Indeed, this is not really a Perl problem, but please do yourself a favor and do not use multiple print's when you only need one. And use the qq operator so you don't have to escape the quotes you should be using:

print qq{
<table border="2" width="100%">
  <tr>
    <td width="100%"><b>Enzyme number $counter</b></td>
  </tr>
  <tr>
    <td width="100%">
      The cleavage site is <b>$recSite</b> for enzyme
      $element denoted by ' ^ '
    </td>
  </tr>
  <tr>
    <td width="100%">
        The annotated sequence is given below along with
        the digested sequence
        <ul>
          <li><b>Annotated:</b> $anotate</li>
          <li><b>Digested:</b> @cut</li>
        </ul>
    </td>
  </tr>
</table>
};
[download]

Also consider using HTML::Template.

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)