Mercurial > repos > jankanis > blast2html

annotate visualise.html.jinja @ 11:7660519f2dc9

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proper layout for alignments, added some links
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 12 May 2014 13:55:04 +0200
parents 2fbdf2eb27b4
children a459c754cdb5
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1 <!DOCTYPE html>
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2 <html>
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3 <head>
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4 <meta charset="UTF-8">
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6 <title>Blast output</title>
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7
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8 <style>
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9 body {
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10 color: #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 #content {
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15 margin: 0 2em;
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16 padding: 0.5em;
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17 border: 1px solid #888888;
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18 background-color: #d3dff5;
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19 }
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20
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21 h1, h2, h3, h4, h5, h6 {
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22 color: #2A6979;
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23 font-family: arial,verdana,sans-serif;
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24 letter-spacing: -1px;
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25 margin: 1.2em 0 0.3em;
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26 }
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28 h1 {
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29 border-bottom: 1px solid #CCCCCC;
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30 font-size: 150%;
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31 padding-bottom: 0.1em;
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32 }
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34 h2 {
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35 font-size: 120%;
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36 font-weight: bold;
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37 }
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38
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39 h4.darkHeader {
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40 color: #4D4D4D;
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41 letter-spacing: 0;
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42 font-weight: bold;
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43 }
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45 #nodata {
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46 font-weight: bold;
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47 }
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48
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49 .headerdata {
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50 font-size: 90%;
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51 }
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52 .headerdata .param {
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53 font-weight: bold;
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54 text-align: right;
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55 padding: 0 1em;
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56 }
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57
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58 .grey {
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59 background-color: #eeeeee;
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60 border: 1px solid #cccccc;
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61 padding: 1em;
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62 }
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63
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64 .white {
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65 background-color: white;
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66 border: 1px solid #cccccc;
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67 padding: 1.5em 2%;
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68 }
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69
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70 .graphicrow {
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71 clear: left;
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72 width: 100%;
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73 }
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74
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75 .graphicitem {
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76 float: left;
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77 }
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78
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79 .graphic {
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80 background-color: white;
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81 border: 2px solid black;
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82 padding: .5em;
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83 align: center;
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84 margin: auto;
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85 }
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86
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87 #graphics .grey {
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88 text-align: center;
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89 }
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91 .centered, #defline, div.legend, div.tablewrapper {
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92 align: center;
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93 margin-left: auto;
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94 margin-right: auto;
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95 }
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96
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97 #defline {
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98 background-color: white;
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99 border: 1px solid black;
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100 margin: .5em auto;
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101 padding-left: .2em;
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102 padding-right: .2em;
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103 max-width: 50em;
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104 text-align: left;
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105 height: 2.8em;
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106 overflow-y: hidden;
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107 }
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108
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109 div.legend {
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110 max-width: 40em;
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111 }
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112 div.legend div {
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113 width: 100%;
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114 color: white;
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115 font-weight: bold;
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116 border-spacing: 0;
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117 }
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118 div.legend div .graphicitem {
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119 width: 20%;
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120 padding: 0;
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121 margin: 0;
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122 border: none;
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123 }
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124
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125 div.tablewrapper {
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126 width: 50%;
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127 min-width: 60em;
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128 }
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129
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130 /* For small widths we give the graphic 100% */
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131 @media (max-width: 70em) {
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132 div.tablewrapper {
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133 width: 100%;
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134 min-width: 0px;
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135 }
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136 }
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137
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138 .scale {
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139 width: 100%;
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140 margin: .5em 0;
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141 font-weight: bold;
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142 }
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143 .scale div {
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144 color: red;
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145 text-align: left;
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146 }
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147 .scale .graphicrow {
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148 margin: .5em 0 .5em 0;
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149 color: white;
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150 }
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151 .scale .graphicitem div {
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152 margin: 0 1px;
