use Algorithm::Combinatorics qw( combinations );
use Set::CrossProduct;

my @base = split //, $str;

for my $exact_distance ( 1 .. $d ) {
    my $change_idx_iter = combinations( [ 0 .. $#base ], $exact_distan
+ce );

    while( my $change_idx = $change_idx_iter->next ) {
        my @base_combo = map {
            my $i = $_;
            [ grep { $base[ $i ] ne $_ } qw( A T C G ) ];
        } @$change_idx;
        # HACK: Set::CrossProduct doesn’t work with a 1-dimensional ma
+trix
        push @base_combo, [ 0 ] if $exact_distance == 1;

        my $bases_iter = Set::CrossProduct->new( \@base_combo );

        my @neighbour = @base;

        while( my $new_bases = $bases_iter->get ) {
            @neighbour[ @$change_idx ] = @$new_bases;
            print @neighbour, "\n";
        }
    }
}
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$_ = "[$_]" for @neighbour[ @$change_idx ];
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Makeshifts last the longest.