Mercurial > repos > jankanis > blast2html

annotate blast_html.html.jinja @ 17:8e61627a87f1

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make html more semantic
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 13 May 2014 12:54:03 +0200
parents db7e4ee3be03
children 67ddcb807b7d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <!DOCTYPE html>
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2 <html>
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3 <head>
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4 <meta charset="UTF-8">
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6 <title>Blast output</title>
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7
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8 <style>
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9 body {
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10 color: #333333;
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11 font-family: Arial,Sans-Serif;
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12 }
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13
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14 :link {
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15 color: #336699;
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16 }
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17
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18 .right {
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19 float: right;
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20 }
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21
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22 #content {
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23 margin: 0 2em;
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24 padding: 0.5em;
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25 border: 1px solid #888888;
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26 background-color: #d3dff5;
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27 }
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28
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29 h1, h2, h3, h4, h5, h6 {
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30 color: #2A6979;
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31 font-family: arial,verdana,sans-serif;
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32 letter-spacing: -1px;
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33 margin: 1.2em 0 0.3em;
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34 }
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36 h1 {
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37 border-bottom: 1px solid #CCCCCC;
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38 font-size: 150%;
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39 padding-bottom: 0.1em;
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40 }
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41
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42 h2 {
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43 font-size: 120%;
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44 font-weight: bold;
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45 }
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46
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47 h4.darkHeader {
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48 color: #4D4D4D;
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49 letter-spacing: 0;
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50 font-weight: bold;
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51 }
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52
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53 #nodata {
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54 font-weight: bold;
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55 }
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56
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57 .headerdata {
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58 font-size: 90%;
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59 }
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60 .headerdata .param {
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61 font-weight: bold;
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62 text-align: right;
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63 padding: 0 1em;
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64 }
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65
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66 .grey {
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67 background-color: #eeeeee;
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68 border: 1px solid #cccccc;
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69 padding: 1em;
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70 }
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71
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72 .white {
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73 background-color: white;
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74 border: 1px solid #cccccc;
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75 padding: 1.5em 2%;
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76 }
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77
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78 .graphicrow {
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79 clear: left;
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80 width: 100%;
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81 }
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82
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83 .graphicitem {
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84 float: left;
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85 }
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86
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88
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89 .graphics .grey {
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90 text-align: center;
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91 }
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92
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93 .graphic {
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94 background-color: white;
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95 border: 2px solid black;
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96 padding: .5em 1.5em;
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97 margin: auto;
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98 }
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99
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100 .centered, #defline, div.legend, div.tablewrapper {
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101 margin-left: auto;
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102 margin-right: auto;
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103 }
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104
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105 #defline {
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106 background-color: white;
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107 border: 1px solid black;
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108 margin: .5em auto;
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109 padding-left: .2em;
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110 padding-right: .2em;
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111 max-width: 50em;
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112 text-align: left;
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113 height: 2.8em;
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114 overflow-y: hidden;
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115 }
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116
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117 div.legend {
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118 max-width: 40em;
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119 }
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120 div.legend div {
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121 width: 100%;
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122 color: white;
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123 font-weight: bold;
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124 border-spacing: 0;
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125 }
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126 div.legend div .graphicitem {
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127 width: 20%;
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128 padding: 0;
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129 margin: 0;
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130 border: none;
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131 }
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132
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133 div.tablewrapper {
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134 width: 50%;
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135 min-width: 60em;
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136 }
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137
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138 /* For small widths we give the graphic 100% */
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139 @media (max-width: 72.5em) {
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140 div.tablewrapper {
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141 width: 100%;
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142 min-width: 0px;
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143 }
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144 }
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145
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146 .scale {
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147 width: 100%;
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148 margin: .5em 0;
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149 font-weight: bold;
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150 }
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151 .scale div {
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152 color: red;
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153 text-align: left;
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154 }
8
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155 .scale .graphicrow {
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parents: 7
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156 margin: .5em 0 .5em 0;
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157 color: white;
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158 }
8
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159 .scale .graphicitem div {
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160 margin: 0 1px;
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diff changeset
161 padding: 0 2px;
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162 text-align: right;
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163 background-color: red;
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164 color: white;
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165 }
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166 .scale .graphicitem:first-child div {
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167 margin-left: 0px;
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168 }
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169 .scale .graphicitem:last-child div {
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170 margin-right: 0px;
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171 }
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parents: 7
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172
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173 a.matchresult {
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diff changeset
174 display: block;
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diff changeset
175 margin: 0;
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parents: 7
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176 padding: 0;
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177 }
8
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178 div.matchrow {
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179 margin-top: 4px;
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180 }
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181 div.matchrow, div.matchitem {
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182 height: 4px;
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183 }
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184
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185
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186 table.descriptiontable {
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187 font-size: 85%;
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188 border: 1px solid #97b0c8;
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diff changeset
189 border-spacing: 0;
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190 color: #222222;
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191 line-height: 1.3em;
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diff changeset
192 background-color: white;