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153 padding: 0 2px;
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diff changeset
154 text-align: right;
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diff changeset
155 background-color: red;
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diff changeset
156 color: white;
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diff changeset
157 }
10
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diff changeset
158 .scale .graphicitem:first-child div {
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diff changeset
159 margin-left: 0px;
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diff changeset
160 }
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diff changeset
161 .scale .graphicitem:last-child div {
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diff changeset
162 margin-right: 0px;
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diff changeset
163 }
8
beb83da5a6b7 div-ified graphics
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parents: 7
diff changeset
164
beb83da5a6b7 div-ified graphics
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
165 a.matchresult {
beb83da5a6b7 div-ified graphics
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parents: 7
diff changeset
166 display: block;
beb83da5a6b7 div-ified graphics
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
167 margin: 0;
beb83da5a6b7 div-ified graphics
Jan Kanis <jan.code@jankanis.nl>
parents: 7
diff changeset
168 padding: 0;
7
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diff changeset
169 }
8
beb83da5a6b7 div-ified graphics
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parents: 7
diff changeset
170 div.matchrow {
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parents: 7
diff changeset
171 margin-top: 4px;
6
d20ce91e1297 slight update
Jan Kanis <jan.code@jankanis.nl>
parents: 5
diff changeset
172 }
8
beb83da5a6b7 div-ified graphics
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parents: 7
diff changeset
173 div.matchrow, div.matchitem {
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diff changeset
174 height: 4px;
7
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parents: 6
diff changeset
175 }
9e7927673089 intermediate commit before converting some tables to divs
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parents: 6
diff changeset
176
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diff changeset
177 div#descriptions {
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diff changeset
178 }
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diff changeset
179
7
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diff changeset
180 table.descriptiontable {
10
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181 font-size: 85%;
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diff changeset
182 border: 1px solid #97b0c8;
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diff changeset
183 border-spacing: 0;
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diff changeset
184 color: #222222;
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diff changeset
185 line-height: 1.3em;
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diff changeset
186 background-color: white;
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parents: 9
diff changeset
187 }
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diff changeset
188 table.descriptiontable col:first-child {
7
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diff changeset
189 width: 100%;
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1df2bfce5c24 first features are working, partial match table
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
190 }
10
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diff changeset
191 table.descriptiontable tr:hover {
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diff changeset
192 background-color: #D5DEE3;
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diff changeset
193 }
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diff changeset
194 table.descriptiontable th {
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diff changeset
195 color: #14376C;
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parents: 10
diff changeset
196 font-weight: normal;
10
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diff changeset
197 background-color: #F0F0F0;
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diff changeset
198 background: linear-gradient(#FFFFFF, #F0F0F0);
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diff changeset
199 border-bottom: 1px solid #D4DFE9;
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diff changeset
200 border-right: 1px solid #CFCFCF;
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diff changeset
201 border-left: 0px solid black;
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diff changeset
202 border-top: 0px solid black;
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diff changeset
203 }
7
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diff changeset
204 table.descriptiontable td {
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diff changeset
205 overflow: hidden;
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diff changeset
206 text-align: center;
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diff changeset
207 padding: .4em .8em;
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parents: 6
diff changeset
208 }
9e7927673089 intermediate commit before converting some tables to divs
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parents: 6
diff changeset
209 table.descriptiontable td div {
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bbdc8fb0de2b fix descriptiontable width
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diff changeset
210 width: 1em;
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parents: 8
diff changeset
211 overflow: visible;
7
9e7927673089 intermediate commit before converting some tables to divs
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diff changeset
212 white-space: nowrap;
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diff changeset
213 text-align: left;
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diff changeset
214 }
11
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diff changeset
215 table.descriptiontable a:link {
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diff changeset
216 color: #336699;
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diff changeset
217 }
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diff changeset
218
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diff changeset
219 #alignments .white {
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diff changeset
220 padding: 1.5em 1em;
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diff changeset
221 }
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diff changeset
222
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diff changeset
223 .alignment {
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diff changeset
224 border-top: 1px solid black;
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diff changeset
225 padding-left: 1em;
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diff changeset
226 padding-right: 1em;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
227 }
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diff changeset
228
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diff changeset
229 div.linkheader {
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diff changeset
230 padding-top: .2em;
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
231 text-align: right;
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
232 font-size: 85%;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
233 color: #14376C;
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
234 }
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
235 div.linkheader a {
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diff changeset
236 color: #14376C;
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
237 text-decoration: none;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
238 }
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diff changeset
239
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
240 .title .hittitle {
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diff changeset
241 color: #22222;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
242 margin-bottom: .3em;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
243 }
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diff changeset
244 .title .titleinfo {
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diff changeset
245 font-size: 80%;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
246 margin-top: 0;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
247 }
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
248 .title .titleinfo .b {
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diff changeset
249 color: #606060;
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Jan Kanis <jan.code@jankanis.nl>
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diff changeset
250 font-weight: bold;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
251 font-size: 90%;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
252 }
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diff changeset
253
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diff changeset
254 .moretitles {
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diff changeset
255 margin: 1.2em;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
256 }
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diff changeset
257 .moretitles .titleinfo {
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diff changeset
258 margin: 0;
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parents: 10
diff changeset
259 padding: 0;
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diff changeset
260 }
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diff changeset
261 .moretitles .hittitle {
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diff changeset
262 margin: .2em 0;
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parents: 10
diff changeset
263 padding: 0;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
264 }
