Mercurial > repos > jankanis > blast2html

annotate visualise.html.jinja @ 12:a459c754cdb5

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add links, refactor, proper commandline arguments
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 12 May 2014 17:12:24 +0200
parents 7660519f2dc9
children
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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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5
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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: #33333;
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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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35
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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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88
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89 .graphic {
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90 background-color: white;
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91 border: 2px solid black;
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92 padding: .5em 1.5em;
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93 align: center;
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94 margin: auto;
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95 }
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96
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97 #graphics .grey {
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98 text-align: center;
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99 }
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100
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101 .centered, #defline, div.legend, div.tablewrapper {
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102 align: center;
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103 margin-left: auto;
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104 margin-right: auto;
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105 }
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106
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107 #defline {
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108 background-color: white;
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109 border: 1px solid black;
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110 margin: .5em auto;
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111 padding-left: .2em;
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112 padding-right: .2em;
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113 max-width: 50em;
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114 text-align: left;
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115 height: 2.8em;
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116 overflow-y: hidden;
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117 }
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118
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119 div.legend {
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120 max-width: 40em;
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121 }
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122 div.legend div {
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123 width: 100%;
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124 color: white;
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125 font-weight: bold;
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126 border-spacing: 0;
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127 }
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128 div.legend div .graphicitem {
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129 width: 20%;
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130 padding: 0;
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131 margin: 0;
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132 border: none;
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133 }
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134
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135 div.tablewrapper {
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136 width: 50%;
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137 min-width: 60em;
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138 }
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139
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140 /* For small widths we give the graphic 100% */
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141 @media (max-width: 72.5em) {
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142 div.tablewrapper {
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143 width: 100%;
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144 min-width: 0px;
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145 }
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146 }
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147
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148 .scale {
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149 width: 100%;
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150 margin: .5em 0;
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151 font-weight: bold;
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152 }
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153 .scale div {
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154 color: red;
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155 text-align: left;
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156 }
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157 .scale .graphicrow {
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158 margin: .5em 0 .5em 0;
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159 color: white;
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160 }
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161 .scale .graphicitem div {
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162 margin: 0 1px;
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163 padding: 0 2px;
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164 text-align: right;
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165 background-color: red;
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166 color: white;
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167 }
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168 .scale .graphicitem:first-child div {
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169 margin-left: 0px;
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170 }
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171 .scale .graphicitem:last-child div {
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172 margin-right: 0px;
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173 }
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174
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175 a.matchresult {
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176 display: block;
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177 margin: 0;
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178 padding: 0;
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179 }
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180 div.matchrow {
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181 margin-top: 4px;
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182 }
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183 div.matchrow, div.matchitem {
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184 height: 4px;
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185 }
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186
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187
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188
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189 div#descriptions {
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190 }
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191
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192 table.descriptiontable {
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193 font-size: 85%;
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194 border: 1px solid #97b0c8;
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195 border-spacing: 0;
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196 color: #222222;
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197 line-height: 1.3em;
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198 background-color: white;
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199 }
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200 table.descriptiontable col:first-child {
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201 width: 100%;
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202 }
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203 table.descriptiontable tr:hover {
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204 background-color: #D5DEE3;
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205 }
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206 table.descriptiontable th {
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207 color: #14376C;
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208 font-weight: normal;
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209 background-color: #F0F0F0;
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210 background: linear-gradient(#FFFFFF, #F0F0F0);
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211 border-bottom: 1px solid #D4DFE9;
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212 border-right: 1px solid #CFCFCF;
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213 border-left: 0px solid black;
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214 border-top: 0px solid black;
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215 }
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216 table.descriptiontable td {
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217 overflow: hidden;
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218 text-align: center;
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219 padding: .4em .8em;
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220 }
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221 table.descriptiontable td div {
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222 width: 1em;
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223 overflow: visible;
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224 white-space: nowrap;
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225 text-align: left;
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226 }
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227
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228
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229
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230 #alignments .white {
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231 padding: 1.5em 1em;
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232 }
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233
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234 .alignment {
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235 border-top: 1px solid black;
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236 padding-left: 1em;
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237 padding-right: 1em;
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238 }
