td>31881..32167 [1]</td>
|
|
|
488 <td>No RBS annotated, None found</td>
|
|
|
489 <td><span style="font-family:monospace">cttcatctct</span></td>
|
|
|
490 </tr>
|
|
|
491 <tr>
|
|
|
492 <td>gene</td>
|
|
|
493 <td>CPT-T1_040.gene</td>
|
|
|
494 <td>32099..32399 [1]</td>
|
|
|
495 <td>Unannotated but valid RBS</td>
|
|
|
496 <td><span style="font-family:monospace"> GAG ttttacc</span></td>
|
|
|
497 </tr>
|
|
|
498 <tr>
|
|
|
499 <td>gene</td>
|
|
|
500 <td>CPT-T1_041.gene</td>
|
|
|
501 <td>32467..33611 [1]</td>
|
|
|
502 <td>No RBS annotated, None found</td>
|
|
|
503 <td><span style="font-family:monospace">tttcattatc</span></td>
|
|
|
504 </tr>
|
|
|
505 <tr>
|
|
|
506 <td>gene</td>
|
|
|
507 <td>CPT-T1_042.gene</td>
|
|
|
508 <td>33673..34166 [1]</td>
|
|
|
509 <td>No RBS annotated, None found</td>
|
|
|
510 <td><span style="font-family:monospace">ttttatagaa</span></td>
|
|
|
511 </tr>
|
|
|
512 <tr>
|
|
|
513 <td>gene</td>
|
|
|
514 <td>CPT-T1_043.gene</td>
|
|
|
515 <td>34226..34415 [1]</td>
|
|
|
516 <td>No RBS annotated, None found</td>
|
|
|
517 <td><span style="font-family:monospace">accacatcga</span></td>
|
|
|
518 </tr>
|
|
|
519 <tr>
|
|
|
520 <td>gene</td>
|
|
|
521 <td>CPT-T1_044.gene</td>
|
|
|
522 <td>34525..34749 [1]</td>
|
|
|
523 <td>No RBS annotated, None found</td>
|
|
|
524 <td><span style="font-family:monospace">gttcaaaaaa</span></td>
|
|
|
525 </tr>
|
|
|
526 <tr>
|
|
|
527 <td>gene</td>
|
|
|
528 <td>CPT-T1_045.gene</td>
|
|
|
529 <td>34739..35237 [1]</td>
|
|
|
530 <td>Unannotated but valid RBS</td>
|
|
|
531 <td><span style="font-family:monospace"> AGG cgcttaa</span></td>
|
|
|
532 </tr>
|
|
|
533 <tr>
|
|
|
534 <td>gene</td>
|
|
|
535 <td>CPT-T1_046.gene</td>
|
|
|
536 <td>35227..35638 [1]</td>
|
|
|
537 <td>No RBS annotated, None found</td>
|
|
|
538 <td><span style="font-family:monospace">acgcatattg</span></td>
|
|
|
539 </tr>
|
|
|
540 <tr>
|
|
|
541 <td>gene</td>
|
|
|
542 <td>CPT-T1_047.gene</td>
|
|
|
543 <td>35761..36179 [-1]</td>
|
|
|
544 <td>No RBS annotated, None found</td>
|
|
|
545 <td><span style="font-family:monospace">caatcctcga</span></td>
|
|
|
546 </tr>
|
|
|
547 <tr>
|
|
|
548 <td>gene</td>
|
|
|
549 <td>CPT-T1_048.gene</td>
|
|
|
550 <td>36173..37755 [-1]</td>
|
|
|
551 <td>No RBS annotated, None found</td>
|
|
|
552 <td><span style="font-family:monospace">tcacgccgtc</span></td>
|
|
|
553 </tr>
|
|
|
554 <tr>
