Mercurial > repos > jankanis > blast2html2

annotate blast_html.html.jinja @ 19:67ddcb807b7d

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make it work with multiple queries
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 13 May 2014 18:06:36 +0200
parents 8e61627a87f1
children 53cd304c5f26
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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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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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 .headerdata {
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59 font-size: 90%;
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60 }
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61 .headerdata .param {
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62 font-weight: bold;
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63 text-align: right;
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64 padding: 0 1em;
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65 }
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66
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67 .grey {
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68 background-color: #eeeeee;
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69 border: 1px solid #cccccc;
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70 padding: 1em;
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71 }
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73 .white {
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74 background-color: white;
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75 border: 1px solid #cccccc;
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76 padding: 1.5em 2%;
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77 }
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78
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79 .graphicrow {
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80 clear: left;
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81 width: 100%;
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82 }
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83
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84 .graphicitem {
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85 float: left;
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86 }
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89
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90 .graphics .grey {
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91 text-align: center;
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92 }
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93
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94 .graphic {
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95 background-color: white;
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96 border: 2px solid black;
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97 padding: .5em 1.5em;
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98 margin: auto;
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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 margin-left: auto;
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103 margin-right: auto;
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104 }
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105
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106 .defline {
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107 background-color: white;
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108 border: 1px solid black;
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109 margin: .5em auto;
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110 padding-left: .2em;
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111 padding-right: .2em;
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112 max-width: 50em;
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113 text-align: left;
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114 height: 2.8em;
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115 overflow-y: hidden;
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116 }
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117
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118 div.legend {
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119 max-width: 40em;
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120 }
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121 div.legend div {
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122 width: 100%;
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123 color: white;
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124 font-weight: bold;
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125 border-spacing: 0;
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126 }
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127 div.legend div .graphicitem {
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128 width: 20%;
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129 padding: 0;
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130 margin: 0;
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131 border: none;
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132 }
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133
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134 div.tablewrapper {
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135 width: 50%;
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136 min-width: 60em;
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137 }
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138
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139 /* For small widths we give the graphic 100% */
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140 @media (max-width: 72.5em) {
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141 div.tablewrapper {
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142 width: 100%;
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143 min-width: 0px;
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144 }
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145 }
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146
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147 .scale {
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148 width: 100%;
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149 margin: .5em 0;
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150 font-weight: bold;
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151 }
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152 .scale div {
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153 color: red;
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154 text-align: left;
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155 }
8
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156 .scale .graphicrow {
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157 margin: .5em 0 .5em 0;
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158 color: white;
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159 }
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160 .scale .graphicitem div {
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161 margin: 0 1px;
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162 padding: 0 2px;
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163 text-align: right;
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164 background-color: red;
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165 color: white;
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166 }
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167 .scale .graphicitem:first-child div {
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168 margin-left: 0px;
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169 }
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170 .scale .graphicitem:last-child div {
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171 margin-right: 0px;
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172 }
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173
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174 a.matchresult {
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175 display: block;
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176 margin: 0;
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177 padding: 0;
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178 }
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179 div.matchrow {
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180 margin-top: 4px;
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181 }
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182 div.matchrow, div.matchitem {
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183 height: 4px;
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184 }
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185
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186
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187 table.descriptiontable {
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188 font-size: 85%;
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189 border: 1px solid #97b0c8;
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190 border-spacing: 0;
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191 color: #222222;
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192 line-height: 1.3em;
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193 background-color: white;
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194 }
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195 table.descriptiontable col:first-child {
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196 width: 100%;
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197 }
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198 table.descriptiontable tr:hover {
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199 background-color: #D5DEE3;
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200 }
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201 table.descriptiontable th {
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202 color: #14376C;
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203 font-weight: normal;
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204 background-color: #F0F0F0;
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205 background: linear-gradient(#FFFFFF, #F0F0F0);
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206 border-bottom: 1px solid #D4DFE9;
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207 border-right: 1px solid #CFCFCF;
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208 border-left: 0px solid black;
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209 border-top: 0px solid black;
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210 }
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211 table.descriptiontable td {
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212 overflow: hidden;
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213 text-align: center;
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214 padding: .4em .8em;
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215 }
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216 table.descriptiontable td div {
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217 width: 1em;
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218 overflow: visible;
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219 white-space: nowrap;
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220 text-align: left;
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221 }
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222
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223
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224
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225 .alignments .white {
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226 padding: 1.5em 1em;
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227 }
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228
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229 .alignment {
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230 border-top: 1px solid black;
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231 padding-left: 1em;
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232 padding-right: 1em;
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233 }
