$seq =  'GGTACACAGAAGCCAAAGCAGGCTCCAGGCTCTGAGCTGTCAGCACAGAGACCGAT';
$mask = 'GGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT';

($srch = $mask) =~ s/(N+)/($1)/g;
$srch           =~ tr/N/./;

$cnt = 1;
($repl = $mask) =~ s/N+/" . lc(\$" . $cnt++ . ") . "/ge;

print $srch, "\n", $repl, "\n\n", $seq, "\n";

$seq =~ s/$srch/$repl/ee;
print $seq, "\n";

##</code><code>##

GGT(....................................................)T
GGT . lc($1) . T

GGTACACAGAAGCCAAAGCAGGCTCCAGGCTCTGAGCTGTCAGCACAGAGACCGAT
GGTacacagaagccaaagcaggctccaggctctgagctgtcagcacagagaccgaT