You might consider replacing the multiple print statements with a heredoc or two. It'll cut down on the backwhacking you've got to do. Or use qq{} rather than ""'s for strings that need to be interpolated which include double quotes.

...

print FILE_OUT <<'EOT';
  $seq =~ /ZZZ/) {
    $match = $&;
EOT

print FILE_OUT qq{    \$name = "$name";\n};

print FILE_OUT <<'EOT';
    $matchlength = length( $match );
    $firstpos = index( $seq, $match );
    print "$name, $match, $matchlength, $firstpos\n";
    print "Got it!\n";
} elsif {
EOT

...
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