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1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
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2 "http://www.w3.org/TR/html4/transitional.dtd">
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3 <html>
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4 <head>
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5 <link rel="stylesheet" type="text/css" href="logo.css" >
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6
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7 <title>CodonLogo - Tests </title>
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8 <meta name="author" content="Gavin E. Crooks" >
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9 <meta name="ID" content="$ID:" >
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10
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11 <style type="text/css">
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12 td {
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13 border-left : white solid 4pt
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14 }
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15 .error {
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16 color: #900;
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17 border-left: red solid +4pt;
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18 }
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19
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20 .err_msg {
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21 color: #900;
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22 }
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23
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24 </style>
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25 </head>
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26
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27 <body style="align:center">
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28
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29
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30 <table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
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31 <tr><td >
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32 <h1> CodonLogo: Tests</h1>
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33
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34 </td><td align = "right">
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35 ·
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36 <a href="./">about</a> ·
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37 <a href="create.cgi">create</a> ·
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38 <a href="examples.html">examples</a> ·
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39 <a href="manual.html">manual</a> ·
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40 <br>
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41
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42 </td></tr>
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43
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44 <tr><td colspan='2'>
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45
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46 Various tests of the CodonLogo webapp. <br >
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47
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48 <hr >
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49
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50 <dl>
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51 <dt>Relative Entropy Test</dt>
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52 <dd>
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53 The entropy should be 2 bits, 1 bit, 0 bits
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54 (The small sample correction should be turned off.)
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55 <br >
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56 <form method="post" action="create.cgi">
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57 <input type="submit" name="cmd_edit" value="Edit" >
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58 <input type="submit" name="cmd_create" value="Create" >
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59 <input type="hidden" name="show_yaxis" value="true" >
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60 <input type="hidden" name="show_xaxis" value="true" >
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61 <input type="hidden" name="show_fineprint" value="true" >
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62 <input type="hidden" name="show_errorbars" value="true" >
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63 <input type="hidden" name="download" value="true" >
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64 <input type="hidden" name="composition" value="comp_none" >
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65
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66 <input type="hidden" name="sequences" value=
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67 ">
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68 GTTGTTGTTGTT
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69 >
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70 GTCGTCGTCGTC
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71 >
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72 GGGGGGGGGGGG
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73 >
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74 GGAGGAGGAGGA
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75 " >
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76 </form>
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77 </dd>
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78
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79
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80 <dt>Title And Labels Test</dt>
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81 <dd>
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82 Replace and display x-label, y-label and title.
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83 <form method="post" action="create.cgi">
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84 <input type="submit" name="cmd_edit" value="Edit" >
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85 <input type="submit" name="cmd_create" value="Create" >
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86 <input type="hidden" name="show_yaxis" value="true" >
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87 <input type="hidden" name="show_xaxis" value="true" >
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88 <input type="hidden" name="show_fineprint" value="true" >
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89 <input type="hidden" name="show_errorbars" value="true" >
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90 <input type="hidden" name="download" value="true" >
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91
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92 <input type="hidden" name="yaxis_label" value="The Y-axis" >
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93 <input type="hidden" name="xaxis_label" value="The X-axis" >
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94 <input type="hidden" name="logo_title" value="This is the TITLE" >
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95 <input type="hidden" name="sequences" value=
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96 ">
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97 AAAGTGAAAGTGAAAGTGAAAGTG
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98 >
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99 AAAGCGAAAGCGAAAGCGAAAGCG
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100 >
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101 TGCCCTTGCCCTTGCCCTTGCCCT
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102 >
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103 TGCCTTTGCCTTTGCCTTTGCCTT
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104 " >
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105 </form>
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106
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107 Same, but do not show axes
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108 <form method="post" action="create.cgi">
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109 <input type="submit" name="cmd_edit" value="Edit" >
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110 <input type="submit" name="cmd_create" value="Create" >
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111 <input type="hidden" name="show_fineprint" value="true" >
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112 <input type="hidden" name="show_errorbars" value="true" >
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113 <input type="hidden" name="download" value="true" >