|
|
|
555 <td>gene</td>
|
|
|
556 <td>CPT-T1_049.gene</td>
|
|
|
557 <td>37741..38294 [-1]</td>
|
|
|
558 <td>No RBS annotated, None found</td>
|
|
|
559 <td><span style="font-family:monospace">gacggcacaa</span></td>
|
|
|
560 </tr>
|
|
|
561 <tr>
|
|
|
562 <td>gene</td>
|
|
|
563 <td>CPT-T1_050.gene</td>
|
|
|
564 <td>38277..38706 [-1]</td>
|
|
|
565 <td>No RBS annotated, None found</td>
|
|
|
566 <td><span style="font-family:monospace">tcaagataac</span></td>
|
|
|
567 </tr>
|
|
|
568 <tr>
|
|
|
569 <td>gene</td>
|
|
|
570 <td>CPT-T1_051.gene</td>
|
|
|
571 <td>38774..38994 [-1]</td>
|
|
|
572 <td>No RBS annotated, None found</td>
|
|
|
573 <td><span style="font-family:monospace">tttacattaa</span></td>
|
|
|
574 </tr>
|
|
|
575 <tr>
|
|
|
576 <td>gene</td>
|
|
|
577 <td>CPT-T1_052.gene</td>
|
|
|
578 <td>38987..39222 [-1]</td>
|
|
|
579 <td>No RBS annotated, None found</td>
|
|
|
580 <td><span style="font-family:monospace">taccaaacaa</span></td>
|
|
|
581 </tr>
|
|
|
582 <tr>
|
|
|
583 <td>gene</td>
|
|
|
584 <td>CPT-T1_053.gene</td>
|
|
|
585 <td>39289..39444 [-1]</td>
|
|
|
586 <td>No RBS annotated, None found</td>
|
|
|
587 <td><span style="font-family:monospace">ggcatatcaa</span></td>
|
|
|
588 </tr>
|
|
|
589 <tr>
|
|
|
590 <td>gene</td>
|
|
|
591 <td>CPT-T1_054.gene</td>
|
|
|
592 <td>39429..39758 [-1]</td>
|
|
|
593 <td>No RBS annotated, None found</td>
|
|
|
594 <td><span style="font-family:monospace">tatcctgact</span></td>
|
|
|
595 </tr>
|
|
|
596 <tr>
|
|
|
597 <td>gene</td>
|
|
|
598 <td>CPT-T1_055.gene</td>
|
|
|
599 <td>39766..39978 [-1]</td>
|
|
|
600 <td>Unannotated but valid RBS</td>
|
|
|
601 <td><span style="font-family:monospace">tagc GGA tcg</span></td>
|
|
|
602 </tr>
|
|
|
603 <tr>
|
|
|
604 <td>gene</td>
|
|
|
605 <td>CPT-T1_056.gene</td>
|
|
|
606 <td>39959..40342 [-1]</td>
|
|
|
607 <td>No RBS annotated, None found</td>
|
|
|
608 <td><span style="font-family:monospace">acatcaacag</span></td>
|
|
|
609 </tr>
|
|
|
610 <tr>
|
|
|
611 <td>gene</td>
|
|
|
612 <td>CPT-T1_057.gene</td>
|
|
|
613 <td>41020..41606 [1]</td>
|
|
|
614 <td>No RBS annotated, None found</td>
|
|
|
615 <td><span style="font-family:monospace">tgtatattga</span></td>
|
|
|
616 </tr>
|
|
|
617 <tr>
|
|
|
618 <td>gene</td>
|
|
|
619 <td>CPT-T1_058.gene</td>
|
|
|
620 <td>41606..41945 [1]</td>
|
|
|
621 <td>Unannotated but valid RBS</td>
|
|
|
