Looks like most responders failed to notice you do not need the count of A/C/G/T in that string, but rather that you're goint to process several strings and count the number of A/C/G/Ts as the first character, second character, ...

Do drop the four separate variables and use a hash of arrays and make sure you declare your variables. That way you do not have to use the switch:

   my @seq = split(//,$string);
   my $i = 0;
   foreach my $letter (@seq){
      $counts{$letter}[$i]++
      $i++;
   }
[download]

Then as others suggested you may want to get rid of the split. You may either use the subtring() as suggested or something like this:

my $i=0;
$counts{$1}[$i++]++ while $string =~ /(.)/g;
[download]

Test for yourself what's quickest.

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