The second draft assembly of the Fugu genome consists of 12,403 contigs, or scaffolds. The individual contigs sizes range from 2-650Kbp. The draft sequence of Fugu Genome available covers 320 Mbases of DNA sequence. We estimate that this covers approximately 90% of the non-repetitive fraction of the genome (which has a total size, including repeats, of around 365Mbases).
The alignments were done with BLAT in translated protein mode requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human genome was masked with RepeatMasker and Tandem Repeat Finder before running BLAT.
Many thanks to Fugu Genomics Project for providing the Fugu sequence.