Don't print hard-coded HTML!

At the very least, use CGI. Better yet, use a template system. I prefer HTML::Template, but there are others. Ask CPAN about templates.

As for the output of the commands, invoke the commands wherever you like. Do the commands all have similar output, or does each one need its own format? Obviously, the actual formatting is going to depend on what commands you invoke.

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TTTATCGGTCGTTATATAGATGTTTGCA