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.

In reply to Re: Seeking help from Perl Monks for counting regular expressions (motifs) and counting lengths between them in a large string by JavaFan
in thread Seeking help from Perl Monks for counting regular expressions (motifs) and counting lengths between them in a large string by supriyoch_2008

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