my $string = "CCATGNNNTAACCNNATGNNTAGCC";

my @substrings;
foreach my $offset ([3, 11], [16, 23]) {
    push @substrings, substr($string, $offset->[0] - 1, $offset->[1] - $offset->[0] + 1);
}

my ($substr1, $substr2) = @substrings;
print "$substr1\n$substr2\n";