Yet another version, trying for speed like davido's using   tr   , but without losing the speed to eval's just to force   tr   to accept the variables.   If this still doesn't go fast enough you'll have to unroll into 4 separate m/// statements.

    my  $temp = <DATA>;
    print "Discarding the file header line.\n";
    print "    ", $temp;
    
    my  @chars = qw( A C G T );
    my  %cnts;
    while( <DATA> ) {
        foreach my $char (@chars) {
#           my  $cnt = () = m/$char/g;
#           $cnts{$char} += $cnt;
#           printf "  For char '%s' I found %d\n", $char, $cnt;
            $cnts{$char} += () = m/$char/g;
        }
    }
    foreach my $char (@chars) {
        printf "  Char '%s':  %6d\n", $char, $cnts{$char};
    }

__DATA__
Generated by a completely confused program yesterday
ACGTGACTAGAGGCCCGGGGAAAAAAAAAACCCCCCC
ACCTGACTAGAGGCCCGGGGAAAAAAAAAACCCCCCC
ACGTGACTAGAGGCCCGGGGAAAAAAAAAACCCCCCC
AGGTGAGTAGAGGGGGGGGGAAAAAAAAAAGGGGGGG
ACGTGACTAGAGGCCCGGGGAAAAAAAAAACCCCCCC
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Outputs

Discarding the file header line.
    Generated by a completely confused program yesterday
  Char 'A':      70
  Char 'C':      49
  Char 'G':      56
  Char 'T':      10