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  # "$ _" is really "$_", and change the qq to a double-quote
  $_ = 
...
  s|.*(\w).*(\w).*\n|$_{$-++ / 9 % 2 ? $2:$ 1}|gex;
  s|(.)(.)(.)(.)|chr (64*$1 + 16*$2 + 4*$3 + $4)|gex;
  eval

  @_{A => C => G => T => } = 0..3;
  # is really...
  @_{'A', 'C', 'G', 'T'}   = 0..3;

  s|
    .*      # greedily match
...
    # strand (see physi's comment for a visual representation of this)
    $_{$-++ / 9 % 2 ? $2:$ 1}
  |gex;

  s|
    # store next four characters into $1,$2,$3, and $4
...
    # replace with a Base4-to-ASCII conversion of those characters
    chr (64*$1 + 16*$2 + 4*$3 + $4)
  |gex;

use strict;

...
    print "$fmt\n";
  }
}