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my @seqlen = (-1,1);    # Memoize sequence length
my $top    = 20;        # Report this many of the top sequences
...
my $mintop = 0;         # Lowest value in @top

GetOptions('top=i' => \$top, 'upper=i' => \$upper);

for (my $start = 3; $start < $upper; $start += 2) {
    my ($n, $len) = ($start, 0);
...
    top($start => $len)            if $len > $mintop  and     $start <
+= $upper;
    top($n * 2 => $seqlen[$n] + 1) if   $n < $upper/2 and $seqlen[$n] 
+> $mintop;
}

sub top {
    my ($n, $len) = @_;
...
    pop @top if @top > $top;
    $mintop = $top[-1][1];
}

real    0m0.848s
user    0m0.835s
sys     0m0.012s