- <ul>
- <li><strong>PID</strong><br>The percentage identity between
- the two sequences at each aligned position.
- <ul>
- <li>PID = Number of equivalent aligned non-gap symbols * 100 /
- Smallest number of non-gap positions in either of both sequences<br>
- <em>This is essentially the 'number of identical bases (or
- residues) per 100 base pairs (or residues)'.</em>
- </li>
- </ul>
- <li><strong>BLOSUM62, PAM250, DNA</strong><br>These options
- use one of the available substitution matrices to compute a sum of
- scores for the residue pairs at each aligned position. For details
- about each model, see the <a href="scorematrices.html">list of
- built-in score matrices.</a></li>
+
+
+ <ul>
+ <li><strong>PID</strong><br>The percentage identity
+ between the two sequences at each aligned position.
+ <ul>
+ <li>PID = Number of equivalent aligned non-gap symbols *
+ 100 / Smallest number of non-gap positions in either of both
+ sequences<br> <em>This is essentially the 'number of
+ identical bases (or residues) per 100 base pairs (or
+ residues)'.</em>
+ </li>
+ </ul>
+ <li><strong>BLOSUM62, PAM250, DNA</strong><br/>These
+ options use one of the available substitution matrices to compute
+ a sum of scores for the residue pairs at each aligned position.
+ <ul><li>For details about each model, see the
+ <a href="scorematrices.html">list of built-in score matrices</a>.
+ </li>
+ </ul></li>