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CAARD:Caulimoviridae - Revision history
2026-06-09T15:00:14Z
Revision history for this page on the wiki
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https://gydb.org/index.php?title=CAARD:Caulimoviridae&diff=526&oldid=prev
imported>Gydbwiki: New page: {{CAARD |pin_output= (BRRV:0.363223,((CVMV:0.637591,(RTBV:0.881718,((TBV:0.539049,(CYMV:0.184009,CSSV:0.236844)N7:0.042530)N6:0.084530,(SBV:0.444779, (KTSV:0.230851,BSV:0.288366)N9:0.18060...
2009-05-08T14:07:59Z
<p>New page: {{CAARD |pin_output= (BRRV:0.363223,((CVMV:0.637591,(RTBV:0.881718,((TBV:0.539049,(CYMV:0.184009,CSSV:0.236844)N7:0.042530)N6:0.084530,(SBV:0.444779, (KTSV:0.230851,BSV:0.288366)N9:0.18060...</p>
<p><b>New page</b></p><div>{{CAARD<br />
|pin_output=<br />
(BRRV:0.363223,((CVMV:0.637591,(RTBV:0.881718,((TBV:0.539049,(CYMV:0.184009,CSSV:0.236844)N7:0.042530)N6:0.084530,(SBV:0.444779, (KTSV:0.230851,BSV:0.288366)N9:0.180600)N8:0.042234)N5:0.312026)N4:0.152466)N3:0.176768,(SVBV:0.384832,(CaMV:0.202691,(CERV:0.300086, (MMV:0.228200,(FMV:0.134410,DMV:0.131026)N14:0.079850)N13:0.050147)N12:0.029419)N11:0.043424)N10:0.147755)N2:0.160175,(SbCMV:0.402013, (PCSV:0.371774,CYLCV:0.350015)N16:0.032916)N15:0.018833); <br />
<br />
|fin_output= <br />
<table class="tabdata"><br />
<tr class="grey"><br />
<td>Name</td><br />
<td>Father</td><br />
<td>Distance to father</td><br />
<td>Sons</td><br />
</tr> <br />
<tr><td>BRRV</td><td>N1</td><td>0.363223</td><td>-</td></tr><tr><td>CVMV</td><td>N3</td><td>0.637591</td><td>-</td></tr><tr><td>RTBV</td><td>N4</td><td>0.881718</td><td>-</td></tr><tr><td>TBV</td><td>N6</td><td>0.539049</td><td>-</td></tr><tr><td>CYMV</td><td>N7</td><td>0.184009</td><td>-</td></tr><tr><td>CSSV</td><td>N7</td><td>0.236844</td><td>-</td></tr><tr><td>SBV</td><td>N8</td><td>0.444779</td><td>-</td></tr><tr><td>KTSV</td><td>N9</td><td>0.230851</td><td>-</td></tr><tr><td>BSV</td><td>N9</td><td>0.288366</td><td>-</td></tr><tr><td>SVBV</td><td>N10</td><td>0.384832</td><td>-</td></tr><tr><td>CaMV</td><td>N11</td><td>0.202691</td><td>-</td></tr><tr><td>CERV</td><td>N12</td><td>0.300086</td><td>-</td></tr><tr><td>MMV</td><td>N13</td><td>0.2282</td><td>-</td></tr><tr><td>FMV</td><td>N14</td><td>0.13441</td><td>-</td></tr><tr><td>DMV</td><td>N14</td><td>0.131026</td><td>-</td></tr><tr><td>SbCMV</td><td>N15</td><td>0.402013</td><td>-</td></tr><tr><td>PCSV</td><td>N16</td><td>0.371774</td><td>-</td></tr><tr><td>CYLCV</td><td>N16</td><td>0.350015</td><td>-</td></tr><tr><td>N1</td><td>root!</td><td>-</td><td>BRRV N2 N15</td></tr><tr><td>N2</td><td>N1</td><td>0.160175</td><td>N3 N10</td></tr><tr><td>N3</td><td>N2</td><td>0.176768</td><td>CVMV N4</td></tr><tr><td>N4</td><td>N3</td><td>0.152466</td><td>RTBV N5</td></tr><tr><td>N5</td><td>N4</td><td>0.312026</td><td>N6 N8</td></tr><tr><td>N6</td><td>N5</td><td>0.0845304</td><td>TBV N7</td></tr><tr><td>N7</td><td>N6</td><td>0.0425305</td><td>CYMV CSSV</td></tr><tr><td>N8</td><td>N5</td><td>0.0422345</td><td>SBV