Mercurial > repos > jankanis > blast2html

annotate blast_html.html.jinja @ 21:9596fea636bb

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style changes
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 15 May 2014 10:45:34 +0200
parents 53cd304c5f26
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 <meta name=generator content="blast_html; see ...">
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6
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7 <title>Blast output</title>
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8
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9 <style>
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10 body {
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11 color: #333333;
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12 font-family: Arial,Sans-Serif;
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13 }
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15 :link {
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16 color: #336699;
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17 }
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18
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19 .right {
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20 float: right;
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21 }
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22
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23 #content {
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24 margin: 0 2em;
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25 padding: 0.5em;
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26 border: 1px solid #888888;
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27 background-color: #d3dff5;
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28 }
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29
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30 h1, h2, h3, h4, h5, h6 {
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31 color: #2A6979;
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32 font-family: arial,verdana,sans-serif;
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33 letter-spacing: -1px;
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34 margin: 1.2em 0 0.3em;
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35 }
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36
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37 h1 {
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38 border-bottom: 1px solid #CCCCCC;
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39 font-size: 150%;
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40 padding-bottom: 0.1em;
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41 }
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42
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43 h2 {
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44 font-size: 120%;
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45 font-weight: bold;
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46 }
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47
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48 h4.darkHeader {
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49 color: #4D4D4D;
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50 letter-spacing: 0;
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51 font-weight: bold;
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52 }
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53
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54 #nodata {
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55 font-weight: bold;
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56 }
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57
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58 .index {
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59 margin-bottom: 3em;
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60 }
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61 .index div.indexentry {
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62 margin: 1.2em 1.6em;
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63 font-weight: bold;
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64 font-size: 100%;
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65 }
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66
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67 .headerdata {
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68 font-size: 90%;
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69 }
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70 .headerdata .param {
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71 font-weight: bold;
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72 text-align: right;
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73 padding: 0 1em;
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74 }
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75
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76 .grey {
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77 background-color: #eeeeee;
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78 border: 1px solid #cccccc;
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79 padding: 1em;
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80 }
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81
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82 .white {
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83 background-color: white;
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84 border: 1px solid #cccccc;
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85 padding: 1.5em 2%;
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86 }
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87
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88 .graphicrow {
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89 clear: left;
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90 width: 100%;
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91 }
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92
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93 .graphicitem {
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94 float: left;
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95 }
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96
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98
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99 .graphics .grey {
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100 text-align: center;
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101 }
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102
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103 .graphic {
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104 background-color: white;
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105 border: 2px solid black;
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106 padding: 1.5em;
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107 margin: auto;
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108 }
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109
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110 .centered, .defline, div.legend, div.tablewrapper {
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111 margin-left: auto;
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112 margin-right: auto;
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113 }
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114
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115 .defline {
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116 background-color: white;
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117 border: 1px solid black;
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118 margin: .5em auto;
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119 padding-left: .2em;
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120 padding-right: .2em;
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121 max-width: 50em;
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122 text-align: left;
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123 height: 2.8em;
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124 overflow-y: hidden;
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125 }
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126
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127 div.legend {
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128 max-width: 40em;
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129 }
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130 div.legend div {
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131 width: 100%;
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132 color: white;
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133 font-weight: bold;
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134 border-spacing: 0;
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135 }
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136 div.legend div .graphicitem {
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137 width: 20%;
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138 padding: 0;
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139 margin: 0;
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140 border: none;
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141 }
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142
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143 div.tablewrapper {
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144 width: 50%;
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145 min-width: 60em;
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146 }
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147
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148 /* For small widths we give the graphic 100% */
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149 @media (max-width: 72.5em) {
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150 div.tablewrapper {
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151 width: 100%;
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152 min-width: 0px;
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153 }
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154 }
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155
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156 .scale {
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157 width: 100%;
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158 margin: .5em 0;
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159 font-weight: bold;
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160 }
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161 .scale div {
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162 color: red;
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163 text-align: left;
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164 }
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165 .scale .graphicrow {
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166 margin: .5em 0 .5em 0;
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167 color: white;
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168 }
