I didn't test it, but see if it works:

([AGCT])(?!\1)([AGCT])(?!\1|\2)([AGCT])(?!\1|\2|\3)[AGCT],([AGCT])(?!\
+4)([AGCT])(?!\4|\5)([AGCT])(?!\4|\5|\6)[AGCT]
[download]

No, it would only do for 4 char strings only on each side.
What about:

my $str = 'some_str';

my @matches = ($str =~ /^([AGCT]{1,4}),([AGCT]{1,4})$/);

if(2 == scalar @matches){
  for my $match (@matches){
    my %letters = ();
    map { $letters{$_} } ($match =~ /(.)/g);
    exit 0 if(scalar keys %letters != length $match);
  }
}else{
  exit 0;
}

print $str;
[download]

:) also didn't test, maybe doesn't work.