my $allow=join '|', qw/AA AG GC GT CA CG TT TC/;
my $disallow=join '|', qw/AC AT GG GA CC CT TG TA/;
# ...
my @chunks=/(?:$allow).*?(?=$disallow)/g;
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my @allowed = qw[ AA AG GC GT CA CG TT TC ];
my $allowed = join "|", @allowed;
my $regex   = qr/ N+ | (?: (?=$allowed) . )*  . /x;

my $data = "CTGTCAGCNNNCCGGTTTTCAAGNNGAGCACACACCAAAAATGCACCAAAGCTTNACA
+TCCATACAAA";

print "$_\n" for $data =~ m/$regex/g;
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This doesn't work for multi-line data. You can either first remove all the newlines from the data, or if you don't want to have the whole file in memory at once, you can do this "inching along" process manually. Take one character at a time, keeping track of the last one you've seen as well. If the last two characters are an allowed sequence, then add the new character to a buffer. If the last two characters are disallowed, then print the buffer (it is a maximal allowed string), and restart the buffer starting with this new character.

Update: Something like this:

my @allowed = qw[ AA AG GC GT CA CG TT TC NN ];
my %allowed = map { $_ => 1 } @allowed;

my $buf;
while ( get next input character as $c ) {
    if ($allowed{ substr($buf,-1).$c }) {
        $buf .= $c;
    } else {
        print "$buf\n";
        $buf = $c;
    }
}
print "$buf\n"; # don't forget last one
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Friends,

I have encountered one problem for the below input because the last character G of first line and the first character C of the next line are @allowed region. But when I get the output, G and C are not in allowed. This is because There is a space after the last character G.

my @allowed = qw[ AA AG GC GT CA CG TT TC ];
my $allowed = join "|", @allowed;
my $regex   = qr/ N+ | (?: (?=$allowed) . )*  . /x;

$data="TGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGATAG
C";
print "$_\n" for $data =~ m/$regex/g;
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ie instead to be printed as GC I get it as

G
C
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which is wrong Please give a solution.

Edit: g0n - code tags