use Modern::Perl;
use Data::Dump qw /dump/;

my @results;

while (<DATA>) {
    my @codon = split '', (split /\s+/)[1];
    while (my ($seq, $char) = each @codon) {
        $results[$seq]{$char}++;
    }
}
say dump(@results);

__DATA__
first  ACGATT--GAT
second AGTTAAC-TTT
third  TTAGCAGG-TA


##</code><code>##

(
  { A => 2, T => 1 },
  { C => 1, G => 1, T => 1 },
  { A => 1, G => 1, T => 1 },
  { A => 1, G => 1, T => 1 },
  { A => 1, C => 1, T => 1 },
  { A => 2, T => 1 },
  { "-" => 1, "C" => 1, "G" => 1 },
  { "-" => 2, "G" => 1 },
  { "-" => 1, "G" => 1, "T" => 1 },
  { A => 1, T => 2 },
  { A => 1, T => 2 },
)


##</code><code>##

while (<DATA>) {
    my $seq;
    $results[$seq++]{$_}++ for split '', (split /\s+/)[1];
}