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114
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115 <input type="hidden" name="yaxis_label" value="This is the Y-axis" >
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116 <input type="hidden" name="xaxis_label" value="This is the X-axis" >
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117 <input type="hidden" name="logo_title" value="This is the TITLE" >
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118 <input type="hidden" name="sequences" value=
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119 ">
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120 AAAGTGAAAGTGAAAGTGAAAGTG
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121 >
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122 AAAGCGAAAGCGAAAGCGAAAGCG
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123 >
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124 TGCCCTTGCCCTTGCCCTTGCCCT
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125 >
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126 TGCCTTTGCCTTTGCCTTTGCCTT
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127 " >
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128 </form>
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129 </dd>
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130
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131
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132
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133 <dt>Format Test</dt>
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134 <dd>
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135 Ensure that this logo can be created in each of the available formats
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136 <form method="post" action="create.cgi">
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137 <input type="submit" name="cmd_edit" value="Edit" >
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138 <input type="submit" name="cmd_create" value="Create" >
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139 <input type="hidden" name="show_yaxis" value="true" >
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140 <input type="hidden" name="show_xaxis" value="true" >
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141 <input type="hidden" name="show_fineprint" value="true" >
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142 <input type="hidden" name="show_errorbars" value="true" >
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143 <input type="hidden" name="download" value="true" >
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144
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145 Format: <select name="format">
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146 <option value="png_print">PNG</option>
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147 <option value="png">PNG (low res.)</option>
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148 <option value="jpeg">JPEG (low res.)</option>
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149 <option value="eps">EPS (vector)</option>
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150 <option value="pdf">PDF (vector)</option>
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151 <option value="txt">data</option>
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152 </select>
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153
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154 <input type="hidden" name="sequences" value=
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155 ">
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156 AAAGTGAAAGTGAAAGTGAAAGTG
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157 >
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158 AAAGCGAAAGCGAAAGCGAAAGCG
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159 >
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160 TGCCCTTGCCCTTGCCCTTGCCCT
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161 >
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162 TGCCTTTGCCTTTGCCTTTGCCTT
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163 " >
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164 </form>
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165 </dd>
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166
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167
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168
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169
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170 <dt>Test Alphabetic Order</dt>
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171 <dd>
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172 Each character in each stack has the same entropy. The letters
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173 should be alphabetized, top down.
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174 <form method="post" action="create.cgi">
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175 <input type="submit" name="cmd_edit" value="Edit" >
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176 <input type="submit" name="cmd_create" value="Create" >
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177 <input type="hidden" name="show_yaxis" value="true" >
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178 <input type="hidden" name="show_xaxis" value="true" >
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179 <input type="hidden" name="show_fineprint" value="true" >
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180 <input type="hidden" name="show_errorbars" value="true" >
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181 <input type="hidden" name="download" value="true" >
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182 <input type="hidden" name="composition" value="comp_none" >
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183 (NA)
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184 <input type="hidden" name="sequences" value=
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185 ">
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186 AAAGTG
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187 >
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188 AAAGCG
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189 >
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190 TGCCCT
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191 >
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192 TGCCTT
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193 " >
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194 </form>
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195
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196 <form method="post" action="create.cgi">
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197 <input type="submit" name="cmd_edit" value="Edit" >
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198 <input type="submit" name="cmd_create" value="Create" >
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199 <input type="hidden" name="show_yaxis" value="true" >
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200 <input type="hidden" name="show_xaxis" value="true" >
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201 <input type="hidden" name="show_fineprint" value="true" >
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202 <input type="hidden" name="show_errorbars" value="true" > (AA)
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203 <input type="hidden" name="download" value="true" >
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204 <input type="hidden" name="sequences" value=
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205 ">
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206 CA
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207 >
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208 CA
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209 >
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210 VA
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211 >
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212 VG
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213 >
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214 KG
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215 >
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216 KG
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217 " >
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218 </form>
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219 </dd>
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220
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221
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222
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223 <dt>One Single Column</dt>
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224 <dd>
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225 Should not die just because there is only 1 stack.
