How to deal with lastz duplicated results

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?

alignment genome

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written 10.1 years ago by Cacau

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

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written 9.9 years ago by microfuge

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