First read the table, or a portion of it. It's easiest if you are sure the sequence of interest won't cross a chunk boundary.

Then use Perl's Pattern Matching feature to find each sequence of interest. By "tagging" do you mean insert a comment at that point where it was found? Use search-and-replace for that. Matching and replacing is a fundamental Perl primitive and one of the hallmarks of the language.

Write the results out.

BTW, I've heard of other people using Perl for DNA stuff, so look in CPAN and see if what you want is already there.