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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
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8 <title>CodonLogo 1.0- Create </title>
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9 <meta name="author" content="Gavin E. Crooks" >
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10
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11
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12 <style type="text/css">
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13 td {
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14 border-left : white solid 4pt
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15 }
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16 .error {
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17 color: #900;
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18 border-left: red solid +4pt;
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19 }
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20
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21 .err_msg {
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22 color: #900;
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23 }
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24
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25 </style>
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26 </head>
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27
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28 <body style="align:center">
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29
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30
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31
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32
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33
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34 <form method="post" action="create.cgi" enctype="multipart/form-data" >
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35 <table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
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36 <tr><td >
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37 <h1> Codonlogo 1.0 : Create</h1>
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38
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39 </td><td align = "right">
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40 ·
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41 <a href="./">about</a> ·
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42 <a class="selected" href="create.cgi">create</a> ·
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43 <a href="examples.html">examples</a> ·
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44 <a href="manual.html">manual</a> ·
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45 <br>
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46 <span style="font-size:small">$version</span>
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47 </td></tr>
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48
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49 <tr><td >
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50 Sequence data
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51 </td><td >
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52 <input type="file" name="sequences_file" >
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53 </td></tr>
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54
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55 <tr><td >
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56 </td><td>
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57 <span style="font-size:small ">(or paste sequence data below)</span>
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58 </td></tr>
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59
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60
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61
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62 <tr><td colspan='2' ${sequences_err} >
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63 <textarea name="sequences" rows="12" cols ="100" style="width:100%">${sequences}</textarea>
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64 </td></tr>
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65
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66
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67
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68 <tr><td>
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69 </td><td align="right">
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70 <input style="font-size:large" type="submit" name="cmd_create" value=" Create Logo " > <br>
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71 <span style="font-size:small"><input type="checkbox" name="download" value="false" >Download</span>
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72 </td></tr>
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73
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74
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75 <!-- Reset defaults must come after create_logo so that hitting enter creates a logo-->
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76 <!--
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77 <tr><td>
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78 <input type="submit" name="cmd_reset" value="Reset defaults" >
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79 </td><td class="err_msg" rowspan="2">
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80 ${error_message}
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81 </td></tr>
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82 <tr><td> </td></tr>
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83 -->
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84
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85 <tr><td colspan='2' style="height:30pt;border-left-width:90pt;" class="err_msg">
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86 ${error_message}
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87 </td></tr>
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88
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89
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90
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91 <tr><td ${format_err} >
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92 Output format </td><td>
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93 <select name="format">
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94 <option ${png} value="png">PNG (low res.)</option>
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95 <option ${png_print} value="png_print">PNG (high res.)</option>
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96 <option ${jpeg} value="jpeg">JPEG (low res.)</option>
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97 <option ${eps} value="eps">EPS (vector)</option>
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98 <option ${pdf} value="pdf">PDF (vector)</option>
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99 <option ${txt} value="txt">Data (plain text)</option>
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100 </select>
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101
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102 </td></tr>
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103
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104 <tr><td ${size_err} >
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105 Logo size
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106 </td><td >
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107 <select name="size" >
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108 <option ${small} >small</option>
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109 <option ${medium}>medium</option>
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110 <option ${large} >large</option>
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111 </select>
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112 </td></tr>
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113
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114
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115 <tr><td ${stacks_per_line_err}>
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116 Stacks per line
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117 </td><td>
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118 <input type="text" name="stacks_per_line" value="${stacks_per_line}" size="4" maxlength="4" >
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119 </td></tr>
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120
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121 <tr><td ${alphabet_err}>
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122 Sequence type </td><td>
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123
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124 <select name="alphabet">
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125 <option ${alphabet_auto} value="alphabet_auto" >auto</option>
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126 <option ${alphabet_protein} value="alphabet_protein">protein</option>
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127 <option ${alphabet_dna} value="alphabet_dna">dna</option>
