Because the danRer3 chrNA and chrUn chromosomes and the tetNig1 random 
chromosomes are comprised of unordered scaffolds separated by 500 <em>N</em>s
and 1000 <em>N</em>s respectively, the blastz alignments and subsequent 
chaining were first performed on the scaffolds, and the coordinates were then 
lifted up to the chromosome level. This avoided false alignments across the 
<em>N</em>s. The M parameter was set to utilize the Blastz dynamic masking 
functionality. The tetraodon sequence was split into 500 kb contigs for the 
non-random chromosomes (lifted up to the chromosome level after chaining) and 
scaffolds for the random chromosomes. Each chunk of danRer3 sequence was 
aligned with all of the tetNig1 sequence in order for dynamic masking to 
occur.