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parents: 10
diff changeset
265
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diff changeset
266 a.showmoretitles {
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267 font-size: 85%;
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parents: 10
diff changeset
268 color: #336699;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
269 }
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diff changeset
270 a.showmoretitles:hover {
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parents: 10
diff changeset
271 }
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diff changeset
272
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diff changeset
273 .hotspot {
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diff changeset
274 color: #606060;
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diff changeset
275 font-family: verdana, arial, sans-serif;
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diff changeset
276 margin-bottom: 2.5em;
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parents: 10
diff changeset
277 }
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diff changeset
278
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diff changeset
279 .hotspot .range {
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280 font-size: 70%;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
281 margin-top: 0;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
282 font-weight: bold;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
283 margin-top: 1em;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
284 margin-bottom: .2em;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
285 }
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parents: 10
diff changeset
286
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diff changeset
287 table.hotspotstable {
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parents: 10
diff changeset
288 border-top: 1px solid;
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parents: 10
diff changeset
289 border-bottom: 1px solid;
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parents: 10
diff changeset
290 text-align: left;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
291 border-collapse: collapse;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
292 }
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parents: 10
diff changeset
293 table.hotspotstable th, table.hotspotstable td {
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diff changeset
294 padding: .1em 1em;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
295 }
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parents: 10
diff changeset
296 table.hotspotstable th {
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diff changeset
297 font-size: 70%;
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parents: 10
diff changeset
298 }
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diff changeset
299 table.hotspotstable td {
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diff changeset
300 min-width: 7em;
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parents: 10
diff changeset
301 color: #222222;
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
302 font-size: 80%;
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parents: 10
diff changeset
303 }
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parents: 10
diff changeset
304
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parents: 10
diff changeset
305 pre.alignmentgraphic {
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Jan Kanis <jan.code@jankanis.nl>
parents: 10
diff changeset
306 color: #222222;
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307 }
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308
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309
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310 </style>
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311
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312 <script type="text/javascript">
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313 function toggle_visibility(id) {
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314 var e = document.getElementById(id);
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315 if(e.style.display != 'block')
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316 e.style.display = 'block';
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317 else
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318 e.style.display = 'none';
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319 }
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320 </script>
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321
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322 </head>
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323
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324
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325 <body>
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326 <div id=content>
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327 <h1>Nucleotide Sequence ({{length}} letters)</h1>
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328
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329 <div id=header>
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330
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331 <table class=headerdata>
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332 {% for param, value in params %}
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333 <tr><td class=param>{{param}}</td><td>{{value}}</td></tr>
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334 {% endfor %}
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335 </table>
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336
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337 </div>
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338
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339 {% if not (blast.BlastOutput_iterations.find('Iteration') and
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340 blast.BlastOutput_iterations.Iteration.Iteration_hits.find('Hit')) %}
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341 <div id=nodata>
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342 <h2>No Results</h2>
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343 <div class=grey>
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344 No Matches
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345 </div>
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346 </div>
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347 {% else %}
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348
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349
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350
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351 <div id=graphics>
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352 <h2>Graphic Summary</h2>
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353
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354 <div class=grey>
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355 <h3 class=centered>Distribution of {{hits|length}} Blast Hits on the Query Sequence</h3>
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356
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357 <div id=defline>Mouse-over to show defline and scores, click to show alignments</div>
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358
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359 <div class=graphic>
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360 <h4 class=darkHeader>Color key for alignment scores</h4>
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361 <div class=legend><div class=graphicrow>
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362 <div class=graphicitem style="background-color: {{colors[0]}}">&lt;40</div>
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363 <div class=graphicitem style="background-color: {{colors[1]}}">40&endash;50</div>
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364 <div class=graphicitem style="background-color: {{colors[2]}}">50-80</div>
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365 <div class=graphicitem style="background-color: {{colors[3]}}">80-200</div>
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366 <div class=graphicitem style="background-color: {{colors[4]}}">200≤</div>
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367 </div></div>
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368 <div style="clear: left"></div>
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369
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370 <div class=tablewrapper>
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371
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372 <div class=scale>
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373 <div>query:</div>
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374 <div class=graphicrow>
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375 {% for s in queryscale %}
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376 <div class=graphicitem
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377 style="width: {{s.width|safe}}%">
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378 <div>{{s.label|safe}}</div>
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379 </div>
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380 {% endfor %}
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381 </div>
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382 <div style="clear: left"></div>
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383 </div>
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384
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385 {% for line in match_colors %}
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386 <a class=matchresult
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387 href="{{line.link}}"
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388 onmouseover='document.getElementById("defline").innerHTML="{{line.defline}}"'
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389 onmouseout='document.getElementById("defline").innerHTML="Mouse-over to show defline and scores, click to show alignments"'
