Here's a pure regex solution that works:
use strict;
use warnings;
while(<DATA>) {
print "$_---\n";
my $m;
while (/([QGYN]{2} # First two characters of the desired class
(?: # Followed by the complex expression...
# Lookback at the previous two chars
(?<=(.)(.))
# Check that the next char differs from at least one of th
+em
(?:(?!\2)|(?!\3))
[QGYN] # Then take another of the desired class
){1,4} # ...1 to 4 times
)/gx) {
$m = $1;
printf "---> $m starting at %d\n", pos($_)-length($m);
}
print "=====\n";
}
__DATA__
QYGNGNG
GGGGGNYGNQYNNNQGYQ
QGYNNN
xxxxxxxGNNNxxxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx
Caution: Contents may have been coded under pressure.