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my %value = (
  G => 0,
...
  T => 2,
  C => 3,
);

$number = $w[$n]*(4**$n) + $w[$n-1]*(4**($n-1)) + ... + $w[0]

sub word_to_number {
  my (@w) = @_;
...
    $res += $value{ pop @w };
  };
};

open my $frequencies, ">+", 'frequencies.bin'
  or die "$!";
...
  seek $requencies, $offset * 4;
  write $frequencies, pack "N", $count;
};