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193 }
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194 table.descriptiontable col:first-child {
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195 width: 100%;
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parents:
diff changeset
196 }
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197 table.descriptiontable tr:hover {
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198 background-color: #D5DEE3;
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diff changeset
199 }
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200 table.descriptiontable th {
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201 color: #14376C;
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diff changeset
202 font-weight: normal;
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diff changeset
203 background-color: #F0F0F0;
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diff changeset
204 background: linear-gradient(#FFFFFF, #F0F0F0);
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205 border-bottom: 1px solid #D4DFE9;
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diff changeset
206 border-right: 1px solid #CFCFCF;
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diff changeset
207 border-left: 0px solid black;
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diff changeset
208 border-top: 0px solid black;
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diff changeset
209 }
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diff changeset
210 table.descriptiontable td {
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diff changeset
211 overflow: hidden;
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212 text-align: center;
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213 padding: .4em .8em;
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214 }
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215 table.descriptiontable td div {
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216 width: 1em;
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217 overflow: visible;
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218 white-space: nowrap;
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219 text-align: left;
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220 }
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221
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222
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diff changeset
223
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224 .alignments .white {
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225 padding: 1.5em 1em;
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226 }
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227
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228 .alignment {
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229 border-top: 1px solid black;
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230 padding-left: 1em;
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231 padding-right: 1em;
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diff changeset
232 }
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233
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234 div.linkheader {
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diff changeset
235 padding-top: .2em;
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236 font-size: 85%;
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diff changeset
237 color: #14376C;
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diff changeset
238 }
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239 div.linkheader a.linkheader {
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240 margin-right: 1em;
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diff changeset
241 }
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diff changeset
242 div.linkheader .right a {
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diff changeset
243 text-decoration: none;
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diff changeset
244 }
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245
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diff changeset
246 .title .hittitle {
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247 color: #222222;
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248 margin-bottom: .3em;
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diff changeset
249 }
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diff changeset
250 .title .titleinfo {
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251 font-size: 80%;
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diff changeset
252 margin-top: 0;
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253 margin-bottom: .3em;
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diff changeset
254 }
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diff changeset
255 .title .titleinfo .b {
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diff changeset
256 color: #606060;
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257 font-weight: bold;
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258 font-size: 90%;
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259 }
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260
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261 .moretitles {
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262 margin: 1.2em;
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263 }
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diff changeset
264 .moretitles .titleinfo {
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diff changeset
265 margin: 0;
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266 padding: 0;
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267 }
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268 .moretitles .hittitle {
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269 margin: .4em 0 .2em 0;
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270 padding: 0;
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diff changeset
271 }
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272
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273 a.showmoretitles {
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274 font-size: 75%;
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275 color: #336699;
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276 font-weight: bold;
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277 margin-top: 0;
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diff changeset
278 }
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279 a.showmoretitles:hover {
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280 }
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281
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282 .hotspot {
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283 color: #606060;
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diff changeset
284 font-family: verdana, arial, sans-serif;
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diff changeset
285 margin-bottom: 2.5em;
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parents: 10
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286 }
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287
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288 .hotspot p.range {
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289 font-size: 70%;
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diff changeset
290 margin-top: 0;
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diff changeset
291 margin-top: 1em;
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diff changeset
292 margin-bottom: .2em;
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diff changeset
293 }
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diff changeset
294 .hotspot p.range span.range {
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295 font-weight: bold;
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parents: 11
diff changeset
296 }
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297 .hotspot p.range a.range {
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298 margin-left: .5em;
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diff changeset
299 }
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300
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diff changeset
301 table.hotspotstable {
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302 border-top: 1px solid;
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diff changeset
303 border-bottom: 1px solid;
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diff changeset
304 text-align: left;
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305 border-collapse: collapse;
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306 }
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307 table.hotspotstable th, table.hotspotstable td {
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308 padding: .1em 1em;
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309 }
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310 table.hotspotstable th {
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311 font-size: 70%;
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312 }
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313 table.hotspotstable td {
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314 min-width: 7em;
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315 color: #222222;
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316 font-size: 80%;
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317 }
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318
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319 pre.alignmentgraphic {
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320 color: #222222;
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321 }
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322
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323
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324 </style>
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325
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326 <script type="text/javascript">
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327 function toggle_visibility(id) {
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328 var e = document.getElementById(id);
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329 if(e.style.display != 'block')
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330 e.style.display = 'block';
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331 else
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332 e.style.display = 'none';
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333 }
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334 </script>
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335
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336 </head>
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337
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338
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339 <body>
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340 <div id=content>
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341 <h1>Nucleotide Sequence ({{length}} letters)</h1>
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342
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343 <section class=header>
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344
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345 <table class=headerdata>
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346 {% for param, value in params %}
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347 <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
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348 {% endfor %}
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349 </table>
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350
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351 </section>
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352
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353 {% if not (blast.BlastOutput_iterations.findall('Iteration') and
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354 blast.BlastOutput_iterations.Iteration.Iteration_hits.findall('Hit')) %}
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355 <section class=nodata>
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356 <h2>No Results</h2>
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357 <div class=grey>
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358 No Matches
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359 </div>
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360 </section>
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361 {% else %}
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362
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363
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364
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365 <section class=graphics>
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366 <h2>Graphic Summary</h2>
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367
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368 <div class=grey>
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369 <h3 class=centered>Distribution of {{hits|length}} Blast Hits on the Query Sequence</h3>
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370
