Because the danRer3 chrNA and chrUn chromosomes and the tetNig1 random chromosomes are comprised of unordered scaffolds separated by 500 Ns and 1000 Ns 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 Ns. 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.