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128 <option ${alphabet_rna} value="alphabet_rna">rna</option>
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129 </select>
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130 </td></tr>
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131
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132 <tr><td>
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133 Ignore lower case
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134 </td><td>
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135 <input type="checkbox" name="ignore_lower_case" value="true" ${ignore_lower_case} >
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136 </td></tr>
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137
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138 <tr><td>
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139 Use codons:
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140 </td><td>
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141 <input type="checkbox" name="altype" value="true" ${altype} >
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142 </td></tr>
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143
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144
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145 <tr><td>
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146 Units </td><td>
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147 <select name="unit_name" >
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148 <option ${probability} >probability</option>
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149 <option ${bits} >bits</option>
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150 <option ${nats} >nats</option>
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151 <option ${kT} >kT</option>
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152 <option ${kJ_mol} >kJ/mol</option>
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153 <option ${kcal_mol} >kcal/mol</option>
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154 </select>
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155
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156 </td></tr>
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157
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158 <tr><td ${first_index_err}>
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159 First position number
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160 </td><td>
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161 <input type="text" name="first_index" value="${first_index}" size="4" maxlength="80" >
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162 </td></tr>
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163
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164 <tr><td ${logo_range_err} >
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165 Logo range </td><td>
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166 <input type="text" name="logo_start" value="${logo_start}" size="4" maxlength="80" > - <input type="text" name="logo_end" value="${logo_end}" size="4" maxlength="80" >
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167 </td></tr>
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168
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169
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170
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171 <tr><td ${composition_err}>
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172 Composition
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173 </td><td>
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174 <select name="composition" >
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175 <option ${comp_none} value = "comp_none" >No adjustment for composition</option>
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176 <option ${comp_auto} value = "comp_auto" >auto</option>
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177 <option ${comp_equiprobable} value = "comp_equiprobable" >equiprobable</option>
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178 <option ${comp_CG} value="comp_CG" >Percentage CG ⇒</option>
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179 <option ${comp_Celegans} value="comp_Celegans" >C. elegans (36%) </option>
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180 <option ${comp_Dmelanogaster} value="comp_Dmelanogaster" >D. melanogaster (43%)</option>
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181 <option ${comp_Ecoli} value="comp_Ecoli" >E. coli (50.5%) </option>
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182 <option ${comp_Hsapiens} value="comp_Hsapiens" >H. sapiens (40%) </option>
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183 <option ${comp_Mmusculus} value="comp_Mmusculus" >M. musculus (42%)</option>
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184 <option ${comp_Scerevisiae} value="comp_Scerevisiae" >S. cerevisiae (38%) </option>
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185 </select>
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186 or
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187 <input type="text" name="percentCG" value="${percentCG}" size="4" maxlength="8" > % CG
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188 </td></tr>
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189
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190 <tr><td>
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191 Scale stack widths
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192 </td><td>
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193 <input type="checkbox" name="scale_width" value="true" ${scale_width} >
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194 </td></tr>
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195
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196 <tr><td>
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197 Error bars
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198 </td><td>
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199 <input type="checkbox" name="show_errorbars" value="true" ${show_errorbars} >
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200 </td></tr>
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201
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202
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203
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204
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205
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206
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207 <tr ><td ${logo_title_err}>
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208 Title
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209 </td><td >
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210 <input type="text" name="logo_title" size="52" maxlength="80" value="${logo_title}" >
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211 </td></tr>
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212
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213 <tr><td>
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214 Figure label</td><td>
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215 <input type="text" name="logo_label" value="${logo_label}" size="4" maxlength="100" >
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216 </td></tr>
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217
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218
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219 <tr><td>
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220 X-axis
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221 </td><td>
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222 <input type="checkbox" name="show_xaxis" value="true" ${show_xaxis} >
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223 Label:
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224 <input type="text" name="xaxis_label" value="${xaxis_label}" size="20" maxlength="100" >
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225 </td></tr>
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226
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227
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228 <tr><td>
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229 Y-axis
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230 </td><td>
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231 <input type="checkbox" name="show_yaxis" value="true" ${show_yaxis} >
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232 Label: <input type="text" name="yaxis_label" value="${yaxis_label}" size="20" maxlength="32" >
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233
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234 </td></tr>
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235
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236 <tr><td ${yaxis_scale_err} >
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237 Y-axis scale:
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238 </td><td>
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239 <input type="text" name="yaxis_scale" value="${yaxis_scale}" size="4" maxlength="100" >
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240 </td></tr>
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241
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242 <tr><td ${yaxis_tic_interval_err} >