622 <td><span style="font-family:monospace">aaaatgt GGA </span></td>
|
|
|
623 </tr>
|
|
|
624 <tr>
|
|
|
625 <td>gene</td>
|
|
|
626 <td>CPT-T1_059.gene</td>
|
|
|
627 <td>42013..42254 [1]</td>
|
|
|
628 <td>Unannotated but valid RBS</td>
|
|
|
629 <td><span style="font-family:monospace">ac GAG atacc</span></td>
|
|
|
630 </tr>
|
|
|
631 <tr>
|
|
|
632 <td>gene</td>
|
|
|
633 <td>CPT-T1_060.gene</td>
|
|
|
634 <td>42247..42487 [1]</td>
|
|
|
635 <td>No RBS annotated, None found</td>
|
|
|
636 <td><span style="font-family:monospace">tcagcacttt</span></td>
|
|
|
637 </tr>
|
|
|
638 <tr>
|
|
|
639 <td>gene</td>
|
|
|
640 <td>CPT-T1_061.gene</td>
|
|
|
641 <td>42473..42594 [1]</td>
|
|
|
642 <td>No RBS annotated, None found</td>
|
|
|
643 <td><span style="font-family:monospace">ggcgacaaca</span></td>
|
|
|
644 </tr>
|
|
|
645 <tr>
|
|
|
646 <td>gene</td>
|
|
|
647 <td>CPT-T1_062.gene</td>
|
|
|
648 <td>42580..42764 [1]</td>
|
|
|
649 <td>No RBS annotated, None found</td>
|
|
|
650 <td><span style="font-family:monospace">ttgctactgt</span></td>
|
|
|
651 </tr>
|
|
|
652 <tr>
|
|
|
653 <td>gene</td>
|
|
|
654 <td>CPT-T1_063.gene</td>
|
|
|
655 <td>42824..43324 [1]</td>
|
|
|
656 <td>No RBS annotated, None found</td>
|
|
|
657 <td><span style="font-family:monospace">ccatcgacaa</span></td>
|
|
|
658 </tr>
|
|
|
659 <tr>
|
|
|
660 <td>gene</td>
|
|
|
661 <td>CPT-T1_064.gene</td>
|
|
|
662 <td>43385..43881 [1]</td>
|
|
|
663 <td>No RBS annotated, None found</td>
|
|
|
664 <td><span style="font-family:monospace">acatcaacca</span></td>
|
|
|
665 </tr>
|
|
|
666 <tr>
|
|
|
667 <td>gene</td>
|
|
|
668 <td>CPT-T1_065.gene</td>
|
|
|
669 <td>43870..44030 [1]</td>
|
|
|
670 <td>No RBS annotated, None found</td>
|
|
|
671 <td><span style="font-family:monospace">actcttgtcc</span></td>
|
|
|
672 </tr>
|
|
|
673 <tr>
|
|
|
674 <td>gene</td>
|
|
|
675 <td>CPT-T1_066.gene</td>
|
|
|
676 <td>44098..44485 [1]</td>
|
|
|
677 <td>No RBS annotated, None found</td>
|
|
|
678 <td><span style="font-family:monospace">gcacgacaac</span></td>
|
|
|
679 </tr>
|
|
|
680 <tr>
|
|
|
681 <td>gene</td>
|
|
|
682 <td>CPT-T1_067.gene</td>
|
|
|
683 <td>44527..44649 [1]</td>
|
|
|
684 <td>No RBS annotated, None found</td>
|
|
|
685 <td><span style="font-family:monospace">gttccccttt</span></td>
|
|
|
686 </tr>
|
|
|
687 <tr>
|
|
|
688 <td>gene</td>
|
|
|
689 <td>CPT-T1_068.gene</td>
|
|
|
690 <td>44625..44852 [1]</td>
