Mercurial > repos > iss > eurl_vtec_wgs_pt

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"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
author iss
date Mon, 21 Mar 2022 15:23:09 +0000
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1 <!DOCTYPE html><html><head><title>EURL VTEC Typer summary report</title>
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2 <style type="text/css">
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3 body {font-family:"sans-serif","lucida Sans Unicode","Lucida Grande","Segoe UI";font-size:13px;}
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4 h1 {font-weight:normal;font-size:2em;margin-top:0.3em;margin-bottom:0.3em;}
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5 h4 {font-size:1.17em;margin-top:0;margin-bottom:0;}
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6 .table-head td {border:1px solid #73ad21;border-radius:6px;}
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7 .table-rep {border-collapse:collapse;font-size:13px;margin:auto;}
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8 .table-rep th, .table-rep td {padding:5px 5px;}
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9 .table-rep .title {caption-side:top;margin-top:12px;margin-bottom:6px;font-size:24px;text-align:left;}
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10 .table-rep tbody td:last-child {border:0;}
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11 .table-rep thead th:last-child {border:0; border-bottom: 1px solid #d7e1da;}
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12 .table-rep thead th {border-right:1px solid #d7e1da;border-bottom:1px solid #d7e1da;}
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13 .table-rep tbody td {color:#353535;border-right:1px solid #d7e1da;text-align:right;}
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14 .table-rep tbody tr:nth-child(odd) td {background-color:#f4fff7;}
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15 .table-rep tbody tr:nth-child(even) td {background-color:#e2e2e2;}
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16 .table-cross tbody td {color:#353535;border-right:1px solid #d7e1da;text-align:right;}
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17 .table-cross {border-collapse:collapse;font-size:13px;margin:auto;}
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18 .table-cross th, .table-cross td {max-width:220px; word-wrap:break-word;}
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19 .table-cross tr:nth-child(2n+1) {background: rgba(178, 178, 178, 0.5) none repeat scroll 0 0;}
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20 .table-cross th:nth-child(2n), .table-cross td:nth-child(2n) {background: rgba(178, 178, 178, 0.5) none repeat scroll 0 0;}
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21 </style> <meta charset='utf-8'>
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22 <body><div style="border: 1px solid #73ad21;max-width:940px;text-align:center;margin:auto;"></br>
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23 <table class="table table-head"><tr><td width="25%"><img src='https://aries.iss.it/static/images/aries.jpg' alt='ARIES' style='float:left;width:50%;padding-left:0.5cm;'>
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24 <img src='https://aries.iss.it/static/images/isseurlvtec.png' alt='ISS-EURL VTEC' style='float:left;width:30%'></td>
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25 <td><h1>EURL VTEC Typer</h1><h2>Report for Strain_1_L2.fastq</h2>2018-05-17 11:16 UTC</td><td style='width: 25%; padding-left: 0.2cm; text-align: left;'><h4>Istituto Superiore di Sanità</h4>
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26 Department of Food Safety, Nutrition and Veterinary Public Health<br/>European Union Reference Laboratory for <i>E. coli</i></td></tr></table>
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27 <h3>Summary</h3>
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28 O26:H11<br/>ST21<br/><p>eae, ehxa, stx1a, stx1b
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29 </p>
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30 <br/><hr/><h3>Raw data quality check</h3>
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31 <p>FASTQC result: <a href='https://galaxy.iss.it/datasets/4b25789cdf945d7e/display/?preview=True'>Webpage</a></p>
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32 <br/><hr/><h3>Trimming analysis</h3>
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33 <table cellpadding="4" class="table table-rep">
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34 <tr><td>Maximum length trimming</td><td>360</td></tr>
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35 <tr><td>Left-side trimming</td><td>10</td></tr>
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36 <tr><td>Right-side trimming</td><td>0</td></tr>
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37 <tr><td>Minimum Phred quality score for right-side trimming</td><td>25</td></tr>
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38 <tr><td>Average Phred quality score for right-side trimming</td><td>27</td></tr>
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39 <tr><td>Minimum length filtering</td><td>50</td></tr>
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40 </table><br/><hr/><h3>Assembly statistics</h3>
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41 <table cellpadding="4" class="table table-rep">
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42 <tr><td>Estimated genome size:</td><td>5000000 bp
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43 </td></tr>
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44 <tr><td>Assembled nucleotides:</td><td>5493390 bp
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45 </td></tr>
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46 <tr><td>Estimated coverage:</td><td>1.1 x
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47 </td></tr>
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48 <tr><td>N. contigs:</td><td>315
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49 </td></tr>
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50 <tr><td>Average contig length:</td><td>17439
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51 </td></tr>