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226 <form method="post" action="create.cgi">
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227 <input type="submit" name="cmd_edit" value="Edit" >
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228 <input type="submit" name="cmd_create" value="Create" >
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229 <input type="hidden" name="download" value="true" >
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230 <input type="hidden" name="sequences" value=
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231 ">
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232 A
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233 >
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234 A
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235 >
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236 G
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237 >
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238 G
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239 >
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240 G
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241 >
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242 G
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243 " >
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244 </form>
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245 </dd>
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246
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247
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248 <dt> Small Sample Correction Test</dt>
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249 <dd>
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250 The samples per column decrease from 32 (left) to 1 (right).
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251 Before the small sample correction the relative entropy of each stack
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252 is 2 bits.
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253 <form method="post" action="create.cgi">
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254 <input type="submit" name="cmd_edit" value="Edit" >
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255 <input type="submit" name="cmd_create" value="Create" >
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256 <input type="hidden" name="show_yaxis" value="true" >
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257 <input type="hidden" name="show_xaxis" value="true" >
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258 <input type="hidden" name="download" value="true" >
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259 <input type="hidden" name="show_fineprint" value="true" >
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260 <select name="composition" >
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261 <option value = "comp_none" >No adjustment for composition</option>
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262 <option value = "comp_auto" >auto</option>
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263 </select>
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264
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265 <input type="hidden" name="sequences" value=
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266 ">
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267 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
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268 >
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269 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG-
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270 >
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271 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG--
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272 >
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273 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG---
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274 >
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275 GGGGGGGGGGGGGGGGGGGGGGGGGGGG----
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276 >
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277 GGGGGGGGGGGGGGGGGGGGGGGGGGG-----
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278 >
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279 GGGGGGGGGGGGGGGGGGGGGGGGGG------
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280 >
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281 GGGGGGGGGGGGGGGGGGGGGGGGG-------
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282 >
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283 GGGGGGGGGGGGGGGGGGGGGGGG--------
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284 >
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285 GGGGGGGGGGGGGGGGGGGGGGG---------
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286 >
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287 GGGGGGGGGGGGGGGGGGGGGG----------
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288 >
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289 GGGGGGGGGGGGGGGGGGGGG-----------
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290 >
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291 GGGGGGGGGGGGGGGGGGGG------------
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292 >
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293 GGGGGGGGGGGGGGGGGGG-------------
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294 >
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295 GGGGGGGGGGGGGGGGGG--------------
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296 >
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297 GGGGGGGGGGGGGGGG----------------
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298 >
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299 GGGGGGGGGGGGGGG-----------------
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300 >
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301 GGGGGGGGGGGGGG------------------
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302 >
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303 GGGGGGGGGGGGG-------------------
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304 >
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305 GGGGGGGGGGGG--------------------
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306 >
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307 GGGGGGGGGGG---------------------
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308 >
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309 GGGGGGGGGG----------------------
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310 >
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311 GGGGGGGGG-----------------------
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312 >
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313 GGGGGGGG------------------------
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314 >
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315 GGGGGGG-------------------------
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316 >
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317 GGGGGG--------------------------
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318 >
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319 GGGGG---------------------------
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320 >
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321 GGGG----------------------------
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322 >
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323 GGG-----------------------------
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324 >
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325 GG------------------------------
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326 >
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327 G-------------------------------
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328 " >
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329 </form>
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330 </dd>
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331
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332
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333
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334 <dt> Test Graceful Failure</dt>
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335 <dd>
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336 Each of these tests should result in a polite and informative error message.
