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@trips = join(" ", @trips);

#!/usr/bin/env perl 
use strict;
...
my @trips = unpack("a3" x (length($sequence)-2), $sequence);
my @shuffled = shuffle(@trips);
print "@shuffled\n";

$ perl /tmp/shuf.pl 
enter sequence and signal end with enter followed by ctrl d
aaabbbcccddd
sequence inserted : aaabbbcccddd
ccc aaa    ddd  bbb