|
|
|
691 <td>No RBS annotated, None found</td>
|
|
|
692 <td><span style="font-family:monospace">gacattatct</span></td>
|
|
|
693 </tr>
|
|
|
694 <tr>
|
|
|
695 <td>gene</td>
|
|
|
696 <td>CPT-T1_069.gene</td>
|
|
|
697 <td>44898..45356 [1]</td>
|
|
|
698 <td>No RBS annotated, None found</td>
|
|
|
699 <td><span style="font-family:monospace">cctacaccaa</span></td>
|
|
|
700 </tr>
|
|
|
701 <tr>
|
|
|
702 <td>gene</td>
|
|
|
703 <td>CPT-T1_070.gene</td>
|
|
|
704 <td>45428..45970 [1]</td>
|
|
|
705 <td>No RBS annotated, None found</td>
|
|
|
706 <td><span style="font-family:monospace">ttaagcaacc</span></td>
|
|
|
707 </tr>
|
|
|
708 <tr>
|
|
|
709 <td>gene</td>
|
|
|
710 <td>CPT-T1_071.gene</td>
|
|
|
711 <td>45941..46451 [1]</td>
|
|
|
712 <td>No RBS annotated, None found</td>
|
|
|
713 <td><span style="font-family:monospace">gcctgtgata</span></td>
|
|
|
714 </tr>
|
|
|
715 <tr>
|
|
|
716 <td>gene</td>
|
|
|
717 <td>CPT-T1_072.gene</td>
|
|
|
718 <td>46444..47026 [1]</td>
|
|
|
719 <td>No RBS annotated, None found</td>
|
|
|
720 <td><span style="font-family:monospace">tcacaaaaag</span></td>
|
|
|
721 </tr>
|
|
|
722 <tr>
|
|
|
723 <td>gene</td>
|
|
|
724 <td>CPT-T1_073.gene</td>
|
|
|
725 <td>47085..47308 [1]</td>
|
|
|
726 <td>No RBS annotated, None found</td>
|
|
|
727 <td><span style="font-family:monospace">ctcatcgaca</span></td>
|
|
|
728 </tr>
|
|
|
729 <tr>
|
|
|
730 <td>gene</td>
|
|
|
731 <td>CPT-T1_074.gene</td>
|
|
|
732 <td>47293..47649 [1]</td>
|
|
|
733 <td>No RBS annotated, None found</td>
|
|
|
734 <td><span style="font-family:monospace">cccgatcgaa</span></td>
|
|
|
735 </tr>
|
|
|
736 <tr>
|
|
|
737 <td>gene</td>
|
|
|
738 <td>CPT-T1_075.gene</td>
|
|
|
739 <td>47637..47879 [1]</td>
|
|
|
740 <td>No RBS annotated, None found</td>
|
|
|
741 <td><span style="font-family:monospace">aagtttttca</span></td>
|
|
|
742 </tr>
|
|
|
743 <tr>
|
|
|
744 <td>gene</td>
|
|
|
745 <td>CPT-T1_076.gene</td>
|
|
|
746 <td>47864..48082 [1]</td>
|
|
|
747 <td>Unannotated but valid RBS</td>
|
|
|
748 <td><span style="font-family:monospace">cgt AGGT aac</span></td>
|
|
|
749 </tr>
|
|
|
750 <tr>
|
|
|
751 <td>gene</td>
|
|
|
752 <td>CPT-T1_077.gene</td>
|
|
|
753 <td>48235..48408 [1]</td>
|
|
|
754 <td>No RBS annotated, None found</td>
|
|
|
755 <td><span style="font-family:monospace">gcggcaacaa</span></td>
|
|
|
756 </tr>
|
|
|
757 <tr>
|
|
|
758 <td>gene</td>
