Mercurial > repos > iuc > meme_dreme

annotate test-data/fimo_output_test2.html @ 1:cb8a2242bf03 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:11:27 -0400
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cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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2 <html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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3 <head>
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4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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5 <meta charset="UTF-8">
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6 <title>FIMO Results</title>
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7 <style type="text/css">
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8 td.left {text-align: left;}
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9 td.right {text-align: right; padding-right: 1cm;}
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10 </style>
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11 </head>
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12 <body bgcolor="#D5F0FF">
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13 <a name="top_buttons"></a>
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14 <hr>
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15 <table summary="buttons" align="left" cellspacing="0">
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16 <tr>
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17 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
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18 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
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19 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
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20 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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21 </table>
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22 <br/>
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23 <br/>
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24 <hr/>
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25 <center><big><b>FIMO - Motif search tool</b></big></center>
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26 <hr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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27 <p>
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28 FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)
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29 </p>
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30 <p>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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31 For further information on how to interpret these results
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32 or to get a copy of the FIMO software please access
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33 <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
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34 <p>If you use FIMO in your research, please cite the following paper:<br>
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35 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
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36 "FIMO: Scanning for occurrences of a given motif",
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37 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
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38 <a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>
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39 <hr>
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40 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
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41 <hr>
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42 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
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43 <p>
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44 DATABASE hsa_chrM.fa
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45 <br />
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46 Database contains 1 sequences, 16569 residues
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47 </p>
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48 <p>
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49 MOTIFS dreme_fimo_input_1.xml (DNA)
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50 <table>
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51 <thead>
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52 <tr>
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53 <th style="border-bottom: 1px dashed;">MOTIF</th>
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54 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
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55 <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
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56 BEST POSSIBLE MATCH
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57 </th>
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58 </tr>
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59 </thead>
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60 <tbody>
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61 <tr>
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62 <td style="text-align:right;">ACTAAYH</td>
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63 <td style="text-align:right;padding-left: 1em;">7</td>
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64 <td style="text-align:left;padding-left: 1em;">ACTAACA</td>
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65 </tr>
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66 <tr>
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67 <td style="text-align:right;">YTAACA</td>
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68 <td style="text-align:right;padding-left: 1em;">6</td>
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69 <td style="text-align:left;padding-left: 1em;">TTAACA</td>
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70 </tr>
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71 <tr>
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72 <td style="text-align:right;">TCTGT</td>
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73 <td style="text-align:right;padding-left: 1em;">5</td>
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74 <td style="text-align:left;padding-left: 1em;">TCTGT</td>
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75 </tr>
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76 <tr>
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77 <td style="text-align:right;">SCCAGG</td>
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78 <td style="text-align:right;padding-left: 1em;">6</td>
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79 <td style="text-align:left;padding-left: 1em;">CCCAGG</td>
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80 </tr>
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81 <tr>
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82 <td style="text-align:right;">CCAGCAY</td>
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83 <td style="text-align:right;padding-left: 1em;">7</td>
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84 <td style="text-align:left;padding-left: 1em;">CCAGCAC</td>
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85 </tr>
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86 <tr>
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87 <td style="text-align:right;">GMATGT</td>
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88 <td style="text-align:right;padding-left: 1em;">6</td>
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89 <td style="text-align:left;padding-left: 1em;">GAATGT</td>
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90 </tr>
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91 </tbody>
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92 </table>
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93 </p>
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94 <p>
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95 Random model letter frequencies (fimo_background_probs_hsa_chrM.txt):
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96 <br/>
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97
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98 A 0.278 C 0.222 G 0.222 T 0.278 </p>
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99 </div>
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100 <hr>
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101 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
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102 <hr>
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103 <ul>
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104 <li>
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105 There were 11 motif occurences with a p-value less than 0.0001.
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106
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107 The full set of motif occurences can be seen in the
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108 tab-delimited plain text output file
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109 <a href="fimo.txt">fimo.txt</a>,
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110 the GFF file
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111 <a href="fimo.gff">fimo.gff</a>
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112 which may be suitable for uploading to the
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113 <a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
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114 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
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115 or the XML file
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116 <a href="fimo.xml">fimo.xml</a>.
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117 </li>
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118 <li>
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119 The p-value of a motif occurrence is defined as the
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120 probability of a random sequence of the same length as the motif
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121 matching that position of the sequence with as good or better a score.
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122 </li>
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123 <li>
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124 The score for the match of a position in a sequence to a motif
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125 is computed by summing the appropriate entries from each column of
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126 the position-dependent scoring matrix that represents the motif.
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127 </li>
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128 <li>
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129 The q-value of a motif occurrence is defined as the
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130 false discovery rate if the occurrence is accepted as significant.