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169 .scale .graphicitem {
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170 position: relative;
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171 }
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172 .scale .graphicitem div {
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173 margin: 0 1px;
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174 padding: 0 2px;
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175 text-align: right;
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176 background-color: red;
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177 color: white;
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178 }
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179 .scale .graphicitem:first-child div {
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180 margin-left: 0px;
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181 }
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182 .scale .graphicitem:last-child div {
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183 margin-right: 0px;
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184 }
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185 .scale .graphicitem .lastlabel {
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186 position: absolute;
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187 top: 0px;
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188 left: 100%;
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189 background-color: transparent;
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190 color: red;
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191 }
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192
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193 a.matchresult {
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194 display: block;
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195 margin: 0;
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196 padding: 0;
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197 }
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198 div.matchrow {
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199 margin-top: 4px;
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200 }
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201 div.matchrow, div.matchitem {
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202 height: 4px;
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203 }
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204
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205
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206 table.descriptiontable {
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207 font-size: 85%;
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208 border: 1px solid #97b0c8;
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209 border-spacing: 0;
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210 color: #222222;
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211 line-height: 1.3em;
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212 background-color: white;
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213 }
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214 table.descriptiontable col:first-child {
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215 width: 100%;
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216 }
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217 table.descriptiontable tr:hover {
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218 background-color: #D5DEE3;
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219 }
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220 table.descriptiontable th {
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221 color: #14376C;
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222 font-weight: normal;
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223 background-color: #F0F0F0;
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224 background: linear-gradient(#FFFFFF, #F0F0F0);
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225 border-bottom: 1px solid #D4DFE9;
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226 border-right: 1px solid #CFCFCF;
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227 border-left: 0px solid black;
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228 border-top: 0px solid black;
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229 }
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230 table.descriptiontable td {
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231 overflow: hidden;
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232 text-align: center;
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233 padding: .4em .8em;
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234 }
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235 table.descriptiontable td div {
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236 width: 1em;
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237 overflow: visible;
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238 white-space: nowrap;
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239 text-align: left;
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240 }
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241
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242
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243
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244 .alignments .white {
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245 padding: 1.5em 1em;
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246 }
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247
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248 .alignment {
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249 border-top: 1px solid black;
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250 padding-left: 1em;
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251 padding-right: 1em;
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252 }
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253
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254 div.linkheader {
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255 padding-top: .2em;
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256 font-size: 85%;
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257 color: #14376C;
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258 }
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259 div.linkheader a.linkheader {
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260 margin-right: 1em;
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261 }
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262 div.linkheader .right a {
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263 text-decoration: none;
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264 }
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265
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266 .title .hittitle {
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267 color: #222222;
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268 margin-bottom: .3em;
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269 }
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270 .title .titleinfo {
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271 font-size: 80%;
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272 margin-top: 0;
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273 margin-bottom: .3em;
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274 }
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275 .title .titleinfo .b {
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276 color: #606060;
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277 font-weight: bold;
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278 font-size: 90%;
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279 }
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280
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281 .moretitles {
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282 margin: 1.2em;
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283 }
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284 .moretitles .titleinfo {
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285 margin: 0;
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286 padding: 0;
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287 }
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288 .moretitles .hittitle {
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289 margin: .4em 0 .2em 0;
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290 padding: 0;
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291 }
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292
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293 a.showmoretitles {
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294 font-size: 75%;
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295 color: #336699;
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296 font-weight: bold;
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297 margin-top: 0;
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diff changeset
298 }
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diff changeset
299 a.showmoretitles:hover {
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300 }
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301
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302 .hotspot {
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303 color: #606060;
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304 font-family: verdana, arial, sans-serif;
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305 margin-bottom: 2.5em;
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306 }
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307
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308 .hotspot p.range {
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309 font-size: 70%;
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310 margin-top: 0;
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311 margin-top: 1em;
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312 margin-bottom: .2em;
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313 }
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314 .hotspot p.range span.range {
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315 font-weight: bold;
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316 }
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317 .hotspot p.range a.range {
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318 margin-left: .5em;
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319 }
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320
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321 table.hotspotstable {
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322 border-top: 1px solid;
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323 border-bottom: 1px solid;
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324 text-align: left;
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325 border-collapse: collapse;
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326 }