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337 <form method="post" action="create.cgi">
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338 <input type="submit" name="cmd_create" value="Fail: No sequence data" >
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339 <input type="hidden" name="show_yaxis" value="true" >
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340 <input type="hidden" name="show_xaxis" value="true" >
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341 <input type="hidden" name="show_fineprint" value="true" >
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342 <input type="hidden" name="download" value="true" >
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343 <input type="hidden" name="show_errorbars" checked="checked" >
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344 <input type="hidden" name="sequences" value="" >
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345 </form>
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346
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347 <form method="post" action="create.cgi">
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348 <input type="submit" name="cmd_create" value="Fail: Malformed sequences" >
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349 <input type="hidden" name="show_yaxis" value="true" >
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350 <input type="hidden" name="download" value="true" >
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351 <input type="hidden" name="show_xaxis" value="true" >
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352 <input type="hidden" name="show_fineprint" value="true" >
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353 <input type="hidden" name="show_errorbars" checked="checked" >
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354 <input type="hidden" name="sequences" value="
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355 asdajksgh
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356 >
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357 GGGGGGGGGGGGGG------------------
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358 >
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359 GGGGGGGGGGGGG-------------------
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360 >
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361 " >
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362 </form>
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363
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364 <form method="post" action="create.cgi">
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365 <input type="submit" name="cmd_create" value="Fail: Unknown format" >
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366 <input type="hidden" name="format" value="NO_SUCH_FORMAT" >
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367 <input type="hidden" name="show_yaxis" value="true" >
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368 <input type="hidden" name="show_xaxis" value="true" >
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369 <input type="hidden" name="show_fineprint" value="true" >
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370 <input type="hidden" name="show_errorbars" checked="checked" >
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371 <input type="hidden" name="download" value="true" >
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372 <input type="hidden" name="sequences" value=">
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373 GGGGGGGGGGGGGG------------------
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374 >
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375 GGGGGGGGGGGGG-------------------
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376 >
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377 " >
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378 </form>
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379
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380 <form method="post" action="create.cgi">
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381 <input type="submit" name="cmd_create" value="Fail: Malformed data" >
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382 <input type="hidden" name="show_yaxis" value="true" >
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383 <input type="hidden" name="show_xaxis" value="true" >
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384 <input type="hidden" name="download" value="true" >
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385 <input type="hidden" name="show_fineprint" value="true" >
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386 <input type="hidden" name="show_errorbars" checked="checked" >
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387 <input type="hidden" name="sequences" value=">
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388 GGGGGGGGGGGGGG------------------
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389 >
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390 GGGGGGGGGGGGG------------------
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391 >
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392 " >
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393 </form>
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394
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395
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396 </dd>
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397
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398
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399
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400 <dt> Logos Sizes</dt>
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401 <dd>
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402 Same sequences, three different sizes.
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403 <form method="post" action="create.cgi">
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404 <input type="submit" name="cmd_edit" value="Edit" >
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405 <input type="hidden" name="download" value="true" >
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406 <input type="submit" name="cmd_create" value="Create" >
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407 <input type="hidden" name="show_yaxis" value="true" >
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408 <input type="hidden" name="show_xaxis" value="true" >
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409 <input type="hidden" name="show_fineprint" value="true" >
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410 Size:
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411 <select name="size" >
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412 <option selected="selected" >small</option>
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413 <option >medium</option>
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414 <option >large</option>
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415 </select>
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416
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417
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418 <input type="hidden" name="sequences" value=
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419 ">aldB -18->4
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420 attcgtgatagctgtcgtaaag
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421 >ansB 103->125
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422 ttttgttacctgcctctaactt
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423 >araB1 109->131
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424 aagtgtgacgccgtgcaaataa
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425 >araB2 147->169
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426 tgccgtgattatagacactttt
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427 >cdd 1 107->129
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428 atttgcgatgcgtcgcgcattt
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429 >cdd 2 57->79
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430 taatgagattcagatcacatat
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431 >crp 1 115->137
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432 taatgtgacgtcctttgcatac
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433 >crp 2
