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

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

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

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