|
|
|
759 <td>CPT-T1_078.gene</td>
|
|
|
760 <td>48377..48574 [1]</td>
|
|
|
761 <td>No RBS annotated, None found</td>
|
|
|
762 <td><span style="font-family:monospace">ctggcgttat</span></td>
|
|
|
763 </tr>
|
|
|
764 <tr>
|
|
|
765 <td>gene</td>
|
|
|
766 <td>CPT-T1_079.gene</td>
|
|
|
767 <td>48564..48803 [1]</td>
|
|
|
768 <td>No RBS annotated, None found</td>
|
|
|
769 <td><span style="font-family:monospace">atattgaatt</span></td>
|
|
|
770 </tr>
|
|
|
771 </tbody>
|
|
|
772 </table>
|
|
|
773 </div>
|
|
|
774
|
|
|
775 <h3 id="weird_starts">Start Codon Usage</h3>
|
|
|
776 <p>This section covers genes with unusual start codons</p>
|
|
|
777 <div class="table-responsive">
|
|
|
778 <table class="table table-striped">
|
|
|
779 <thead>
|
|
|
780 <tr>
|
|
|
781 <th>Start Codon</th>
|
|
|
782 <th>Count</th>
|
|
|
783 </tr>
|
|
|
784 </thead>
|
|
|
785 <tbody>
|
|
|
786 <tr><td>ATG</td><td>74</td></tr>
|
|
|
787 <tr><td>GTG</td><td>3</td></tr>
|
|
|
788 <tr><td>TTG</td><td>2</td></tr>
|
|
|
789 </tbody>
|
|
|
790 </table>
|
|
|
791 </div>
|
|
|
792
|
|
|
793 <div class="table-responsive">
|
|
|
794 <table class="table table-striped">
|
|
|
795 <thead>
|
|
|
796 <tr>
|
|
|
797 <th>Feature Type</th>
|
|
|
798 <th>ID</th>
|
|
|
799 <th>Location</th>
|
|
|
800 <th>Error</th>
|
|
|
801 </tr>
|
|
|
802 </thead>
|
|
|
803 <tbody>
|
|
|
804 </tbody>
|
|
|
805 </table>
|
|
|
806 </div>
|
|
|
807
|
|
|
808 <h3 id="excessive_gaps">Intergenic Gaps</h3>
|
|
|
809 <p>Phage genomes are under pressure to maintain high coding density. Large intergenic gaps may be a sign of incorrect gene starts or missing genes.</p>
|
|
|
810 <div class="table-responsive">
|
|
|
811 <table class="table table-striped">
|
|
|
812 <thead>
|
|
|
813 <tr>
|
|
|
814 <th>Region</th>
|
|
|
815 <th>Size</th>
|
|
|
816 <th>Bounding Gene Transcription Direction</th>
|
|
|
817 <th>Message</th>
|
|
|
818 </tr>
|
|
|
819 </thead>
|
|
|
820 <tbody>
|
|
|
821 <tr>
|
|
|
822 <td>2184 .. 2238</td>
|
|
|
823 <td>54</td>
|
|
|
824 <td>→ →</td>
|
|
|
825 <td>
|
|
|
826 </td>
|
|
|
827 </tr>
|
|
|
828 <tr>
|
|
|
829 <td>5876 .. 5937</td>
|
|
|
830 <td>61</td>
|
|
|
831 <td>→ →</td>
|
|
|
832 <td>
|
|
|
833 </td>
|
|
|
834 </tr>
|
|
|
835 <tr>
|
|
|
836 <td>6705 .. 6795</td>
|
|
|
837 <td>90</td>
|
|
|
838 <td>→ →</td>
|
|
|
839 <td>
|
|
|
840 </td>
|
|
|
841 </tr>
|
|
|
842 <tr>
|
|
|
843 <td>10414 .. 10527</td>
