How to achieve blast results according to the intuitive interpretation of `-max_target_seqs`?
The -max_target_seqs is also related to -evalue which does not work as one would think. Looking at the blast news one finds that since version BLAST 2.2.27+ released, one should use the -max_target_seqs: 


  4.) The output for reports without separate descriptions and alignments sections (all –outfmt greater than 4) should now use –max_target_seqs to control the output rather than –num_descriptions and –num_alignments.


So it seems that num_alignments is also misunderstood. I came to the conclusion that one cannot expect to get the best n alignments, unless you get all and filter yourself the best ones.