I wouldn't use a regex for this, there aren't any patterns, just plain old string matching 
my $super = 'AAAAATT';
my $sub   =  'AT';

print "1\n" if (index($super, $sub) != -1);

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my name's not Keith, and I'm not reasonable.

In reply to Re^2: Testing if a string is a substring by reasonablekeith
in thread Testing if a string is a substring by monkfan

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