N9</td></tr><tr><td>N9</td><td>N8</td><td>0.1806</td><td>KTSV BSV</td></tr><tr><td>N10</td><td>N2</td><td>0.147755</td><td>SVBV N11</td></tr><tr><td>N11</td><td>N10</td><td>0.0434235</td><td>CaMV N12</td></tr><tr><td>N12</td><td>N11</td><td>0.0294185</td><td>CERV N13</td></tr><tr><td>N13</td><td>N12</td><td>0.0501468</td><td>MMV N14</td></tr><tr><td>N14</td><td>N13</td><td>0.07985</td><td>FMV DMV</td></tr><tr><td>N15</td><td>N1</td><td>0.0188328</td><td>SbCMV N16</td></tr><tr><td>N16</td><td>N15</td><td>0.0329159</td><td>PCSV CYLCV</td></tr><br />
</table><br />
<br />
<br />
|jpf_output=<br />
<table class="tabdata"><br />
<tr class="grey"><br />
<td>Position</td><br />
<td>Joint probability</td><br />
<td>Position</td><br />
<td>Joint probability</td><br />
<td>Position</td><br />
<td>Joint probability</td><br />
<td>Position</td><br />
<td>Joint probability</td><br />
</tr><br />
<tr class="text"><td>0</td><td>7.29263e-011</td><td>32</td><td>2.97321e-014</td><td>64</td><td>7.34051e-017</td><td>96</td><td>0.000296046</td></tr><tr class="text"><td>1</td><td>2.08886e-005</td><td>33</td><td>3.58782e-013</td><td>65</td><td>6.92923e-020</td><td>97</td><td>7.00137e-015</td></tr><tr class="text"><td>2</td><td>8.03596e-007</td><td>34</td><td>1.17773e-026</td><td>66</td><td>1.76561e-020</td><td>98</td><td>1.53441e-010</td></tr><tr class="text"><td>3</td><td>0.000494463</td><td>35</td><td>3.15967e-013</td><td>67</td><td>2.84189e-028</td><td>99</td><td>1.2218e-017</td></tr><tr class="text"><td>4</td><td>1.39289e-007</td><td>36</td><td>2.35722e-019</td><td>68</td><td>2.76896e-005</td><td>100</td><td>6.51548e-014</td></tr><tr class="text"><td>5</td><td>2.27823e-011</td><td>37</td><td>5.58372e-011</td><td>69</td><td>4.12527e-027</td><td>101</td><td>2.1351e-012</td></tr><tr class="text"><td>6</td><td>1.49912e-017</td><td>38</td><td>0.000115678</td><td>70</td><td>6.42354e-012</td><td>102</td><td>3.95936e-019</td></tr><tr class="text"><td>7</td><td>0.00022636</td><td>39</td><td>1.53633e-010</td><td>71</td><td>0.00719497</td><td>103</td><td>0.0024444</td></tr><tr class="text"><td>8</td><td>5.77138e-006</td><td>40</td><td>1.62056e-011</td><td>72</td><td>0.00758651</td><td>104</td><td>0.00300215</td></tr><tr class="text"><td>9</td><td>7.07139e-015</td><td>41</td><td>4.45526e-019</td><td>73</td><td>0.0024444</td><td>105</td><td>0.00262271</td></tr><tr class="text"><td>10</td><td>5.38338e-019</td><td>42</td><td>0.000253743</td><td>74</td><td>0.019163</td><td>106</td><td>0.00300215</td></tr><tr class="text"><td>11</td><td>1.6775e-022</td><td>43</td><td>2.56186e-025</td><td>75</td><td>3.91079e-007</td><td>107</td><td>0.00152142</td></tr><tr class="text"><td>12</td><td>1.56167e-012</td><td>44</td><td>3.46782e-027</td><td>76</td><td>1.58051e-019</td><td>108</td><td>0.00719497</td></tr><tr class="text"><td>13</td><td>9.41236e-016</td><td>45</td><td>4.32692e-024</td><td>77</td><td>1.70366e-008</td><td>109</td><td>0.00464171</td></tr><tr