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52 <tr><td>Median contig length:</td><td>4504
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53 </td></tr>
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54 <tr><td>Maximum contig length:</td><td>164788
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55 </td></tr>
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56 <tr><td>N. contigs >= 200 bp:</td><td>315 (100.0 %)
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57 </td></tr>
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58 <tr><td>N. contigs >= 2,000 bp:</td><td>224 (71.1 %)
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59 </td></tr>
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60 <tr><td>N50:</td><td>52450
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61 </td></tr>
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62 <tr><td>NG50:</td><td>59152
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63 </td></tr>
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64 </table><br/><hr/><h3>Serotyping</h3>
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65 <table cellpadding="4" class="table table-rep">
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66 <tr><th>sseqid</th><th>pident</th><th>length</th><th>positive
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67 </th></tr>
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68 <tr><td>wzx_208_AF529080_O26</td><td>100.00</td><td>1263</td><td>1263
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69 </td></tr>
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70 <tr><td>wzy_192_AF529080_O26</td><td>100.00</td><td>1023</td><td>1023
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71 </td></tr>
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72 <tr><td>fliC_269_AY337465_H11</td><td>99.93</td><td>1459</td><td>1458
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73 </td></tr>
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74 <tr><td>fliC_276_AY337472_H11</td><td>99.79</td><td>1459</td><td>1456
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75 </td></tr>
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76 </table><br/><hr/><h3>Multi Locus Sequence Typing</h3>
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77 <table cellpadding="4" class="table table-rep">
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78 <tr><th>Sample</th><th>ST</th><th>adk</th><th>fumC</th><th>gyrB</th><th>icd</th><th>mdh</th><th>purA</th><th>recA</th><th>mismatches</th><th>uncertainty</th><th>depth</th><th>maxMAF
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79 </th></tr>
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80 <tr><td>dataset_10081</td><td>21</td><td>16</td><td>4</td><td>12</td><td>16</td><td>9</td><td>7</td><td>7</td><td>0</td><td>-</td><td>31.5927142857</td><td>0.333333333333
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81 </td></tr>
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82 </table><br/><hr/><h3>Virulotyping</h3>
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83 <p>This table is filtered for results with >90% gene coverage, unfiltered results can be found <a href='https://galaxy.iss.it/datasets/977c7565c45fc8c2/display/?preview=True'>here</a></p>
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84 <table cellpadding="4" class="table table-cross">
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85 <tr><th>#gene</th><th>percentage gene coverage</th><th>gene mean read coverage</th><th>percentage gene identity
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86 </th></tr>
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87 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/hm138194'>ehxa_7_hm138194</a></td><td>100.0</td><td>22.75</td><td>100.0
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88 </td></tr>
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89 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ae005174'>nlea_8_ae005174</a></td><td>99.92</td><td>27.36</td><td>99.85
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90 </td></tr>
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91 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af540491'>celb_8_af540491</a></td><td>100.0</td><td>254.92</td><td>98.61
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92 </td></tr>
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93 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/cu928160'>iss_13_cu928160</a></td><td>100.0</td><td>28.49</td><td>99.71
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94 </td></tr>
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95 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/cp001164'>nlea_7_cp001164</a></td><td>99.92</td><td>17.8</td><td>99.85
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96 </td></tr>
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97 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010960'>nlea_13_ap010960</a></td><td>93.95</td><td>14.56</td><td>99.92
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98 </td></tr>
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99 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab011549'>katp_1_ab011549</a></td><td>100.0</td><td>108.79</td><td>100.0
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100 </td></tr>
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101 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af054421'>espb_13_af054421</a></td><td>93.12</td><td>10.91</td><td>99.89
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102 </td></tr>
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103 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab456530'>toxb_3_ab456530</a></td><td>100.0</td><td>27.15</td><td>99.98
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104 </td></tr>
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105 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/am230663'>stx1b_14_am230663_a</a></td><td>100.0</td><td>18.51</td><td>100.0
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106 </td></tr>
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107 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/x06119'>celb_9_x06119</a></td><td>100.0</td><td>177.13</td><td>99.31
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108 </td></tr>
