Depending on the length and number of your nucleic acids, and the number of comparisons you are making it might be better to store and compare bit strings generated with the vec command rather than character strings. You could convert each character in the original string with a for loop and a hash table ie something like
my $char_string = "AAATAT";
my $bit_string = "";
my %lookup_table = ("A" => "00", "T" => "01", "C" => "10", "G" => "11
+");
my @char_array=(split //, $char_string);
for (my $i=0; $i <= $#char_array ; $i++) {
vec($bit_string,$i,2) = $lookup_table{$char_array[$i]};
}
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