#! perl -slw
use strict;
use Time::HiRes qw[ time ];
use List::Util qw[sum];;

my $sequence = join'', map{ ( qw[ A C G T ] )[ rand 4 ] } 1 .. 600_000;

my $start = time;
my( %one, %two, %three );
$one{ $_ }++ for unpack '(A1)*', $sequence;
$two{ $_ }++ for unpack '(A2X)*', $sequence;
delete @two{ (qw'A C G T') };;
$three{ $_ }++ for unpack '(A3XX)*', $sequence;
delete @three{ (qw'AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT') };

printf "Elapsed: %3f seconds\n", time - $start;

print sum values %one;
print sum values %two;
print sum values %three;

__END__
P:\test>junk
Elapsed: 3.390625 seconds
600000
599999
599998