How to deal with lastz duplicated results

Question

[Cacau]

I am using lastz to align two genomes. I found there are some regions in genome A aligned to two regions in genome B. I want to find out the alignment with the best quality. How should I deal with that? Can I keep both alignments?

[microfuge]

Here are the detailed steps http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto