# "$ _" is really "$_", and change the qq to a double-quote
  $_ = 
  "CG
  T--A
  A---T
  A----T
   C----G
    T----A
     A---T
      and 
       so 
       on
  ";
  @_{A => C => G => T => } = 0..3;
  s|.*(\w).*(\w).*\n|$_{$-++ / 9 % 2 ? $2:$ 1}|gex;
  s|(.)(.)(.)(.)|chr (64*$1 + 16*$2 + 4*$3 + $4)|gex;
  eval

##</code><code>##

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

##</code><code>##

  s|
    .*      # greedily match
    (\w)    # match first letter, and store into $1
    .*      # greedily match
    (\w)    # match last letter, and store into $2
    .*\n    # eat up remainder of line
  |
    # this expression maps the relevant character to its Base4 digit from 
    # the %_ hash. The $- is used as a line counter (it defaults to 0). When 
    # the DNA strands flip positions, this continues decoding on the correct
    # strand (see physi's comment for a visual representation of this)
    $_{$-++ / 9 % 2 ? $2:$ 1}
  |gex;

##</code><code>##

  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;

##</code><code>##

use strict;

my $BASE = 4;
my %NUC_PAIRS = (
  A => T =>
  C => G =>
  G => C =>
  T => A =>
);
my @DIGIT_TO_NUC = qw( A C G T );
my $FMT_DNA = <<END;
 01
0--1
0---1
0----1
 0----1
  0---1
   0--1
    01
    10
   1--0
  1---0
 1----0
1----0
1---0
1--0
 10
END
my @FMT_DNA = split "\n",$FMT_DNA;

my $str = 'print"Just Another Perl Hacker\n"';

my @str_digits;
for (split//, $str) {
  my $ord = ord($_);
  my @digits = (0) x 4;
  print "$ord:\t";
  my $i = 0;
  while ($ord) {
    $digits[4 - ++$i] = $ord % $BASE;
    $ord = int ($ord / $BASE);
  }
  print "@digits\n";
  push @str_digits, [@digits];
}

my $i = 0;
for (@str_digits) {
  for (@$_) {
    my $fmt     = $FMT_DNA[$i++ % @FMT_DNA];
    my $nuc0 = $DIGIT_TO_NUC[$_];
    my $nuc1 = $NUC_PAIRS{$nuc0};
    $fmt =~ s/0/$nuc0/;
    $fmt =~ s/1/$nuc1/;
    print "$fmt\n";
  }
}