my $regex = '(([QGYN])';
$regex .= '((?!\\' . $_ . ')[QGYN]|\\' . $_. '(?!\\${_}))' for 2 .. 3;
$regex .= '(?:((?!\\' . $_ . ')[QGYN]|\\' . $_ . '(?!\\' . $_ . '))' for 4 .. 5;
$regex .= '[QGYN]?)?)?)';
$regex = qr/$regex/;

while ($seq{$k} =~ /$regex/g)
{
    print "\n$k";
    print $1." begins at position ", (pos($seq{$k})-length($s)) , "\n";
}