IIUC your question, which I'm not completely sure about, and taking into account Skeeve's comment, I'm giving you a (hopefully correct) hint/incomplete solution: 
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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In reply to Re: Extracting a substring according to some criteria by blazar
in thread Extracting a substring according to some criteria by Benson

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