|
|
|
844 <td>113</td>
|
|
|
845 <td>→ →</td>
|
|
|
846 <td>
|
|
|
847 </td>
|
|
|
848 </tr>
|
|
|
849 <tr>
|
|
|
850 <td>14432 .. 14511</td>
|
|
|
851 <td>79</td>
|
|
|
852 <td>→ →</td>
|
|
|
853 <td>
|
|
|
854 2 ORFs found in this region
|
|
|
855 </td>
|
|
|
856 </tr>
|
|
|
857 <tr>
|
|
|
858 <td>16621 .. 16698</td>
|
|
|
859 <td>77</td>
|
|
|
860 <td>→ →</td>
|
|
|
861 <td>
|
|
|
862 </td>
|
|
|
863 </tr>
|
|
|
864 <tr>
|
|
|
865 <td>21506 .. 21765</td>
|
|
|
866 <td>259</td>
|
|
|
867 <td>→ →</td>
|
|
|
868 <td>
|
|
|
869 </td>
|
|
|
870 </tr>
|
|
|
871 <tr>
|
|
|
872 <td>21906 .. 22033</td>
|
|
|
873 <td>127</td>
|
|
|
874 <td>→ →</td>
|
|
|
875 <td>
|
|
|
876 </td>
|
|
|
877 </tr>
|
|
|
878 <tr>
|
|
|
879 <td>24289 .. 24350</td>
|
|
|
880 <td>61</td>
|
|
|
881 <td>→ →</td>
|
|
|
882 <td>
|
|
|
883 1 ORFs found in this region
|
|
|
884 </td>
|
|
|
885 </tr>
|
|
|
886 <tr>
|
|
|
887 <td>27573 .. 27634</td>
|
|
|
888 <td>61</td>
|
|
|
889 <td>→ →</td>
|
|
|
890 <td>
|
|
|
891 </td>
|
|
|
892 </tr>
|
|
|
893 <tr>
|
|
|
894 <td>28087 .. 28180</td>
|
|
|
895 <td>93</td>
|
|
|
896 <td>→ →</td>
|
|
|
897 <td>
|
|
|
898 </td>
|
|
|
899 </tr>
|
|
|
900 <tr>
|
|
|
901 <td>30612 .. 30679</td>
|
|
|
902 <td>67</td>
|
|
|
903 <td>→ →</td>
|
|
|
904 <td>
|
|
|
905 1 ORFs found in this region
|
|
|
906 </td>
|
|
|
907 </tr>
|
|
|
908 <tr>
|
|
|
909 <td>31641 .. 31707</td>
|
|
|
910 <td>66</td>
|
|
|
911 <td>→ →</td>
|
|
|
912 <td>
|
|
|
913 </td>
|
|
|
914 </tr>
|
|
|
915 <tr>
|
|
|
916 <td>32399 .. 32477</td>
|
|
|
917 <td>78</td>
|
|
|
918 <td>→ →</td>
|
|
|
919 <td>
|
|
|
920 1 ORFs found in this region
|
|
|
921 </td>
|
|
|
922 </tr>
|
|
|
923 <tr>
|
|
|
924 <td>33611 .. 33683</td>
|
|
|
925 <td>72</td>
|
|
|
926 <td>→ →</td>
|
|
|
927 <td>
|
|
|
928 </td>
|
|
|
929 </tr>
|
|
|
930 <tr>
|
|
|
931 <td>34166 .. 34238</td>
|
|
|
932 <td>72</td>
|
|
|
933 <td>→ →</td>
|
|
|
934 <td>
|
|
|
935 </td>
|
|
|
936 </tr>
|
|
|
937 <tr>
|
|
|
938 <td>34415 .. 34533</td>
|
|
|
939 <td>118</td>
|
|
|
940 <td>→ →</td>
|
|
|
941 <td>
|
|
|
942 </td>
|
|
|
943 </tr>
|
|
|
944 <tr>
|
|
|
945 <td>35638 .. 35760</td>
|
|
|
946 <td>122</td>
|
|
|
947 <td>→ →</td>
|
|
|
948 <td>
|
|
|
949 2 ORFs found in this region
|
|
|
950 </td>
|
|
|
951 </tr>
|
|
|
952 <tr>
|
|
|
953 <td>38693 .. 38773</td>
|
|
|
954 <td>80</td>
|
|
|
955 <td>→ →</td>
|
|
|
956 <td>
|
|
|