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327 table.hotspotstable th, table.hotspotstable td {
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328 padding: .1em 1em;
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329 }
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330 table.hotspotstable th {
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331 font-size: 70%;
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332 }
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333 table.hotspotstable td {
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334 min-width: 7em;
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335 color: #222222;
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336 font-size: 80%;
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337 }
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338
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339 pre.alignmentgraphic {
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340 color: #222222;
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341 }
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342
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343
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344 </style>
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345
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346 <script type="text/javascript">
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347 function toggle_visibility(id) {
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348 var e = document.getElementById(id);
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349 if(e.style.display != 'block')
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350 e.style.display = 'block';
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351 else
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352 e.style.display = 'none';
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353 }
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354 </script>
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355
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356 </head>
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357
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358
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359 <body>
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360 <div id=content>
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361
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362 {% if not blast.BlastOutput_iterations.findall('Iteration') %}
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363 <section class=nodata>
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364 <h1>No data</h1>
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365 <div class=grey>
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366 No matches
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367 </div>
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368 </section>
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369
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370 {% else %}
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371
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372 {% if blast.BlastOutput_iterations.findall('Iteration') | length > 1 %}
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373 <section class=index>
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374 <h1>Queries</h1>
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375
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376 {% for result in blast.BlastOutput_iterations.Iteration %}
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377 <div class=indexentry><a href="#match{{result['Iteration_iter-num']}}">
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378 {% set hits = result|hits %}
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379 {{result['Iteration_query-ID']}}: {{result['Iteration_query-def']}}
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380 ({{result|len}} letters, {{hits|length}} hits)
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381 </a></div>
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382 {% endfor %}
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383
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384 </section>
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385 {% endif %}
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386
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387 {% for result in blast.BlastOutput_iterations.Iteration %}
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388
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389 <section class=match id=match{{result['Iteration_iter-num']}}>
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390
19
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391 <h1>Nucleotide Sequence ({{result|len}} letters)</h1>
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392
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393 <section class=header>
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394
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395 <table class=headerdata>
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396 {% for param, value in params %}
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397 <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
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398 {% endfor %}
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399 </table>
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400
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401 </section>
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402
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403 {% set hits = result|hits %}
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404 {% if not hits %}
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405 <section>
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406 <h2>No Hits</h2>
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diff changeset
407 <div class=grey>
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408 This query did not match anywhere
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409 </div>
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410 </section>
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411 {% else %}
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412
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413 <section class=graphics>
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414 <h2>Graphic Summary</h2>
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415
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416 <div class=grey>
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417 <h3 class=centered>Distribution of {{result|length}} Blast Hits on the Query Sequence</h3>
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418
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419 <div class=defline id=defline{{result['Iteration_iter-num']}}>
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420 Mouse-over to show defline and scores, click to show alignments
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diff changeset
421 </div>
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422
19
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423 <div class=graphic>
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424 <h4 class=darkHeader>Color key for alignment scores</h4>
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diff changeset
425 <div class=legend><div class=graphicrow>
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426 <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
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427 <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
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428 <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
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429 <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
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diff changeset
430 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
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diff changeset
431 </div></div>
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diff changeset
432 <div style="clear: left"></div>
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diff changeset
433
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diff changeset
434 <div class=tablewrapper>
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diff changeset
435
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diff changeset
436 <div class=scale>
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diff changeset
437 <div>query:</div>
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diff changeset
438 <div class=graphicrow>
20
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diff changeset
439 <div>
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diff changeset
440 {% for s in result|queryscale %}
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diff changeset
441 <div class=graphicitem style="width: {{s.width}}%">
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442 {% if s.width > 3.0 %}
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443 <div>{{s.label}}</div>
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444 {% else %}
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diff changeset
445 <div>&nbsp;</div>
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diff changeset
446 <div class=lastlabel>{{s.label}}</div>
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diff changeset
447 {% endif %}
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diff changeset
448 </div>
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449 {% endfor %}
19
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450 </div>
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diff changeset
451 </div>
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diff changeset
452 <div style="clear: left"></div>
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453 </div>
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454
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455 {% for line in result|match_colors %}
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456 <a class=matchresult
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457 href="{{line.link}}"
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458 onmouseover='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="{{line.defline|js_string_escape}}"'
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459 onmouseout='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
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460 title="{{line.defline}}">
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461 <div class="matchrow graphicrow">
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462 {% for hit in line.colors %}
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463 <div class="matchitem graphicitem"
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464 style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div>
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465 {% endfor %}
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466 </div>
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467 </a>
