mdv1.rnaml

mfold

<?xml version="1.0"?>
<!DOCTYPE rnaml PUBLIC "-//University of Montreal//RNAML 1.1//EN" "http://www-lbit.iro.umontreal.ca/rnaml/current/rnaml.dtd">

<rnaml version="1.1" comment="Output from mFold">

  <analysis id="mfold">
    <program>
      <prog-name>mFold</prog-name>
      <prog-version>3.2</prog-version>
    </program>
  </analysis>


  <!-- 1st sequence and its associated foldings ******************* -->
  <molecule id="MDV-1__-__RNA" type="rna">
    <sequence circular="false" strand="1">
      <seq-data>
        GGGGAACCCC CCUUCGGGGG UCACCUCGCG CAGCGGGCUG CGCGAAGGGG CCACGCUGCG
        AAGCAGCGUG GCGGUUCUCG UGCGUUACCG AAACGCACGA AGGUCGCGCC UCUUCACGAG
        GCGUCACCUG GGAGAGCGCG AAAGCGCUAG CCCGUGACUC GUCACGGUCG AACUCCCGUA
        CGAGGUGCCC GCACCUCGUC CCCCCUUCCG GGGGGUCCCC A
      </seq-data>
    </sequence>

    <structure analysis-ids="mfold">
      <!-- Start of folding 1 for sequence 1 ************************ -->
      <model id="_1.1">
        <model-info>
          <free-energy>-145.30</free-energy>
        </model-info>

        <str-annotation>
          <helix>
            <base-id-5p>
              <base-id>
                <position>1</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>220</position>
              </base-id>
            </base-id-3p>
            <length>4</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>6</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>216</position>
              </base-id>
            </base-id-3p>
            <length>7</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>16</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>205</position>
              </base-id>
            </base-id-3p>
            <length>5</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>24</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>48</position>
              </base-id>
            </base-id-3p>
            <length>2</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>26</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>45</position>
              </base-id>
            </base-id-3p>
            <length>8</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>50</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>72</position>
              </base-id>
            </base-id-3p>
            <length>10</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>78</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>100</position>
              </base-id>
            </base-id-3p>
            <length>9</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>102</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>128</position>
              </base-id>
            </base-id-3p>
            <length>3</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>106</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>124</position>
              </base-id>
            </base-id-3p>
            <length>7</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>130</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>177</position>
              </base-id>
            </base-id-3p>
            <length>5</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>136</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>147</position>
              </base-id>
            </base-id-3p>
            <length>4</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>152</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>167</position>
              </base-id>
            </base-id-3p>
            <length>6</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>180</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>199</position>
              </base-id>
            </base-id-3p>
            <length>8</length>
          </helix>
        </str-annotation>
      </model>
      <!-- End of folding 1 for sequence 1 ************************ -->

      <!-- Start of folding 2 for sequence 1 ************************ -->
      <model id="_1.2">
        <model-info>
          <free-energy>-141.80</free-energy>
        </model-info>

        <str-annotation>
          <helix>
            <base-id-5p>
              <base-id>
                <position>1</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>220</position>
              </base-id>
            </base-id-3p>
            <length>4</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>6</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>216</position>
              </base-id>
            </base-id-3p>
            <length>7</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>16</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>205</position>
              </base-id>
            </base-id-3p>
            <length>5</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>26</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>45</position>
              </base-id>
            </base-id-3p>
            <length>8</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>47</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>177</position>
              </base-id>
            </base-id-3p>
            <length>3</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>50</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>72</position>
              </base-id>
            </base-id-3p>
            <length>10</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>74</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>173</position>
              </base-id>
            </base-id-3p>
            <length>4</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>79</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>99</position>
              </base-id>
            </base-id-3p>
            <length>8</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>101</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>129</position>
              </base-id>
            </base-id-3p>
            <length>4</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>106</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>124</position>
              </base-id>
            </base-id-3p>
            <length>7</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>130</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>153</position>
              </base-id>
            </base-id-3p>
            <length>3</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>135</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>148</position>
              </base-id>
            </base-id-3p>
            <length>5</length>
          </helix>
          <helix>
            <base-id-5p>
              <base-id>
                <position>154</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>165</position>
              </base-id>
            </base-id-3p>