class="text"><td>14</td><td>1.0096e-020</td><td>46</td><td>2.51807e-025</td><td>78</td><td>2.01149e-014</td><td>110</td><td>1.70753e-008</td></tr><tr class="text"><td>15</td><td>2.60008e-014</td><td>47</td><td>3.57657e-022</td><td>79</td><td>1.86842e-016</td><td>111</td><td>1.36581e-012</td></tr><tr class="text"><td>16</td><td>2.82417e-011</td><td>48</td><td>3.72296e-023</td><td>80</td><td>1.02466e-011</td><td>112</td><td>7.12848e-007</td></tr><tr class="text"><td>17</td><td>1.88843e-018</td><td>49</td><td>2.05744e-018</td><td>81</td><td>6.74726e-008</td><td>113</td><td>8.24521e-014</td></tr><tr class="text"><td>18</td><td>1.02598e-016</td><td>50</td><td>3.68767e-017</td><td>82</td><td>1.6437e-005</td><td>114</td><td>4.51991e-008</td></tr><tr class="text"><td>19</td><td>1.41563e-011</td><td>51</td><td>9.92609e-017</td><td>83</td><td>4.43852e-018</td><td>115</td><td>3.79039e-021</td></tr><tr class="text"><td>20</td><td>4.92493e-007</td><td>52</td><td>1.18994e-011</td><td>84</td><td>5.38862e-021</td><td>116</td><td>1.39614e-016</td></tr><tr class="text"><td>21</td><td>4.69162e-027</td><td>53</td><td>1.55043e-027</td><td>85</td><td>1.78583e-019</td><td>117</td><td>1.28258e-022</td></tr><tr class="text"><td>22</td><td>0.00223868</td><td>54</td><td>3.52359e-015</td><td>86</td><td>1.68585e-011</td><td>118</td><td>3.72019e-020</td></tr><tr class="text"><td>23</td><td>2.19534e-011</td><td>55</td><td>4.9967e-023</td><td>87</td><td>1.78766e-010</td><td>119</td><td>0.00378599</td></tr><tr class="text"><td>24</td><td>3.25178e-016</td><td>56</td><td>5.39737e-006</td><td>88</td><td>2.24791e-018</td><td>120</td><td>1.9553e-010</td></tr><tr class="text"><td>25</td><td>1.84511e-007</td><td>57</td><td>2.31023e-014</td><td>89</td><td>9.28698e-018</td><td>121</td><td>1.90183e-018</td></tr><tr class="text"><td>26</td><td>0.000389014</td><td>58</td><td>5.03191e-034</td><td>90</td><td>6.16295e-021</td><td>122</td><td>2.39151e-008</td></tr><tr class="text"><td>27</td><td>2.57658e-026</td><td>59</td><td>7.33408e-013</td><td>91</td><td>7.92811e-011</td><td>123</td><td>4.02254e-013</td></tr><tr class="text"><td>28</td><td>2.07038e-015</td><td>60</td><td>0.0034186</td><td>92</td><td>3.46343e-013</td><td>124</td><td>4.89559e-016</td></tr><tr class="text"><td>29</td><td>2.08338e-013</td><td>61</td><td>0.00880089</td><td>93</td><td>0.000494463</td><td>125</td><td>1.5219e-023</td></tr><tr class="text"><td>30</td><td>8.49017e-011</td><td>62</td><td>0.00719497</td><td>94</td><td>2.84725e-013</td><td>126</td><td>7.17307e-022</td></tr><tr class="text"><td>31</td><td>1.54163e-012</td><td>63</td><td>0.00701351</td><td>95</td><td>2.09331e-008</td><td>127</td><td>9.47549e-012</td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-3706.46</td></tr><br />
</table><br />
<br />
<br />
|jrof_output=<br />
<align id="caulimoviridae" folder="jrof"></align><br />
<br />
<br />
|mpf_output=<br />
<table class="tabdata"><br />
<tbody><tr class="grey"><br />
<td>Position</td><br />
<td>Joint probability</td><br />
<td>Position</td><br />
<td>Joint probability</td><br />
<td>Position</td><br />
