help/html/calculations/scorematrices.html

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  20 <head>
  21 <title>Substitution matrices in Jalview</title>
  22 </head>
  23 <body>
  24 <strong>Substitution Matrices available in Jalview</strong>
  25 <p>Jalview includes a small number of built in substitution matrices, used for different types of analysis.</p>
  26 <ul>
  27 <li><a href="#blosum62">BLOSUM62</a> is the standard protein sequence alignment and analysis matrix.</li>
  28 <li><a href="#pam250">PAM250</a> is another standard protein matrix, but not currently available for use from Jalview's user interface.</li>
  29 <li><a href="#simplenucleotide">Simple Nucleotide Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.
  30 </li>
  31 </ul>
  32
  33 <p><strong><a name="blosum62"></a>BLOSUM62</strong><br/>
  34 <table border="1">
  35 <tr><td></td><td>&nbsp;A&nbsp;</td><td>&nbsp;B&nbsp;</td><td>&nbsp;C&nbsp;</td><td>&nbsp;D&nbsp;</td><td>&nbsp;E&nbsp;</td><td>&nbsp;F&nbsp;</td><td>&nbsp;G&nbsp;</td><td>&nbsp;H&nbsp;</td><td>&nbsp;I&nbsp;</td><td>&nbsp;K&nbsp;</td><td>&nbsp;L&nbsp;</td><td>&nbsp;M&nbsp;</td><td>&nbsp;N&nbsp;</td><td>&nbsp;P&nbsp;</td><td>&nbsp;Q&nbsp;</td><td>&nbsp;R&nbsp;</td><td>&nbsp;S&nbsp;</td><td>&nbsp;T&nbsp;</td><td>&nbsp;U&nbsp;</td><td>&nbsp;V&nbsp;</td><td>&nbsp;W&nbsp;</td><td>&nbsp;X&nbsp;</td><td>&nbsp;Y&nbsp;</td><td>&nbsp;Z&nbsp;</td></tr>
  36 <tr><td>A</td><td>4</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>-3</td><td>0</td><td>-2</td><td>-1</td></tr>
  37 <tr><td>B</td><td>-2</td><td>4</td><td>-3</td><td>4</td><td>1</td><td>-3</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>3</td><td>-2</td><td>0</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-3</td><td>1</td></tr>
  38 <tr><td>C</td><td>0</td><td>-3</td><td>9</td><td>-3</td><td>-4</td><td>-2</td><td>-3</td><td>-3</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td><td>-3</td><td>-3</td><td>3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-3</td></tr>
  39 <tr><td>D</td><td>-2</td><td>4</td><td>-3</td><td>6</td><td>2</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td><td>-1</td><td>-4</td><td>-3</td><td>1</td><td>-1</td><td>0</td><td>-2</td><td>0</td><td>-1</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-3</td><td>1</td></tr>
  40 <tr><td>E</td><td>-1</td><td>1</td><td>-4</td><td>2</td><td>5</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-3</td><td>-2</td><td>0</td><td>-1</td><td>2</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>4</td></tr>
  41 <tr><td>F</td><td>-2</td><td>-3</td><td>-2</td><td>-3</td><td>-3</td><td>6</td><td>-3</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>0</td><td>-3</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>1</td><td>-1</td><td>3</td><td>-3</td></tr>
  42 <tr><td>G</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-2</td><td>-3</td><td>6</td><td>-2</td><td>-4</td><td>-2</td><td>-4</td><td>-3</td><td>0</td><td>-2</td><td>-2</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td></tr>
  43 <tr><td>H</td><td>-2</td><td>0</td><td>-3</td><td>-1</td><td>0</td><td>-1</td><td>-2</td><td>8</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>1</td><td>-2</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>2</td><td>0</td></tr>
  44 <tr><td>I</td><td>-1</td><td>-3</td><td>-1</td><td>-3</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>4</td><td>-3</td><td>2</td><td>1</td><td>-3</td><td>-3</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>-1</td><td>3</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td></tr>
  45 <tr><td>K</td><td>-1</td><td>0</td><td>-3</td><td>-1</td><td>1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>5</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>1</td><td>2</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>1</td></tr>