957 2 ORFs found in this region
|
|
|
958 </td>
|
|
|
959 </tr>
|
|
|
960 <tr>
|
|
|
961 <td>39211 .. 39288</td>
|
|
|
962 <td>77</td>
|
|
|
963 <td>→ →</td>
|
|
|
964 <td>
|
|
|
965 </td>
|
|
|
966 </tr>
|
|
|
967 <tr>
|
|
|
968 <td>40330 .. 41030</td>
|
|
|
969 <td>700</td>
|
|
|
970 <td>→ →</td>
|
|
|
971 <td>
|
|
|
972 7 ORFs found in this region
|
|
|
973 </td>
|
|
|
974 </tr>
|
|
|
975 <tr>
|
|
|
976 <td>41945 .. 42023</td>
|
|
|
977 <td>78</td>
|
|
|
978 <td>→ →</td>
|
|
|
979 <td>
|
|
|
980 </td>
|
|
|
981 </tr>
|
|
|
982 <tr>
|
|
|
983 <td>42764 .. 42835</td>
|
|
|
984 <td>71</td>
|
|
|
985 <td>→ →</td>
|
|
|
986 <td>
|
|
|
987 </td>
|
|
|
988 </tr>
|
|
|
989 <tr>
|
|
|
990 <td>43324 .. 43395</td>
|
|
|
991 <td>71</td>
|
|
|
992 <td>→ →</td>
|
|
|
993 <td>
|
|
|
994 </td>
|
|
|
995 </tr>
|
|
|
996 <tr>
|
|
|
997 <td>44030 .. 44110</td>
|
|
|
998 <td>80</td>
|
|
|
999 <td>→ →</td>
|
|
|
1000 <td>
|
|
|
1001 </td>
|
|
|
1002 </tr>
|
|
|
1003 <tr>
|
|
|
1004 <td>44485 .. 44538</td>
|
|
|
1005 <td>53</td>
|
|
|
1006 <td>→ →</td>
|
|
|
1007 <td>
|
|
|
1008 </td>
|
|
|
1009 </tr>
|
|
|
1010 <tr>
|
|
|
1011 <td>44852 .. 44909</td>
|
|
|
1012 <td>57</td>
|
|
|
1013 <td>→ →</td>
|
|
|
1014 <td>
|
|
|
1015 </td>
|
|
|
1016 </tr>
|
|
|
1017 <tr>
|
|
|
1018 <td>45356 .. 45439</td>
|
|
|
1019 <td>83</td>
|
|
|
1020 <td>→ →</td>
|
|
|
1021 <td>
|
|
|
1022 6 ORFs found in this region
|
|
|
1023 </td>
|
|
|
1024 </tr>
|
|
|
1025 <tr>
|
|
|
1026 <td>47026 .. 47098</td>
|
|
|
1027 <td>72</td>
|
|
|
1028 <td>→ →</td>
|
|
|
1029 <td>
|
|
|
1030 </td>
|
|
|
1031 </tr>
|
|
|
1032 <tr>
|
|
|
1033 <td>48082 .. 48246</td>
|
|
|
1034 <td>164</td>
|
|
|
1035 <td>→ →</td>
|
|
|
1036 <td>
|
|
|
1037 2 ORFs found in this region
|
|
|
1038 </td>
|
|
|
1039 </tr>
|
|
|
1040 </tbody>
|
|
|
1041 </table>
|
|
|
1042 </div>
|
|
|
1043
|
|
|
1044 <h3 id="excessive_overlap">Overlapping Genes </h3>
|
|
|
1045 <p>Large gene overlaps may indicate an incorrect gene start or miscalled gene.</p>
|
|
|
1046 <div class="table-responsive">
|
|
|
1047 <table class="table table-striped">
|
|
|
1048 <thead>
|
|
|
1049 <tr>
|
|
|
1050 <th>Feature A</th>
|
|
|
1051 <th>Feature B</th>
|
|
|
1052 <th>Shared Region</th>
|
|
|
1053 <th>Overlap Length</th>
|
|
|
1054 </tr>
|
|
|
1055 </thead>
|
|
|
1056 <tbody>
|
|
|
1057 <tr>
|
|
|
1058 <td>CPT-T1_015.gene ([10516:10845](+))</td>
|
|
|