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434 gaaggcgacctgggtcatgctg
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435 >cya 151->173
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436 aggtgttaaattgatcacgttt
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437 >cytR 1 125->147
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438 cgatgcgaggcggatcgaaaaa
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439 >cytR 2 106->128
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440 aaattcaatattcatcacactt
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441 >dadAX 1 95->117
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442 agatgtgagccagctcaccata
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443 >dadAX 2 32->54
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444 agatgtgattagattattattc
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445 >deoP2 1 75->97
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446 aattgtgatgtgtatcgaagtg
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447 >deoP2 2 128->150
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448 ttatttgaaccagatcgcatta
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449 >fur 136->158
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450 aaatgtaagctgtgccacgttt
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451 >gal 56->78
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452 aagtgtgacatggaataaatta
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453 >glpACB (glpTQ) 1 54->76
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454 ttgtttgatttcgcgcatattc
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455 >glpACB (glpTQ) 2 94->116
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456 aaacgtgatttcatgcgtcatt
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457 >glpACB (glpTQ) 144->166
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458 atgtgtgcggcaattcacattt
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459 >glpD (glpE) 95->117
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460 taatgttatacatatcactcta
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461 >glpFK 1 120->142
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462 ttttatgacgaggcacacacat
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463 >glpFK 2 95->117
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464 aagttcgatatttctcgttttt
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465 >gut (srlA) 72->94
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466 ttttgcgatcaaaataacactt
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467 >ilvB 87->109
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468 aaacgtgatcaacccctcaatt
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469 >lac 1 (lacZ) 88->110
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470 taatgtgagttagctcactcat
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471 >lac 2 (lacZ) 16->38
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472 aattgtgagcggataacaattt
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473 >malEpKp1 110->132
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474 ttgtgtgatctctgttacagaa
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475 >malEpKp2 139->161
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476 TAAtgtggagatgcgcacaTAA
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477 >malEpKp3 173->195
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478 TTTtgcaagcaacatcacgAAA
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479 >malEpKp4 205->227
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480 GACctcggtttagttcacaGAA
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481 >malT 121->143
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482 aattgtgacacagtgcaaattc
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483 >melR 52->74
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484 aaccgtgctcccactcgcagtc
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485 >mtl 302->324
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486 TCTTGTGATTCAGATCACAAAG
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487 >nag 156->178
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488 ttttgtgagttttgtcaccaaa
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489 >nupG2 97->119
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|
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490 aaatgttatccacatcacaatt
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491 >nupG1 47->69
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|
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492 ttatttgccacaggtaacaaaa
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493 >ompA 166->188
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494 atgcctgacggagttcacactt
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495 >ompR 161->183
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496 taacgtgatcatatcaacagaa
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497 >ptsH A 316->338
|
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498 Ttttgtggcctgcttcaaactt
|
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499 >ptsH B 188->210
|
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500 ttttatgatttggttcaattct
|
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501 >rhaS (rhaB) 161->183
|
|
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502 aattgtgaacatcatcacgttc
|
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503 >rot 1 (ppiA) 182->204
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|
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504 ttttgtgatctgtttaaatgtt
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505 >rot 2 (ppiA) 129->151
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506 agaggtgattttgatcacggaa
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507 >tdcA 60->82
|
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508 atttgtgagtggtcgcacatat
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509 >tnaL 73->95
|
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510 gattgtgattcgattcacattt
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511 >tsx 2 146->168
|
|
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512 gtgtgtaaacgtgaacgcaatc
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|
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513 >tsx 1 107->129
|
|
|
514 aactgtgaaacgaaacatattt
|
|
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515 >uxuAB 165->187
|
|
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516 TCTTGTGATGTGGTTAACCAAT
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517 " >
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518 </form>
|
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519 </dd>
|
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520
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521
|
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522
|
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523
|
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524 </dl>
|
|
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525
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526
|
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527
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528 </td></tr>
|
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529
|
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530
|
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531
|
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532
|
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533 </table>
|
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534
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535 <script type="text/javascript">
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536 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
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537 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
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538 </script>
|
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539 <script type="text/javascript">
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540 var pageTracker = _gat._getTracker("UA-5951066-1");
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541 pageTracker._trackPageview();
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542 </script>
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543 </body></html>
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