I'll leave the interaction with the environment to you.

$_ = "ATGCCCGATATATATCCCNNNATATATGCGCATGCTGCT";
say length $1 while /\G(.*?)AT/g;
say length $';
__END__
0
5
0
0
0
6
0
0
4
6
[download]

Or:

$_ = "ATGCCCGATATATATCCCNNNATATATGCGCATGCTGCT";

my ($l, $m) = (-2, 0);
$m = length $', say -$l - 2 + ($l = length($`)) while /AT/g;
say $m;
__END__
0
5
0
0
0
6
0
0
4
6
[download]

For those readers who get trigger happy when they see a use of $' or $`, feel free to use /p instead if you're going to use the above code.