<td>Joint probability</td><br />
<td>Position</td><br />
<td>Joint probability</td><br />
</tr><br />
<tr class="text"><td>0</td><td>2.24686e-010</td><td>32</td><td>6.60519e-013</td><td>64</td><td>5.178e-016</td><td>96</td><td>0.00029637</td></tr><tr class="text"><td>1</td><td>2.11068e-005</td><td>33</td><td>1.14485e-012</td><td>65</td><td>5.24355e-019</td><td>97</td><td>3.53869e-014</td></tr><tr class="text"><td>2</td><td>8.26475e-007</td><td>34</td><td>3.98971e-025</td><td>66</td><td>7.12634e-020</td><td>98</td><td>1.46028e-009</td></tr><tr class="text"><td>3</td><td>0.000494827</td><td>35</td><td>7.53204e-013</td><td>67</td><td>1.84336e-027</td><td>99</td><td>9.29422e-017</td></tr><tr class="text"><td>4</td><td>1.44025e-007</td><td>36</td><td>4.31719e-019</td><td>68</td><td>2.77707e-005</td><td>100</td><td>1.66008e-013</td></tr><tr class="text"><td>5</td><td>3.57387e-011</td><td>37</td><td>9.38688e-011</td><td>69</td><td>5.10582e-026</td><td>101</td><td>1.13323e-011</td></tr><tr class="text"><td>6</td><td>2.04533e-016</td><td>38</td><td>0.000924235</td><td>70</td><td>2.12919e-011</td><td>102</td><td>3.31153e-018</td></tr><tr class="text"><td>7</td><td>0.000621205</td><td>39</td><td>7.46959e-010</td><td>71</td><td>0.058676</td><td>103</td><td>0.068765</td></tr><tr class="text"><td>8</td><td>5.78327e-006</td><td>40</td><td>3.77395e-011</td><td>72</td><td>0.032102</td><td>104</td><td>0.053761</td></tr><tr class="text"><td>9</td><td>1.50239e-014</td><td>41</td><td>1.00036e-017</td><td>73</td><td>0.068765</td><td>105</td><td>0.058565</td></tr><tr class="text"><td>10</td><td>7.99407e-018</td><td>42</td><td>0.0027651</td><td>74</td><td>0.091904</td><td>106</td><td>0.053761</td></tr><tr class="text"><td>11</td><td>9.66623e-022</td><td>43</td><td>6.87009e-024</td><td>75</td><td>3.95952e-007</td><td>107</td><td>0.022944</td></tr><tr class="text"><td>12</td><td>1.37372e-011</td><td>44</td><td>8.43915e-026</td><td>76</td><td>1.12859e-018</td><td>108</td><td>0.058676</td></tr><tr class="text"><td>13</td><td>1.83124e-015</td><td>45</td><td>1.42096e-022</td><td>77</td><td>7.29653e-008</td><td>109</td><td>0.051544</td></tr><tr class="text"><td>14</td><td>3.69497e-020</td><td>46</td><td>6.08814e-024</td><td>78</td><td>5.42501e-014</td><td>110</td><td>3.59132e-008</td></tr><tr class="text"><td>15</td><td>1.04341e-013</td><td>47</td><td>3.25807e-021</td><td>79</td><td>9.71813e-016</td><td>111</td><td>1.00523e-011</td></tr><tr class="text"><td>16</td><td>2.95014e-011</td><td>48</td><td>4.37383e-022</td><td>80</td><td>6.28351e-011</td><td>112</td><td>4.91441e-006</td></tr><tr class="text"><td>17</td><td>1.68511e-017</td><td>49</td><td>7.62289e-018</td><td>81</td><td>1.46962e-007</td><td>113</td><td>1.03763e-013</td></tr><tr class="text"><td>18</td><td>1.11897e-015</td><td>50</td><td>3.41581e-016</td><td>82</td><td>0.000112293</td><td>114</td><td>7.57141e-008</td></tr><tr class="text"><td>19</td><td>4.50512e-010</td><td>51</td><td>5.53589e-016</td><td>83</td><td>2.69454e-017</td><td>115</td><td>2.4569e-019</td></tr><tr