A slight simplification can be gained by using the 'nsort_by' function from List::UtilsBy (or its XS equivalent). You can also use the special variable '$,' rather than 'join' to control the print.

use strict;
use warnings;
use List::UtilsBy::XS qw(nsort_by);

my $string = "AAATTTAGTTCTTAAGGCTGACATCGGTTTACGTCAGCGTTACCCCCCAAGTTATT
+GGGGACTTT";
my @matches;
push @matches, $& while ($string=~m/([AGCT])\1+/g);
local $, = "\n";
print nsort_by {length} @matches ;
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