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371 <div id=defline>Mouse-over to show defline and scores, click to show alignments</div>
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372
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373 <div class=graphic>
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374 <h4 class=darkHeader>Color key for alignment scores</h4>
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375 <div class=legend><div class=graphicrow>
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376 <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
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377 <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
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378 <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
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379 <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
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380 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
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381 </div></div>
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382 <div style="clear: left"></div>
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383
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384 <div class=tablewrapper>
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385
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386 <div class=scale>
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387 <div>query:</div>
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388 <div class=graphicrow>
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389 {% for s in queryscale %}
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390 <div class=graphicitem style="width: {{s.width}}%">
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391 <div>{{s.label}}</div>
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392 </div>
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393 {% endfor %}
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394 </div>
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395 <div style="clear: left"></div>
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396 </div>
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397
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398 {% for line in match_colors %}
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399 <a class=matchresult
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400 href="{{line.link}}"
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401 onmouseover='document.getElementById("defline").innerHTML="{{line.defline|js_string_escape}}"'
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402 onmouseout='document.getElementById("defline").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
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403 title="{{line.defline}}">
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404 <div class="matchrow graphicrow">
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405 {% for match in line.colors %}
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406 <div class="matchitem graphicitem"
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407 style="background-color: {{match[1]}}; width: {{match[0]}}%"></div>
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408 {% endfor %}
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409 </div>
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410 </a>
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411
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412 {% endfor %}
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413 </div>
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414 </div>
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415 </div>
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416 </section>
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417
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418
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419
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420 <section class=descriptions>
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421 <h2>Descriptions</h2>
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422
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423 <div class=grey><div class=white>
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424 <h4 class=darkHeader>Sequences producing significant alignments:</h4>
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425
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426 <table class=descriptiontable>
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427 <col/><col/><col/><col/><col/><col/><col/>
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428 <tr>
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429 <th>Description</th>
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430 <th>Max score</th>
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431 <th>Total score</th>
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432 <th>Query cover</th>
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433 <th>E value</th>
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434 <th>Ident</th>
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435 <th>Accession</th>
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436 </tr>
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437 {% for hit in hit_info %}
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438 <tr>
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439 <td><div><a href="#hit{{hit.link_id}}"
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440 title="{{hit.title}}"
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441 id="description{{hit.link_id}}">
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442 {{hit.title}}
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443 </a></div></td>
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444 <td>{{hit.maxscore}}</td>
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445 <td>{{hit.totalscore}}</td>
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446 <td>{{hit.cover}}</td>
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447 <td>{{hit.e_value}}</td>
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448 <td>{{hit.ident}}</td>
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449 <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
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450 </tr>
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451 {% endfor %}
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452 </table>
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453
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454 </div></div>
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455 </section>
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456
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457
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458
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459 <section class=alignments>
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460 <h2>Alignments</h2>
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461
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462 <div class=grey><div class=white>
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463 {% for hit in hits %}
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464 <div class=alignment id=hit{{hit.Hit_num}}>
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465
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466 <div class=linkheader>
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467 <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
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468 <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
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469 <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
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470 </div>
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471
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472 <div class=title>
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473 <p class=hittitle>{{hit|firsttitle}}</p>
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474 <p class=titleinfo>
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475 <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
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476 <span class=b>Length:</span> {{hit.Hit_len}}
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477 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
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478 </p>
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479 </div>
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480
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481 {% if hit|othertitles|length %}
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482 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''>
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483 See {{hit|othertitles|length}} more title(s)
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484 </a>
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485
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486 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
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487 {% for title in hit|othertitles %}
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488 <div class=title>
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489 <p class=hittitle>{{title.title}}</p>
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490 <p class=titleinfo>
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491 <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
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492 </p>
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493 </div>
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494 {% endfor %}
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495 </div>
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496 {% endif %}
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497
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498 {% for hsp in hit.Hit_hsps.Hsp %}
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499 <div class=hotspot>
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500 <p class=range>
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501 <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
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502 <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
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503 <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
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504 </p>
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505
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506 <table class=hotspotstable>
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507 <tr>
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508 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
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509 </tr>
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510 <tr>
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511 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
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512 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
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513 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
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514 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
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515 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
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516 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
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517 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
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518 </tr>
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519 </table>
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520
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521 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
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522 </div>
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523 {% endfor %}
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524
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525 </div>
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526
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527 {% endfor %}
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528 </div></div>
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529 </section>
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530
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531 {% endif %}
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532 </div>
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533 </body>
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534 </html>
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535
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536 {#
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537 Local Variables:
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538 tab-width: 2
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539 indent-tabs-mode: nil
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540 End:
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541 #}