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468
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469 {% endfor %}
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470 </div>
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471 </div>
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472 </div>
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473 </section>
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474
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475
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476
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477 <section class=descriptions>
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478 <h2>Descriptions</h2>
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479
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480 <div class=grey><div class=white>
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481 <h4 class=darkHeader>Sequences producing significant alignments:</h4>
10
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482
19
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483 <table class=descriptiontable>
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484 <col/><col/><col/><col/><col/><col/><col/>
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485 <tr>
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486 <th>Description</th>
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487 <th>Max score</th>
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488 <th>Total score</th>
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489 <th>Query cover</th>
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490 <th>E value</th>
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491 <th>Ident</th>
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492 <th>Accession</th>
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493 </tr>
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494 {% for hit in result|hit_info %}
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495 <tr>
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496 <td><div><a href="#hit{{hit.link_id}}"
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497 title="{{hit.title}}"
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498 id="description{{hit.link_id}}">
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499 {{hit.title}}
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500 </a></div></td>
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501 <td>{{hit.maxscore}}</td>
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502 <td>{{hit.totalscore}}</td>
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503 <td>{{hit.cover}}</td>
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504 <td>{{hit.e_value}}</td>
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505 <td>{{hit.ident}}</td>
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506 <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
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507 </tr>
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508 {% endfor %}
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509 </table>
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510
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511 </div></div>
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diff changeset
512 </section>
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513
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514
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diff changeset
515
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diff changeset
516 <section class=alignments>
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517 <h2>Alignments</h2>
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518
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519 <div class=grey><div class=white>
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520 {% for hit in hits %}
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diff changeset
521 <div class=alignment id=hit{{hit.Hit_num}}>
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522
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diff changeset
523 <div class=linkheader>
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diff changeset
524 <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
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diff changeset
525 <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
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526 <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
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diff changeset
527 </div>
5
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528
19
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diff changeset
529 <div class=title>
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parents: 17
diff changeset
530 <p class=hittitle>{{hit|firsttitle}}</p>
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parents: 17
diff changeset
531 <p class=titleinfo>
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532 <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
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diff changeset
533 <span class=b>Length:</span> {{hit.Hit_len}}
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diff changeset
534 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
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535 </p>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
536 </div>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
537
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diff changeset
538 {% if hit|othertitles|length %}
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diff changeset
539 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
540 See {{hit|othertitles|length}} more title(s)
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
541 </a>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
542
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diff changeset
543 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
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diff changeset
544 {% for title in hit|othertitles %}
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diff changeset
545 <div class=title>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
546 <p class=hittitle>{{title.title}}</p>
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diff changeset
547 <p class=titleinfo>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
548 <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
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parents: 17
diff changeset
549 </p>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
550 </div>
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diff changeset
551 {% endfor %}
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diff changeset
552 </div>
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diff changeset
553 {% endif %}
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
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parents: 9
diff changeset
554
19
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diff changeset
555 {% for hsp in hit.Hit_hsps.Hsp %}
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parents: 17
diff changeset
556 <div class=hotspot>
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diff changeset
557 <p class=range>
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diff changeset
558 <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
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diff changeset
559 <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
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diff changeset
560 <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
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diff changeset
561 </p>
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parents: 17
diff changeset
562
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
563 <table class=hotspotstable>
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parents: 17
diff changeset
564 <tr>
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diff changeset
565 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
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diff changeset
566 </tr>
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parents: 17
diff changeset
567 <tr>
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diff changeset
568 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
569 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
570 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
571 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
572 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
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diff changeset
573 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
574 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
575 </tr>
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Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
576 </table>
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
577
67ddcb807b7d make it work with multiple queries
Jan Kanis <jan.code@jankanis.nl>
parents: 17
diff changeset
578 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
67ddcb807b7d make it work with multiple queries
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parents: 17
diff changeset
579 </div>
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diff changeset
580 {% endfor %}
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parents: 17
diff changeset
581
16
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parents: 13
diff changeset
582 </div>
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
Jan Kanis <jan.code@jankanis.nl>
parents: 9
diff changeset
583
19
67ddcb807b7d make it work with multiple queries
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diff changeset
584 {% endfor %}
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parents: 17
diff changeset
585 </div></div>
67ddcb807b7d make it work with multiple queries
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diff changeset
586 </section>
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
587 {% endif %}
10
2fbdf2eb27b4 All data is displayed now, still some formatting to do
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parents: 9
diff changeset
588
19
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diff changeset
589 {% endfor %}
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parents: 17
diff changeset
590 {% endif %}
5
1df2bfce5c24 first features are working, partial match table
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diff changeset
591 </div>
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
592 </body>
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
593 </html>
1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
594
16
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diff changeset
595 {#
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diff changeset
596 Local Variables:
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diff changeset
597 tab-width: 2
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diff changeset
598 indent-tabs-mode: nil
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diff changeset
599 End:
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
600 #}