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my @allowed = qw[ AA AG GC GT CA CG TT TC ];
my $allowed = join "|", @allowed;
...
my $data = "CTGTCAGCNNNCCGGTTTTCAAGNNGAGCACACACCAAAAATGCACCAAAGCTTNACA
+TCCATACAAA";

print "$_\n" for $data =~ m/$regex/g;

my @allowed = qw[ AA AG GC GT CA CG TT TC NN ];
my %allowed = map { $_ => 1 } @allowed;
...
}
print "$buf\n"; # don't forget last one