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239
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240 div.linkheader {
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241 padding-top: .2em;
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242 font-size: 85%;
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243 color: #14376C;
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244 }
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245 div.linkheader a.linkheader {
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246 margin-right: 1em;
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247 }
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248 div.linkheader .right a {
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249 text-decoration: none;
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250 }
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251
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252 .title .hittitle {
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253 color: #22222;
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254 margin-bottom: .3em;
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255 }
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256 .title .titleinfo {
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257 font-size: 80%;
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258 margin-top: 0;
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259 margin-bottom: .3em;
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260 }
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261 .title .titleinfo .b {
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262 color: #606060;
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263 font-weight: bold;
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264 font-size: 90%;
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265 }
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266
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267 .moretitles {
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268 margin: 1.2em;
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269 }
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270 .moretitles .titleinfo {
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271 margin: 0;
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272 padding: 0;
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273 }
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274 .moretitles .hittitle {
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275 margin: .4em 0 .2em 0;
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276 padding: 0;
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277 }
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278
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279 a.showmoretitles {
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280 font-size: 75%;
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281 color: #336699;
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282 font-weight: bold;
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283 margin-top: 0;
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284 }
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285 a.showmoretitles:hover {
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286 }
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287
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288 .hotspot {
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289 color: #606060;
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290 font-family: verdana, arial, sans-serif;
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291 margin-bottom: 2.5em;
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292 }
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293
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294 .hotspot p.range {
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295 font-size: 70%;
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diff changeset
296 margin-top: 0;
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297 margin-top: 1em;
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298 margin-bottom: .2em;
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299 }
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300 .hotspot p.range span.range {
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301 font-weight: bold;
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302 }
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303 .hotspot p.range a.range {
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304 margin-left: .5em;
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305 }
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306
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307 table.hotspotstable {
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308 border-top: 1px solid;
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309 border-bottom: 1px solid;
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310 text-align: left;
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311 border-collapse: collapse;
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312 }
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313 table.hotspotstable th, table.hotspotstable td {
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314 padding: .1em 1em;
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315 }
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316 table.hotspotstable th {
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317 font-size: 70%;
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318 }
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319 table.hotspotstable td {
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320 min-width: 7em;
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321 color: #222222;
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322 font-size: 80%;
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323 }
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324
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325 pre.alignmentgraphic {
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326 color: #222222;
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327 }
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328
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329
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330 </style>
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331
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332 <script type="text/javascript">
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333 function toggle_visibility(id) {
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334 var e = document.getElementById(id);
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335 if(e.style.display != 'block')
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336 e.style.display = 'block';
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337 else
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338 e.style.display = 'none';
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339 }
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340 </script>
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341
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342 </head>
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343
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344
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345 <body>
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346 <div id=content>
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347 <h1>Nucleotide Sequence ({{length}} letters)</h1>
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348
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349 <div id=header>
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350
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351 <table class=headerdata>
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352 {% for param, value in params %}
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353 <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
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354 {% endfor %}
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355 </table>
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356
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357 </div>
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358
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359 {% if not (blast.BlastOutput_iterations.findall('Iteration') and
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360 blast.BlastOutput_iterations.Iteration.Iteration_hits.findall('Hit')) %}
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361 <div id=nodata>
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362 <h2>No Results</h2>
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363 <div class=grey>
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364 No Matches
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365 </div>
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366 </div>
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367 {% else %}
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368
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369
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370
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371 <div id=graphics>
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372 <h2>Graphic Summary</h2>
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373
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374 <div class=grey>
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375 <h3 class=centered>Distribution of {{hits|length}} Blast Hits on the Query Sequence</h3>
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376
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377 <div id=defline>Mouse-over to show defline and scores, click to show alignments</div>
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378
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379 <div class=graphic>
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380 <h4 class=darkHeader>Color key for alignment scores</h4>
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381 <div class=legend><div class=graphicrow>
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382 <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
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383 <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
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384 <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
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385 <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
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386 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
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387 </div></div>
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388 <div style="clear: left"></div>
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389
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390 <div class=tablewrapper>
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391
7
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392 <div class=scale>
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393 <div>query:</div>
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394 <div class=graphicrow>
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395 {% for s in queryscale %}
