Don't use $&, it will slow down every regular expression in the program. 

my $string = "CCATGNNNTAACCNNATGNNTAGCC";
while ( $string =~ /([AG]TG.*?T[AG][AG])/ig ) {
  print "matched at $-[0]: $1\n";
}

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In reply to Re^2: Request to correct the perl code for getting substrings by jwkrahn
in thread Request to correct the perl code for getting substrings by supriyoch_2008

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