Thanks for your reply! If I implement it like below. It doesn't change the order of codons.

 print "enter sequence and signal end with enter followed by ctrl d\n"
+;
$sequence = <STDIN>;
chomp $sequence;
print "sequence inserted : $sequence\n";
@trips = unpack("a3" x (length($sequence)-2), $sequence);
@trips = join(" ", @trips);

my @shuftrips = &myshuffle( @trips );

print "@shuftrips\n";

sub myshuffle
  {
  map $_->[0],
    sort { $a->[1] <=> $b->[1] }
    map [ $_, rand ], @_;
  }
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