You can use a regexp, but you ought to make it work in one pass. It's a little tricky, but it benches favorably with ikegami's solution.

sub roy {
   my %count;
   while ($seq =~ /(?=(((.).).))/g) {
      ++$count{$1};
      ++$count{$2};
      ++$count{$3};
   }
   # pick up the last two chars
   $seq =~ /((.)(.))$/;
      ++$count{$1};
      ++$count{$2};
      ++$count{$3};
   1;
}
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$seq should be at least 3 chars long.