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396 <div class=graphicitem
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397 style="width: {{s.width|safe}}%">
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398 <div>{{s.label|safe}}</div>
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399 </div>
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400 {% endfor %}
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401 </div>
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402 <div style="clear: left"></div>
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403 </div>
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404
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405 {% for line in match_colors %}
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406 <a class=matchresult
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407 href="{{line.link}}"
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408 onmouseover='document.getElementById("defline").innerHTML="{{line.defline}}"'
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409 onmouseout='document.getElementById("defline").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
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410 title="{{line.defline}}">
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411 <div class="matchrow graphicrow">
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412 {% for match in line.colors %}
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413 <div class="matchitem graphicitem"
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414 style="background-color: {{match[1]}}; width: {{match[0]}}%"></div>
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415 {% endfor %}
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416 </div>
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417 </a>
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418
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419 {% endfor %}
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420 </div>
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421 </div>
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422 </div>
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423 </div>
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424
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425
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426
7
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427 <div id=descriptions>
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428 <h2>Descriptions</h2>
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429
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430 <div class=grey><div class=white>
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431 <h4 class=darkHeader>Sequences producing significant alignments:</h4>
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432
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433 <table class=descriptiontable>
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434 <col/><col/><col/><col/><col/><col/><col/>
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435 <tr>
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436 <th>Description</th>
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437 <th>Max score</th>
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438 <th>Total score</th>
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439 <th>Query cover</th>
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440 <th>E value</th>
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441 <th>Ident</th>
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442 <th>Accession</th>
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443 </tr>
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444 {% for hit in hit_info %}
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445 <tr>
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446 <td><div><a href="#hit{{hit.link_id}}"
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447 title="{{hit.title}}"
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448 name=description{{hit.link_id}}>
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449 {{hit.title}}
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450 </a></div></td>
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451 <td>{{hit.maxscore}}</td>
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452 <td>{{hit.totalscore}}</td>
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453 <td>{{hit.cover}}</td>
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454 <td>{{hit.e_value}}</td>
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455 <td>{{hit.ident}}</td>
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456 <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
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457 </tr>
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458 {% endfor %}
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459 </table>
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460
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461 </div></div>
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462 </div>
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463
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464
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465
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466 <div id=alignments>
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467 <h2>Alignments</h2>
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468
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469 <div class=grey><div class=white>
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470 {% for hit in hits %}
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471 <div class=alignment id=hit{{hit.Hit_num}}>
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472
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473 <div class=linkheader>
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474 <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
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475 <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
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476 <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
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477 </div>
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478
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479 <div class=title>
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480 <p class=hittitle>{{hit|firsttitle}}</p>
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481 <p class=titleinfo>
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482 <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
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483 <span class=b>Length:</span> {{hit.Hit_len}}
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484 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
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485 </p>
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486 </div>
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487
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488 {% if hit|othertitles|length %}
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489 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num}}'); return false;" href=''>
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490 See {{hit|othertitles|length}} more title(s)
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491 </a>
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492
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493 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
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494 {% for title in hit|othertitles %}
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495 <div class=title>
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496 <p class=hittitle>{{title.title}}</p>
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497 <p class=titleinfo>
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498 <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
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499 </p>
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500 </div>
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501 {% endfor %}
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502 </div>
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503 {% endif %}
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504
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505 {% for hsp in hit.Hit_hsps.Hsp %}
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506 <div class=hotspot>
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507 <p class=range>
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508 <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
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509 <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
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510 <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
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511 </p>
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512
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513 <table class=hotspotstable>
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514 <tr>
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515 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
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516 </tr>
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517 <tr>
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518 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
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519 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
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520 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
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521 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
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522 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
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523 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
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524 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
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525 </tr>
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526 </table>
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527
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528 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
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529 </div>
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530 {% endfor %}
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531
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532 </div>
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533
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534 {% endfor %}
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535 </div></div>
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536 </div>
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537
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538 {% endif %}
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539 </div>
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540 </body>
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541 </html>
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parents:
diff changeset
542