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use strict;
use warnings;
...
    for sort { $prompted_seqs{$a}{len} <=> $prompted_seqs{$b}{len} }
        keys %prompted_seqs
        ;

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Win8 Strawberry 5.8.9.5 (32)  Sun 09/20/2020 22:47:03
C:\@Work\Perl\monks\shabird
...
  first: dddddd (6)
  4th: gggggg (6)
  third: ffffffffff (10)