  46 <tr><td>L</td><td>-1</td><td>-4</td><td>-1</td><td>-4</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>2</td><td>-2</td><td>4</td><td>2</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>1</td><td>-2</td><td>-1</td><td>-1</td><td>-3</td></tr>
  47 <tr><td>M</td><td>-1</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>-1</td><td>2</td><td>5</td><td>-2</td><td>-2</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td></tr>
  48 <tr><td>N</td><td>-2</td><td>3</td><td>-3</td><td>1</td><td>0</td><td>-3</td><td>0</td><td>1</td><td>-3</td><td>0</td><td>-3</td><td>-2</td><td>6</td><td>-2</td><td>0</td><td>0</td><td>1</td><td>0</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-2</td><td>0</td></tr>
  49 <tr><td>P</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-1</td><td>-4</td><td>-2</td><td>-2</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>-2</td><td>7</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-4</td><td>-2</td><td>-3</td><td>-1</td></tr>
  50 <tr><td>Q</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>2</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-2</td><td>0</td><td>0</td><td>-1</td><td>5</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>3</td></tr>
  51 <tr><td>R</td><td>-1</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>2</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>1</td><td>5</td><td>-1</td><td>-1</td><td>-1</td><td>-3</td><td>-3</td><td>-1</td><td>-2</td><td>0</td></tr>
  52 <tr><td>S</td><td>1</td><td>0</td><td>-1</td><td>0</td><td>0</td><td>-2</td><td>0</td><td>-1</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>1</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>1</td><td>0</td><td>-2</td><td>-3</td><td>0</td><td>-2</td><td>0</td></tr>
  53 <tr><td>T</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>5</td><td>0</td><td>0</td><td>-2</td><td>0</td><td>-2</td><td>-1</td></tr>
  54 <tr><td>U</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td></tr>
  55 <tr><td>V</td><td>0</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>-3</td><td>3</td><td>-2</td><td>1</td><td>1</td><td>-3</td><td>-2</td><td>-2</td><td>-3</td><td>-2</td><td>0</td><td>-1</td><td>4</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td></tr>
  56 <tr><td>W</td><td>-3</td><td>-4</td><td>-2</td><td>-4</td><td>-3</td><td>1</td><td>-2</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>-4</td><td>-4</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-3</td><td>11</td><td>-2</td><td>2</td><td>-3</td></tr>
  57 <tr><td>X</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td></tr>
  58 <tr><td>Y</td><td>-2</td><td>-3</td><td>-2</td><td>-3</td><td>-2</td><td>3</td><td>-3</td><td>2</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>2</td><td>-1</td><td>7</td><td>-2</td></tr>
  59 <tr><td>Z</td><td>-1</td><td>1</td><td>-3</td><td>1</td><td>4</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-3</td><td>-1</td><td>0</td><td>-1</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>4</td></tr>
  60 </table>
  61 <p><strong><a name="pam250">PAM250</a></strong><br/>
  62 <table border="1">
  63 <tr><td></td><td>&nbsp;A&nbsp;</td><td>&nbsp;B&nbsp;</td><td>&nbsp;C&nbsp;</td><td>&nbsp;D&nbsp;</td><td>&nbsp;E&nbsp;</td><td>&nbsp;F&nbsp;</td><td>&nbsp;G&nbsp;</td><td>&nbsp;H&nbsp;</td><td>&nbsp;I&nbsp;</td><td>&nbsp;K&nbsp;</td><td>&nbsp;L&nbsp;</td><td>&nbsp;M&nbsp;</td><td>&nbsp;N&nbsp;</td><td>&nbsp;P&nbsp;</td><td>&nbsp;Q&nbsp;</td><td>&nbsp;R&nbsp;</td><td>&nbsp;S&nbsp;</td><td>&nbsp;T&nbsp;</td><td>&nbsp;U&nbsp;</td><td>&nbsp;V&nbsp;</td><td>&nbsp;W&nbsp;</td><td>&nbsp;X&nbsp;</td><td>&nbsp;Y&nbsp;</td><td>&nbsp;Z&nbsp;</td></tr>
  64 <tr><td>A</td><td>2</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>0</td><td>1</td><td>0</td><td>-2</td><td>1</td><td>1</td><td>0</td><td>0</td><td>-6</td><td>0</td><td>-3</td><td>0</td></tr>
  65 <tr><td>B</td><td>0</td><td>3</td><td>-4</td><td>3</td><td>3</td><td>-4</td><td>0</td><td>1</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>2</td><td>-1</td><td>1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-5</td><td>-1</td><td>-3</td><td>2</td></tr>