1059 <td>CPT-T1_016.gene ([10516:11162](+))</td>
|
|
|
1060 <td>10527..10844</td>
|
|
|
1061 <td>317 bp</td>
|
|
|
1062 </tr>
|
|
|
1063 <tr>
|
|
|
1064 <td>CPT-T1_030.gene ([24351:26550](-))</td>
|
|
|
1065 <td>CPT-T1_031.gene ([26447:26600](-))</td>
|
|
|
1066 <td>26446..26536</td>
|
|
|
1067 <td>90 bp</td>
|
|
|
1068 </tr>
|
|
|
1069 <tr>
|
|
|
1070 <td>CPT-T1_039.gene ([31881:32167](+))</td>
|
|
|
1071 <td>CPT-T1_040.gene ([32099:32399](+))</td>
|
|
|
1072 <td>32111..32166</td>
|
|
|
1073 <td>55 bp</td>
|
|
|
1074 </tr>
|
|
|
1075 </tbody>
|
|
|
1076 </table>
|
|
|
1077 </div>
|
|
|
1078 <!--<h3 id="coding_density">Coding Density Issues <small>99 / 100</small></h3>
|
|
|
1079 <div class="table-responsive">
|
|
|
1080 <p>
|
|
|
1081 You have a coding density of 93 which scores
|
|
|
1082 99 / 100. Most genomes should be in the 90% to
|
|
|
1083 100% coding density range
|
|
|
1084 </p>
|
|
|
1085 </div>-->
|
|
|
1086
|
|
|
1087 <h2 class="sub-header" id="antisense">Antisense Genes</h2>
|
|
|
1088 <h3 id="morons">Possible Morons <small>78 / 79 (Doesn't count towards score)</small></h3>
|
|
|
1089 <div class="table-responsive">
|
|
|
1090 <table class="table table-striped">
|
|
|
1091 <thead>
|
|
|
1092 <tr>
|
|
|
1093 <th>Feature</th>
|
|
|
1094 <th>RBS</th>
|
|
|
1095 <th>Surrounding Features</th>
|
|
|
1096 </tr>
|
|
|
1097 </thead>
|
|
|
1098 <tbody>
|
|
|
1099 <tr>
|
|
|
1100 <td>CPT-T1_025.gene</td>
|
|
|
1101 <td>No RBS Available</td>
|
|
|
1102 <td class="moron">
|
|
|
1103 →
|
|
|
1104 →
|
|
|
1105 <span class="strand_emph">←</span>
|
|
|
1106 →
|
|
|
1107 →
|
|
|
1108 </div>
|
|
|
1109 </td>
|
|
|
1110 </tr>
|
|
|
1111 </tbody>
|
|
|
1112 </table>
|
|
|
1113 </div>
|
|
|
1114
|
|
|
1115
|
|
|
1116 <h2 class="sub-header" id="annotations">Annotation Issues</h2>
|
|
|
1117 <h3 id="missing_product">Missing Product Tags <small>79 / 79</small></h3>
|
|
|
1118 <div class="table-responsive">
|
|
|
1119 <table class="table table-striped">
|
|
|
1120 <thead>
|
|
|
1121 <tr>
|
|
|
1122 <th>Feature</th>
|
|
|
1123 <th>Qualifiers</th>
|
|
|
1124 </tr>
|
|
|
1125 </thead>
|
|
|
1126 <tbody>
|
|
|
1127 </tbody>
|
|
|
1128 </table>
|
|
|
1129 </div>
|
|
|
1130
|
|
|
1131
|
|
|
1132
|
|
|
1133
|
|
|
1134
|
|
|
1135 </div>
|
|
|
1136 </div>
|
|
|
1137 </div>
|
|
|
1138
|
|
|
1139
|
|
|
1140 <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
|
|
|
1141 </body>
|
|
|
1142 </html>
|