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109 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>iha_5_ap010953</a></td><td>100.0</td><td>38.17</td><td>100.0
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110 </td></tr>
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111 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/gq259888'>espp_3_gq259888</a></td><td>100.0</td><td>41.34</td><td>100.0
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112 </td></tr>
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113 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af461168'>stx1a_15_af461168_a</a></td><td>99.89</td><td>20.92</td><td>99.79
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114 </td></tr>
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115 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/aj225018'>espa_23_aj225018</a></td><td>100.0</td><td>9.57</td><td>100.0
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116 </td></tr>
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117 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010960'>nlec_6_ap010960</a></td><td>100.0</td><td>18.57</td><td>99.8
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118 </td></tr>
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119 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>lpfa_3_ap010953</a></td><td>100.0</td><td>15.77</td><td>100.0
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120 </td></tr>
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121 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af453441'>nleb_11_af453441</a></td><td>97.58</td><td>12.94</td><td>99.9
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122 </td></tr>
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123 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fj386569'>toxb_4_fj386569</a></td><td>100.0</td><td>25.5</td><td>99.97
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124 </td></tr>
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125 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ae014075'>iss_11_ae014075</a></td><td>100.0</td><td>15.83</td><td>97.66
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126 </td></tr>
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127 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/x94129'>ehxa_4_x94129</a></td><td>93.56</td><td>16.28</td><td>99.71
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128 </td></tr>
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129 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fm201463'>espa_22_fm201463</a></td><td>100.0</td><td>18.99</td><td>100.0
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130 </td></tr>
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131 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/am422003'>nlea_12_am422003</a></td><td>100.0</td><td>21.17</td><td>100.0
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132 </td></tr>
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133 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab071620'>stx1b_11_ab071620_c</a></td><td>100.0</td><td>11.84</td><td>99.63
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134 </td></tr>
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135 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ecu59503'>eae_45_ecu59503</a></td><td>92.62</td><td>28.63</td><td>99.85
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136 </td></tr>
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137 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab011549'>espp_4_ab011549</a></td><td>95.62</td><td>29.83</td><td>99.87
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138 </td></tr>
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139 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/hm138194'>espp_1_hm138194</a></td><td>99.03</td><td>37.41</td><td>99.97
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140 </td></tr>
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141 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ay128535'>cif_2_ay128535</a></td><td>99.88</td><td>19.24</td><td>99.88
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142 </td></tr>
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143 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ay128537'>cif_1_ay128537</a></td><td>99.88</td><td>18.14</td><td>99.88
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144 </td></tr>
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145 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab303060'>espj_1_ab303060</a></td><td>100.0</td><td>63.45</td><td>100.0
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146 </td></tr>
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147 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fm201463'>nleb_12_fm201463</a></td><td>93.54</td><td>16.32</td><td>99.57
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148 </td></tr>
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149 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>nlec_3_ap010953</a></td><td>94.53</td><td>20.93</td><td>99.46
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150 </td></tr>
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151 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fj386569'>ehxa_5_fj386569</a></td><td>99.63</td><td>23.12</td><td>99.97
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152 </td></tr>
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153 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/cu928158'>iss_12_cu928158</a></td><td>100.0</td><td>23.77</td><td>99.42
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154 </td></tr>
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155 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/d00021'>celb_10_d00021</a></td><td>100.0</td><td>150.01</td><td>98.61
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156 </td></tr>
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157 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/gq259888'>toxb_2_gq259888</a></td><td>99.29</td><td>24.57</td><td>99.98
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158 </td></tr>
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159 </table><br/></div></body></html>
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