  66 <tr><td>C</td><td>-2</td><td>-4</td><td>12</td><td>-5</td><td>-5</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-5</td><td>-6</td><td>-5</td><td>-4</td><td>-3</td><td>-5</td><td>-4</td><td>0</td><td>-2</td><td>-3</td><td>-2</td><td>-8</td><td>-3</td><td>0</td><td>-5</td></tr>
  67 <tr><td>D</td><td>0</td><td>3</td><td>-5</td><td>4</td><td>3</td><td>-6</td><td>1</td><td>1</td><td>-2</td><td>0</td><td>-4</td><td>-3</td><td>2</td><td>-1</td><td>2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-7</td><td>-1</td><td>-4</td><td>3</td></tr>
  68 <tr><td>E</td><td>0</td><td>3</td><td>-5</td><td>3</td><td>4</td><td>-5</td><td>0</td><td>1</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>-1</td><td>2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-7</td><td>-1</td><td>-4</td><td>3</td></tr>
  69 <tr><td>F</td><td>-3</td><td>-4</td><td>-4</td><td>-6</td><td>-5</td><td>9</td><td>-5</td><td>-2</td><td>1</td><td>-5</td><td>2</td><td>0</td><td>-3</td><td>-5</td><td>-5</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>7</td><td>-5</td></tr>
  70 <tr><td>G</td><td>1</td><td>0</td><td>-3</td><td>1</td><td>0</td><td>-5</td><td>5</td><td>-2</td><td>-3</td><td>-2</td><td>-4</td><td>-3</td><td>0</td><td>0</td><td>-1</td><td>-3</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-7</td><td>-1</td><td>-5</td><td>0</td></tr>
  71 <tr><td>H</td><td>-1</td><td>1</td><td>-3</td><td>1</td><td>1</td><td>-2</td><td>-2</td><td>6</td><td>-2</td><td>0</td><td>-2</td><td>-2</td><td>2</td><td>0</td><td>3</td><td>2</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>0</td><td>2</td></tr>
  72 <tr><td>I</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>5</td><td>-2</td><td>2</td><td>2</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>-5</td><td>-1</td><td>-1</td><td>-2</td></tr>
  73 <tr><td>K</td><td>-1</td><td>1</td><td>-5</td><td>0</td><td>0</td><td>-5</td><td>-2</td><td>0</td><td>-2</td><td>5</td><td>-3</td><td>0</td><td>1</td><td>-1</td><td>1</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-4</td><td>0</td></tr>
  74 <tr><td>L</td><td>-2</td><td>-3</td><td>-6</td><td>-4</td><td>-3</td><td>2</td><td>-4</td><td>-2</td><td>2</td><td>-3</td><td>6</td><td>4</td><td>-3</td><td>-3</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>2</td><td>-2</td><td>-1</td><td>-1</td><td>-3</td></tr>
  75 <tr><td>M</td><td>-1</td><td>-2</td><td>-5</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>2</td><td>0</td><td>4</td><td>6</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>-1</td><td>-1</td><td>2</td><td>-4</td><td>-1</td><td>-2</td><td>-2</td></tr>
  76 <tr><td>N</td><td>0</td><td>2</td><td>-4</td><td>2</td><td>1</td><td>-3</td><td>0</td><td>2</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>2</td><td>0</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>-2</td><td>-4</td><td>0</td><td>-2</td><td>1</td></tr>
  77 <tr><td>P</td><td>1</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-5</td><td>0</td><td>0</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>6</td><td>0</td><td>0</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-6</td><td>-1</td><td>-5</td><td>0</td></tr>
  78 <tr><td>Q</td><td>0</td><td>1</td><td>-5</td><td>2</td><td>2</td><td>-5</td><td>-1</td><td>3</td><td>-2</td><td>1</td><td>-2</td><td>-1</td><td>1</td><td>0</td><td>4</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-5</td><td>-1</td><td>-4</td><td>3</td></tr>
  79 <tr><td>R</td><td>-2</td><td>-1</td><td>-4</td><td>-1</td><td>-1</td><td>-4</td><td>-3</td><td>2</td><td>-2</td><td>3</td><td>-3</td><td>0</td><td>0</td><td>0</td><td>1</td><td>6</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>2</td><td>-1</td><td>-4</td><td>0</td></tr>
  80 <tr><td>S</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>1</td><td>-1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>-1</td><td>-2</td><td>0</td><td>-3</td><td>0</td></tr>
