...

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

...