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234
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235 div.linkheader {
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236 padding-top: .2em;
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237 font-size: 85%;
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238 color: #14376C;
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239 }
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240 div.linkheader a.linkheader {
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241 margin-right: 1em;
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242 }
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243 div.linkheader .right a {
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244 text-decoration: none;
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245 }
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246
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247 .title .hittitle {
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248 color: #222222;
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249 margin-bottom: .3em;
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250 }
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251 .title .titleinfo {
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252 font-size: 80%;
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253 margin-top: 0;
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254 margin-bottom: .3em;
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255 }
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diff changeset
256 .title .titleinfo .b {
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257 color: #606060;
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258 font-weight: bold;
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259 font-size: 90%;
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260 }
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261
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262 .moretitles {
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263 margin: 1.2em;
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264 }
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265 .moretitles .titleinfo {
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266 margin: 0;
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267 padding: 0;
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268 }
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269 .moretitles .hittitle {
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270 margin: .4em 0 .2em 0;
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271 padding: 0;
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272 }
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273
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274 a.showmoretitles {
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275 font-size: 75%;
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276 color: #336699;
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277 font-weight: bold;
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278 margin-top: 0;
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279 }
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280 a.showmoretitles:hover {
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281 }
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282
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283 .hotspot {
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284 color: #606060;
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diff changeset
285 font-family: verdana, arial, sans-serif;
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diff changeset
286 margin-bottom: 2.5em;
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287 }
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288
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289 .hotspot p.range {
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290 font-size: 70%;
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diff changeset
291 margin-top: 0;
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diff changeset
292 margin-top: 1em;
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293 margin-bottom: .2em;
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diff changeset
294 }
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295 .hotspot p.range span.range {
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296 font-weight: bold;
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diff changeset
297 }
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298 .hotspot p.range a.range {
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diff changeset
299 margin-left: .5em;
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diff changeset
300 }
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301
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diff changeset
302 table.hotspotstable {
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303 border-top: 1px solid;
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diff changeset
304 border-bottom: 1px solid;
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305 text-align: left;
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306 border-collapse: collapse;
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307 }
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308 table.hotspotstable th, table.hotspotstable td {
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309 padding: .1em 1em;
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310 }
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311 table.hotspotstable th {
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312 font-size: 70%;
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313 }
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314 table.hotspotstable td {
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315 min-width: 7em;
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316 color: #222222;
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317 font-size: 80%;
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318 }
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319
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320 pre.alignmentgraphic {
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321 color: #222222;
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322 }
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323
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324
5
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325 </style>
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326
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327 <script type="text/javascript">
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328 function toggle_visibility(id) {
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329 var e = document.getElementById(id);
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330 if(e.style.display != 'block')
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331 e.style.display = 'block';
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332 else
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333 e.style.display = 'none';
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334 }
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335 </script>
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336
5
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337 </head>
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338
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339
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340 <body>
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341 <div id=content>
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342
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343 {% if not blast.BlastOutput_iterations.findall('Iteration') %}
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344 <section class=nodata>
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345 <h1>No data</h1>
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346 <div class=grey>
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347 No matches
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348 </div>
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349 </section>
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350
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351 {% else %}
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352 {% for result in blast.BlastOutput_iterations.Iteration %}
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353
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354 <section class=match>
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355
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356 <h1>Nucleotide Sequence ({{result|len}} letters)</h1>
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357
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358 <section class=header>
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359
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360 <table class=headerdata>
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361 {% for param, value in params %}
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362 <tr><td class=param>{{param}}:</td><td>{{value}}</td></tr>
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363 {% endfor %}
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364 </table>
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365
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366 </section>
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367
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368 {% set hits = result|hits %}
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369 {% if not hits %}
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370 <section>
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371 <h2>No Hits</h2>
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372 <div class=grey>
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373 This query did not match anywhere
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374 </div>
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375 </section>
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376 {% else %}
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377
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378 <section class=graphics>
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379 <h2>Graphic Summary</h2>
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380
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381 <div class=grey>
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382 <h3 class=centered>Distribution of {{result|length}} Blast Hits on the Query Sequence</h3>
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383
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384 <div class=defline id=defline{{result['Iteration_iter-num']}}>
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385 Mouse-over to show defline and scores, click to show alignments
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386 </div>
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387
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388 <div class=graphic>
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389 <h4 class=darkHeader>Color key for alignment scores</h4>
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390 <div class=legend><div class=graphicrow>
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391 <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
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392 <div class=graphicitem style="background-color: {{colors[1]}}">40–50</div>
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393 <div class=graphicitem style="background-color: {{colors[2]}}">50–80</div>
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394 <div class=graphicitem style="background-color: {{colors[3]}}">80–200</div>
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395 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
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396 </div></div>
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397 <div style="clear: left"></div>
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398
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399 <div class=tablewrapper>
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400
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401 <div class=scale>
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402 <div>query:</div>
