The simplest way to do it, demonstrated in the debugger
DB<39> $_ = "AAATTTAGTTCTTAAGGCTGACATCGGTTTACGTCAGCGTTACCCCCCAAGTTAT
+TGGGGACTTT";
DB<40> push @substr, $1 while /((\w)\2+)/g
DB<41> @sorted = sort { length($b) <=> length($a) } @substr
DB<42> x @sorted
0 'CCCCCC'
1 'GGGG'
2 'AAA'
3 'TTT'
4 'TTT'
5 'TTT'
6 'TT'
7 'TT'
8 'AA'
9 'GG'
10 'GG'
11 'TT'
12 'AA'
13 'TT'
14 'TT'
DB<43>
Storing the length in @substr for a Schwartzian transform might be faster, but I wouldn't bet on this.
IMHO is length only doing a simple lookup of the pre-calculated length inside Perl's data-structure for strings and should be pretty fast.
HTH! :)
update
you could also do sort and dump in one line:
DB<43> print join "\n", sort { length($b)<=>length($a) } @substr
CCCCCC
GGGG
AAA
TTT
TTT
TTT
TT
TT
AA
GG
GG
TT
AA
TT
TT
DB<44>
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