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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

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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In reply to Re^3: list of unique strings, also eliminating matching substrings by BrowserUk
in thread list of unique strings, also eliminating matching substrings by lindsay_grey

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