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131 </li>
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132 <li>The table is sorted by increasing p-value.</li>
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133 </ul>
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134 <table border="1">
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135 <thead>
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136 <tr>
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137 <th>Motif ID</th>
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138 <th>Alt ID</th>
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139 <th>Sequence Name</th>
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140 <th>Strand</th>
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141 <th>Start</th>
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142 <th>End</th>
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143 <th>p-value</th>
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144 <th>q-value</th>
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145 <th>Matched Sequence</th>
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146 </tr>
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147 </thead>
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148 <tbody>
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149 <tr>
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150 <td style="text-align:left;">CCAGCAY</td>
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151 <td style="text-align:left;">DREME-5</td>
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152 <td style="text-align:left;">chrM</td>
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153 <td style="text-align:center;">+</td>
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154 <td style="text-align:left;">510</td>
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155 <td style="text-align:left;">516</td>
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156 <td style="text-align:left;">4.15e-05</td>
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iuc
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157 <td style="text-align:left;">0.668</td>
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158 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
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159 </tr>
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160 <tr>
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161 <td style="text-align:left;">CCAGCAY</td>
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162 <td style="text-align:left;">DREME-5</td>
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163 <td style="text-align:left;">chrM</td>
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164 <td style="text-align:center;">+</td>
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165 <td style="text-align:left;">5137</td>
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iuc
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166 <td style="text-align:left;">5143</td>
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167 <td style="text-align:left;">4.15e-05</td>
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iuc
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168 <td style="text-align:left;">0.668</td>
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169 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
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170 </tr>
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171 <tr>
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172 <td style="text-align:left;">ACTAAYH</td>
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173 <td style="text-align:left;">DREME-1</td>
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174 <td style="text-align:left;">chrM</td>
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175 <td style="text-align:center;">+</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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diff changeset
176 <td style="text-align:left;">440</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
177 <td style="text-align:left;">446</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
178 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
179 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
180 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
181 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
182 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
183 <td style="text-align:left;">ACTAAYH</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
184 <td style="text-align:left;">DREME-1</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
185 <td style="text-align:left;">chrM</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
186 <td style="text-align:center;">-</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
187 <td style="text-align:left;">2093</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
188 <td style="text-align:left;">2099</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
189 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
190 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
191 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
192 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
193 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
194 <td style="text-align:left;">ACTAAYH</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
195 <td style="text-align:left;">DREME-1</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
196 <td style="text-align:left;">chrM</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
197 <td style="text-align:center;">-</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
198 <td style="text-align:left;">2299</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
199 <td style="text-align:left;">2305</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
200 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
201 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
202 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
203 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
204 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
205 <td style="text-align:left;">ACTAAYH</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
206 <td style="text-align:left;">DREME-1</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
207 <td style="text-align:left;">chrM</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
208 <td style="text-align:center;">+</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
209 <td style="text-align:left;">5186</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
210 <td style="text-align:left;">5192</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
211 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
212 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
213 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
214 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
215 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
216 <td style="text-align:left;">ACTAAYH</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
217 <td style="text-align:left;">DREME-1</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
218 <td style="text-align:left;">chrM</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
219 <td style="text-align:center;">+</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
220 <td style="text-align:left;">6530</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
221 <td style="text-align:left;">6536</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
222 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
223 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
224 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
225 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
226 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
227 <td style="text-align:left;">ACTAAYH</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
228 <td style="text-align:left;">DREME-1</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
229 <td style="text-align:left;">chrM</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
230 <td style="text-align:center;">+</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
231 <td style="text-align:left;">7742</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
232 <td style="text-align:left;">7748</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
233 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
234 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
235 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
236 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
237 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
238 <td style="text-align:left;">ACTAAYH</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
239 <td style="text-align:left;">DREME-1</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
240 <td style="text-align:left;">chrM</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
241 <td style="text-align:center;">+</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
242 <td style="text-align:left;">13657</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
243 <td style="text-align:left;">13663</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
244 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
245 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
246 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
247 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
248 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
249 <td style="text-align:left;">ACTAAYH</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
250 <td style="text-align:left;">DREME-1</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
251 <td style="text-align:left;">chrM</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
252 <td style="text-align:center;">+</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
253 <td style="text-align:left;">13741</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
254 <td style="text-align:left;">13747</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
255 <td style="text-align:left;">8.2e-05</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
256 <td style="text-align:left;">0.327</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
257 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
258 </tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
259 <tr>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
260 <td style="text-align:left;">CCAGCAY</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
261 <td style="text-align:left;">DREME-5</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
diff changeset
262 <td style="text-align:left;">chrM</td>
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263 <td style="text-align:center;">+</td>
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264 <td style="text-align:left;">4241</td>
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265 <td style="text-align:left;">4247</td>
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266 <td style="text-align:left;">9.37e-05</td>
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267 <td style="text-align:left;">1</td>
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268 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAT</td>
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269 </tr>
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270 </tbody>
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271 </table>
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272
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273 <hr>
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274 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
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275 <hr>
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276 <p>
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277 Command line:
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278 </p>
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279 <pre>
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280 fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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281 </pre>
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282 <p>
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283 Settings:
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284 </p>
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285 <pre>
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286 <table>
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287 <tr>
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288 <td style="padding-right: 2em">output_directory = fimo_test2_out</td>
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289 <td style="padding-left: 5em; padding-right: 2em">MEME file name = dreme_fimo_input_1.xml</td>
cb8a2242bf03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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290 <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>
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291 </tr> <tr>
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292 <td style="padding-right: 2em">background file name = fimo_background_probs_hsa_chrM.txt</td>
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293 <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
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294 <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
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295 </tr> <tr>
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296 <td style="padding-right: 2em">allow clobber = true</td>
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297 <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
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298 <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td>
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299 </tr>
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300 <tr>
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301 <td style="padding-right: 2em">text only = false</td>
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302 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
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303 <td style="padding-left: 5em; padding-right: 2em">max strand = false</td>
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304 </tr>
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305 <tr>
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306 <td style="padding-right: 2em">threshold type = p-value</td>
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307 <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
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308 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
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309 </tr>
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310 <tr>
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311 <td style="padding-right: 2em">alpha = 1</td>
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312 <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
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313 <td style="padding-left: 5em; padding-right: 2em"></td>
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314 </tr>
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315
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316 </table>
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317 </pre>
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318 <p>
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319 This information can be useful in the event you wish to report a
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320 problem with the FIMO software.
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321 </p>
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322 <hr>
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323 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
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324 </body>
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325 </html>