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

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

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

GGTACACAGAAGCCAAAGCAGGCTCCAGGCTCTGAGCTGTCAGCACAGAGACCGAT
GGTacacagaagccaaagcaggctccaggctctgagctgtcagcacagagaccgaT