I used this generator to create a 10000 string file where the first 5000 string are just randomly generated and the other 5000 are random substring extracted from the first 5000. Thus, you'd expect at most 5000 unique strings with a very slight possibility of there being fewer:

#! perl -slw
use strict;

sub rndStr{ join'', @_[ map{ rand $#_ } 1 .. shift ] }

our $N //= 10e3;

my $halfN = $N >> 1;

my @data; $#data = $N;

$data[ $_ ] = rndStr( 200 +int( rand 200 ), 'A', 'C', 'G', 'T', 'N' )
    for 0 .. $halfN;

$data[ $_ + $halfN ] = substr(
    $data[ $_ ], 10, 10 + int( rand( length( $data[ $_ ] ) - 20 ) )
) for 0 .. $halfN;

print for @data;
__END__
C:\test> 906020-gen -N=10e3 > 906020.10e3
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When I run your code on this file it misses some dups:

C:\test>906020-robo 906020.10e3
5551 unique items
4450 rejected.
5 seconds.
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