class="text"><td>20</td><td>2.40285e-006</td><td>52</td><td>2.31814e-010</td><td>84</td><td>1.28873e-020</td><td>116</td><td>9.05718e-016</td></tr><tr class="text"><td>21</td><td>3.62092e-025</td><td>53</td><td>2.24395e-026</td><td>85</td><td>5.18683e-018</td><td>117</td><td>3.8267e-021</td></tr><tr class="text"><td>22</td><td>0.00827945</td><td>54</td><td>5.17243e-014</td><td>86</td><td>9.12423e-011</td><td>118</td><td>1.33308e-019</td></tr><tr class="text"><td>23</td><td>3.65651e-011</td><td>55</td><td>2.16515e-022</td><td>87</td><td>1.80825e-010</td><td>119</td><td>0.053761</td></tr><tr class="text"><td>24</td><td>1.88297e-014</td><td>56</td><td>5.83295e-005</td><td>88</td><td>2.63726e-017</td><td>120</td><td>8.92577e-010</td></tr><tr class="text"><td>25</td><td>2.92338e-007</td><td>57</td><td>8.26904e-014</td><td>89</td><td>2.7358e-017</td><td>121</td><td>4.45872e-018</td></tr><tr class="text"><td>26</td><td>0.00638423</td><td>58</td><td>9.2202e-032</td><td>90</td><td>8.79648e-020</td><td>122</td><td>2.52176e-008</td></tr><tr class="text"><td>27</td><td>2.21044e-024</td><td>59</td><td>1.80081e-012</td><td>91</td><td>1.01543e-010</td><td>123</td><td>6.10079e-013</td></tr><tr class="text"><td>28</td><td>2.67111e-015</td><td>60</td><td>0.040752</td><td>92</td><td>6.02062e-013</td><td>124</td><td>2.28424e-015</td></tr><tr class="text"><td>29</td><td>3.42442e-012</td><td>61</td><td>0.040126</td><td>93</td><td>0.000494827</td><td>125</td><td>9.74988e-023</td></tr><tr class="text"><td>30</td><td>1.00294e-009</td><td>62</td><td>0.058676</td><td>94</td><td>7.6988e-013</td><td>126</td><td>1.18715e-020</td></tr><tr class="text"><td>31</td><td>5.11742e-011</td><td>63</td><td>0.06183</td><td>95</td><td>2.1933e-008</td><td>127</td><td>2.20721e-010</td></tr><tr><td colspan="7" class="grey right">Total log likelihood of joint reconstruction: </td><td class="grey">-3476.31</td></tr><br />
</table> <br />
<br />
<br />
|mrof_output=<br />
<align id="caulimoviridae" folder="mrof"></align><br />
<br />
|sequence_logo=<br />
[[Image:Logo_caulimoviridae.png|500px|center]]<br />
<br />
|hmms=<br />
<pre><br />
>AP_caulimoviruses profile HMM generated consensus sequence<br />
iDTGAtlCiasekivpkewkenkekpikirianssvivirkvkkdgklwIadekFlIPt<br />
tYPmqqesGidmIIGnNFlrslygpfrIqygdtItF<br />
</pre><br />
<br />
|pairwise_alignment=<br />
<pre><br />
Domain 1 of 1, from 1 to 89: score 63.1, E = 1e-19<br />
<br />
DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs<br />
+DTGA++ +++s+ ++ k ++++k ++P+<br />
AP_caulimo 1 IDTGATL-CIASEK--IVPKEWKENK-----------------EKPI 27 <br />
<br />
sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe<br />
k ir+a+ +++ i ++k + G <br />
AP_caulimo 28 -K--------IRIANS----------SVIVI-------RKVKKD-G---- 46 <br />
<br />
venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvh.idl<-*<br />
+ ++++++ fl+++t p++q+s++d+I+G+ fLr l+++++i++ <br />
AP_caulimo 47 --KLWIADEK-FLIPtTYPMQQESGIDMIIGN-NFLRSLYGPFrIQY 89 <br />
</pre><br />
}}</div>
imported>Gydbwiki