TIMTOWTDI

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11122267
use warnings;

my $string = "AAATTTAGTTCTTAAGGCTGACATCGGTTTACGTCAGCGTTACCCCCCAAGTTATT
+GGGGACTTT";
my @substrings;

push @{ $substrings[length $1] }, $1 while $string =~ /(([ACTG])\2+)/g
+;

my @sorted = map @{ $_ // [] }, reverse @substrings;

use Data::Dump 'dd'; dd \@sorted;
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Outputs:

[
  "CCCCCC",
  "GGGG",
  "AAA",
  "TTT",
  "TTT",
  "TTT",
  "TT",
  "TT",
  "AA",
  "GG",
  "GG",
  "TT",
  "AA",
  "TT",
  "TT",
]
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