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390 title="{{line.defline}}">
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391 <div class="matchrow graphicrow">
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392 {% for match in line.colors %}
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393 <div class="matchitem graphicitem"
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394 style="background-color: {{match[1]}}; width: {{match[0]}}%"></div>
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395 {% endfor %}
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396 </div>
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397 </a>
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398
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399 {% endfor %}
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400 </div>
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401 </div>
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402 </div>
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403 </div>
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404
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405
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406
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407 <div id=descriptions>
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408 <h2>Descriptions</h2>
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409
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410 <div class=grey><div class=white>
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411 <h4 class=darkHeader>Sequences producing significant alignments:</h4>
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412
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413 <table class=descriptiontable>
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414 <col/><col/><col/><col/><col/><col/><col/>
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415 <tr>
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416 <th>Description</th>
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417 <th>Max score</th>
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418 <th>Total score</th>
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419 <th>Query cover</th>
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420 <th>E value</th>
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421 <th>Ident</th>
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422 <th>Accession</th>
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423 </tr>
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424 {% for hit in hit_info %}
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425 <tr>
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426 <td><div><a href="#hit{{hit.link_id}}"
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427 title="{{hit.title}}"
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428 name=description{{hit.link_id}}>
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429 {{hit.title}}
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430 </a></div></td>
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431 <td>{{hit.maxscore}}</td>
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432 <td>{{hit.totalscore}}</td>
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433 <td>{{hit.cover}}</td>
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434 <td>{{hit.e_value}}</td>
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435 <td>{{hit.ident}}</td>
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436 <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/{{hit.hit|hitid}}?report=genbank&log$=nucltop&blast_rank=1">{{hit.accession}}</a></td>
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437 </tr>
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438 {% endfor %}
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439 </table>
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440
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441 </div></div>
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442 </div>
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443
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444
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445
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446 <div id=alignments>
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447 <h2>Alignments</h2>
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448
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449 <div class=grey><div class=white>
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450 {% for hit in hits %}
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451 <div class=alignment id=hit{{hit.Hit_num}}>
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452
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453 <div class=linkheader>
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454 <a href="#description{{hit.Hit_num}}">Descriptions</a>
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455 </div>
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456
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457 <div class=title>
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458 <p class=hittitle>{{hit|firsttitle}}</p>
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459 <p class=titleinfo>
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460 <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/{{hit|hitid}}?report=genbank&log$=nuclalign&blast_rank=1">{{hit|seqid}}</a>
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461 <span class=b>Length:</span> {{hit.Hit_len}}
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462 <span class=b>Number of Matches:</span> {{hit.Hit_hsps.Hsp|length}}
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463 </p>
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464 </div>
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465
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466 {% if hit|othertitles|length %}
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467 <a class=showmoretitles onclick="toggle_visibility('moretitles{{hit.Hit_num}}'); return false;" href=''>
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468 See {{hit|othertitles|length}} more title(s)
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469 </a>
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470
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471 <div class=moretitles id=moretitles{{hit.Hit_num}} style="display: none">
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472 {% for title in hit|othertitles %}
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473 <div class=title>
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474 <p class=hittitle>{{title.title}}</p>
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475 <p class=titleinfo>
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476 <span class=b>Sequence ID:</span> {{title.id}}
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477 </p>
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478 </div>
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479 {% endfor %}
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480 </div>
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481 {% endif %}
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482
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483 {% for hsp in hit.Hit_hsps.Hsp %}
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484 <div class=hotspot>
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485 <p class=range>Range {{hsp.Hsp_num}}: {{hsp['Hsp_hit-from']}} to {{hsp['Hsp_hit-to']}} <a href="http://www.ncbi.nlm.nih.gov/nucleotide/{{hit|hitid}}?report=genbank&log$=nuclalign&blast_rank=1&from={{hsp['Hsp_hit-from']}}&to={{hsp['Hsp_hit-to']}}">GenBank</a></p>
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486
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487 <table class=hotspotstable>
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488 <tr>
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489 <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>
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490 </tr>
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491 <tr>
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492 <td>{{hsp['Hsp_bit-score']|fmt('.1f')}} bits({{hsp.Hsp_score}})</td>
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493 <td>{{hsp.Hsp_evalue|fmt('.1f')}}</td>
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494 <td>{{ hsp.Hsp_identity }}/{{ hsp|len }}({{
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495 (hsp.Hsp_identity/hsp|len) |fmt('.0%') }})</td>
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496 <td>{{ hsp.Hsp_gaps }}/{{ hsp|len
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497 }}({{ (hsp.Hsp_gaps / hsp|len) | fmt('.0%') }})</td>
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498 <td>{{ hsp['Hsp_query-frame']|asframe }}/{{ hsp['Hsp_hit-frame']|asframe }}</td>
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499 </tr>
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500 </table>
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501
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502 <pre class=alignmentgraphic>{{hsp|alignment_pre}}</pre>
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503 </div>
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504 {% endfor %}
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505
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506 </div>
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507
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508 {% endfor %}
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509 </div></div>
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510 </div>
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511
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512 {% endif %}
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513 </div>
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514 </body>
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515 </html>
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516