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403 <div class=graphicrow>
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404 {% for s in result|queryscale %}
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405 <div class=graphicitem style="width: {{s.width}}%">
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406 <div>{{s.label}}</div>
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407 </div>
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408 {% endfor %}
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409 </div>
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410 <div style="clear: left"></div>
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411 </div>
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412
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413 {% for line in result|match_colors %}
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414 <a class=matchresult
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415 href="{{line.link}}"
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416 onmouseover='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="{{line.defline|js_string_escape}}"'
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417 onmouseout='document.getElementById("defline{{result['Iteration_iter-num']}}").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
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418 title="{{line.defline}}">
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419 <div class="matchrow graphicrow">
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420 {% for hit in line.colors %}
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421 <div class="matchitem graphicitem"
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422 style="background-color: {{hit[1]}}; width: {{hit[0]}}%"></div>
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423 {% endfor %}
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424 </div>
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diff changeset
425 </a>
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426
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427 {% endfor %}
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diff changeset
428 </div>
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429 </div>
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430 </div>
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431 </section>
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432
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diff changeset
433
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434
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435 <section class=descriptions>
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436 <h2>Descriptions</h2>
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437
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438 <div class=grey><div class=white>
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439 <h4 class=darkHeader>Sequences producing significant alignments:</h4>
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440
19
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441 <table class=descriptiontable>
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442 <col/><col/><col/><col/><col/><col/><col/>
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443 <tr>
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444 <th>Description</th>
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445 <th>Max score</th>
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446 <th>Total score</th>
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447 <th>Query cover</th>
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448 <th>E value</th>
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449 <th>Ident</th>
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450 <th>Accession</th>
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451 </tr>
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452 {% for hit in result|hit_info %}
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453 <tr>
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454 <td><div><a href="#hit{{hit.link_id}}"
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455 title="{{hit.title}}"
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456 id="description{{hit.link_id}}">
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diff changeset
457 {{hit.title}}
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458 </a></div></td>
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459 <td>{{hit.maxscore}}</td>
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460 <td>{{hit.totalscore}}</td>
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461 <td>{{hit.cover}}</td>
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462 <td>{{hit.e_value}}</td>
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463 <td>{{hit.ident}}</td>
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464 <td><a href="{{genelink(hit.hit|hitid)}}">{{hit.accession}}</a></td>
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465 </tr>
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466 {% endfor %}
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467 </table>
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468
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469 </div></div>
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470 </section>
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471
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472
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473
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474 <section class=alignments>
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475 <h2>Alignments</h2>
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476
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477 <div class=grey><div class=white>
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478 {% for hit in hits %}
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479 <div class=alignment id=hit{{hit.Hit_num}}>
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480
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481 <div class=linkheader>
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482 <div class=right><a href="#description{{hit.Hit_num}}">Descriptions</a></div>
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483 <a class=linkheader href="{{genelink(hit|hitid)}}">GenBank</a>
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484 <a class=linkheader href="{{genelink(hit|hitid, 'graph')}}">Graphics</a>
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485 </div>
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486
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487 <div class=title>
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488 <p class=hittitle>{{hit|firsttitle}}</p>
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489 <p class=titleinfo>
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490 <span class=b>Sequence ID:</span> <a href="{{genelink(hit|hitid)}}">{{hit|seqid}}</a>
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491 <span class=b>Length:</span> {{hit.Hit_len}}
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492 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
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493 </p>
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494 </div>
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495
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496 {% if hit|othertitles|length %}
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497 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num|js_string_escape}}'); return false;" href=''>
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498 See {{hit|othertitles|length}} more title(s)
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499 </a>
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500
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501 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
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502 {% for title in hit|othertitles %}
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503 <div class=title>
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504 <p class=hittitle>{{title.title}}</p>
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505 <p class=titleinfo>
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506 <span class=b>Sequence ID:</span> <a href="{{genelink(title.hitid)}}">{{title.id}}</a>
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507 </p>
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508 </div>
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509 {% endfor %}
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510 </div>
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511 {% endif %}
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512
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513 {% for hsp in hit.Hit_hsps.Hsp %}
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514 <div class=hotspot>
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515 <p class=range>
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516 <span class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}}</span>
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517 <a class=range href="{{genelink(hit|hitid, 'genbank', hsp)}}">GenBank</a>
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518 <a class=range href="{{genelink(hit|hitid, 'graph', hsp)}}">Graphics</a>
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519 </p>
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520
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521 <table class=hotspotstable>
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522 <tr>
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523 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
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524 </tr>
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525 <tr>
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526 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
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527 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
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528 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
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529 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
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530 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
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531 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
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532 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
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533 </tr>
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534 </table>
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535
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536 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
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537 </div>
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538 {% endfor %}
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539
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540 </div>
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541
19
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542 {% endfor %}
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543 </div></div>
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544 </section>
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545 {% endif %}
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546
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547 {% endfor %}
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548 {% endif %}
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549 </div>
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550 </body>
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551 </html>
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552
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553 {#
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554 Local Variables:
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555 tab-width: 2
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556 indent-tabs-mode: nil
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557 End:
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558 #}