Question 3 

foreach my $i (0..$#lines) {
    my $k1 = get_key( (($i >> 6) & 7) * 6 + 17 );
    my $k2 = get_key( (($i >> 3) & 7) * 6 + 17 );
    my $k3 = get_key( ($i & 7)        * 6 + 17 );
    my $frag = $lines[$i];
    $frag_id{$frag} ||= shift @keys;
    $map{$i} = [ $frag_id{$frag}, $k1, $k2, $k3 ];
}

sub get_key {
    my($bin) = @_;
    my $word = shift @keys;
    $used{$word} = $bin;
    return $word;
}