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243 Y-axis tic spacing:
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244 </td><td>
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245 <input type="text" name="yaxis_tic_interval" value="${yaxis_tic_interval}" size="4" maxlength="100" >
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246 </td></tr>
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247
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248
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249
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250 <tr><td>
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251 Sequence end labels
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252 </td><td>
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253 <input type="checkbox" name="show_ends" value="true" ${show_ends} >
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254 </td></tr>
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255
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256 <tr><td>
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257 Version fineprint
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258 </td><td>
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259 <input type="checkbox" name="show_fineprint" value="true" ${show_fineprint} >
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260 </td></tr>
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261
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262
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263
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264
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265 <tr><td ${color_scheme_err}>Color scheme
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266 </td><td>
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267 <select name="color_scheme" >
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268 <option ${color_auto} value="color_auto">Auto</option>
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269 <option ${color_monochrome} value="color_monochrome" >Monochrome</option>
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270 <option ${color_base_pairing} value="color_base_pairing">Base pairing (NA default)</option>
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271 <option ${color_classic} value="color_classic">Classic (NA)</option>
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272 <option ${color_hydrophobicity} value="color_hydrophobicity">Hydrophobicity (AA default)</option>
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273 <option ${color_chemistry} value="color_chemistry">Chemistry (AA)</option>
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274 <option ${color_charge} value="color_charge">Charge (AA)</option>
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275 <option ${color_custom} value="color_custom">Custom (Specify below)</option>
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276 </select>
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277 <!-- Color key:
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278 <input type="checkbox" name="show_color_key" value="true" ${show_color_key} disabled >
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279 -->
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280 </td></tr>
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281
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282 <tr><td></td><td>
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283 <table cellpadding="0" cellspacing="0" style="font-size:small">
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284 <tr>
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285 <td>Symbols</td><td>Color</td> <!--<td>Description</td>-->
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286 </tr>
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287
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288 <tr >
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289 <td ${color0_err}><input name="symbols0" type="text" size="16" maxlength="64" value="${symbols0}"></td>
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290 <td><input name="color0" type="text" size="16" maxlength="64" value="${color0}"></td>
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291 <!--<td><input name="desc0" size="16" maxlength="64" value="${desc0}"></td> -->
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292 </tr>
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293
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294 <tr >
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295 <td ${color1_err}><input name="symbols1" type="text" size="16" maxlength="64" value="${symbols1}"></td>
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296 <td><input name="color1" type="text" size="16" maxlength="64" value="${color1}"></td>
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297 <!--<td><input name="desc1" size="16" maxlength="64" value="${desc1}"></td>-->
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298 </tr>
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299
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300 <tr>
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301 <td ${color2_err}><input name="symbols2" type="text" size="16" maxlength="64" value="${symbols2}"></td>
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302 <td><input name="color2" type="text" size="16" maxlength="64" value="${color2}"></td>
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303 <!--<td><input name="desc2" size="16" maxlength="64" value="${desc2}"></td>-->
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304 </tr>
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305
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306 <tr>
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307 <td ${color3_err}><input name="symbols3" type="text" size="16" maxlength="64" value="${symbols3}"></td>
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308 <td><input name="color3" type="text" size="16" maxlength="64" value="${color3}"></td>
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309 <!--<td><input name="desc3" size="16" maxlength="64" value="${desc3}"></td>-->
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310 </tr>
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311
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312 <tr>
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313 <td ${color4_err}><input name="symbols4" type="text" size="16" maxlength="64" value="${symbols4}"></td>
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314 <td><input name="color4" type="text" size="16" maxlength="64" value="${color4}"></td>
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315 <!--<td><input name="desc4" size="16" maxlength="64" value="${desc4}"></td>-->
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316 </tr>
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317
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318
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319
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320 </table>
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321 </td></tr>
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322
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323 <tr><td>
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324
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325 </td><td>
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326
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327 </td></tr>
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328
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329 <tr><td>
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330 <input type="submit" name="cmd_reset" value="Reset defaults" >
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331 </td><td align="right">
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332 <input style="font-size:large" type="submit" name="cmd_create" value=" Create Logo " >
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333 </td></tr>
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334
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335
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336
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337
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338 </table>
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339 </form>
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340
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341 <script type="text/javascript">
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342 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
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343 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
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344 </script>
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345 <script type="text/javascript">
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346 var pageTracker = _gat._getTracker("UA-5951066-1");
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347 pageTracker._trackPageview();
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348 </script>
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349 </body>
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350 </html>
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