  81 <tr><td>T</td><td>1</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>0</td><td>-1</td><td>0</td><td>0</td><td>-2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>1</td><td>3</td><td>0</td><td>0</td><td>-5</td><td>0</td><td>-3</td><td>-1</td></tr>
  82 <tr><td>U</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-1</td></tr>
  83 <tr><td>V</td><td>0</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>4</td><td>-2</td><td>2</td><td>2</td><td>-2</td><td>-1</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>-6</td><td>-1</td><td>-2</td><td>-2</td></tr>
  84 <tr><td>W</td><td>-6</td><td>-5</td><td>-8</td><td>-7</td><td>-7</td><td>0</td><td>-7</td><td>-3</td><td>-5</td><td>-3</td><td>-2</td><td>-4</td><td>-4</td><td>-6</td><td>-5</td><td>2</td><td>-2</td><td>-5</td><td>-4</td><td>-6</td><td>17</td><td>-4</td><td>0</td><td>-6</td></tr>
  85 <tr><td>X</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-1</td></tr>
  86 <tr><td>Y</td><td>-3</td><td>-3</td><td>0</td><td>-4</td><td>-4</td><td>7</td><td>-5</td><td>0</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-2</td><td>-5</td><td>-4</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>0</td><td>-2</td><td>10</td><td>-4</td></tr>
  87 <tr><td>Z</td><td>0</td><td>2</td><td>-5</td><td>3</td><td>3</td><td>-5</td><td>0</td><td>2</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-6</td><td>-1</td><td>-4</td><td>3</td></tr>
  88 </table>
  89
  90 <p><strong><a name="simplenucleotide">Simple Nucleotide Substitution</a></strong></br>
  91 This is an ad-hoc matrix which, in addition to penalising mutations between the common nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA.
  92 In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, and N is allowed to match any other base weakly. This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match any of (ACGTU), and unfavourably match each other.
  93 <table border="1">
  94 <tr><td></td><td>&nbsp;A&nbsp;</td><td>&nbsp;C&nbsp;</td><td>&nbsp;G&nbsp;</td><td>&nbsp;I&nbsp;</td><td>&nbsp;N&nbsp;</td><td>&nbsp;R&nbsp;</td><td>&nbsp;T&nbsp;</td><td>&nbsp;U&nbsp;</td><td>&nbsp;X&nbsp;</td><td>&nbsp;Y&nbsp;</td></tr>
  95 <tr><td>A</td><td>10</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>1</td><td>-8</td></tr>
  96 <tr><td>C</td><td>-8</td><td>10</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td></tr>
  97 <tr><td>G</td><td>-8</td><td>-8</td><td>10</td><td>1</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>1</td><td>-8</td></tr>
  98 <tr><td>I</td><td>1</td><td>1</td><td>1</td><td>10</td><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td><td>0</td></tr>
  99 <tr><td>N</td><td>1</td><td>1</td><td>1</td><td>1</td><td>10</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr>
 100 <tr><td>R</td><td>1</td><td>-8</td><td>1</td><td>0</td><td>1</td><td>10</td><td>-8</td><td>-8</td><td>0</td><td>-8</td></tr>
 101 <tr><td>T</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>10</td><td>10</td><td>1</td><td>1</td></tr>
 102 <tr><td>U</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>10</td><td>10</td><td>1</td><td>1</td></tr>
 103 <tr><td>X</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>1</td><td>10</td><td>0</td></tr>
 104 <tr><td>Y</td><td>-8</td><td>1</td><td>-8</td><td>0</td><td>1</td><td>-8</td><td>1</td><td>1</td><td>0</td><td>10</td></tr>
 105 </table>
 106 <strong><em>This nucleotide matrix was introduced in
 107                                 Jalview 2.8. If you'd like to improve it - please take a look at <a
 108                                 href="http://issues.jalview.org/browse/JAL-1027">Issue JAL-1027
 109                                         - introduce a nucleotide substitution matrix that supports RNA/DNA
 110                                         and ambiguity codes</a>
 111                 </em></strong>
 112                 </body>
 113 </html>