A valid pair of fosmid end sequences must be at least 32Kb but no more than 47Kb away from each other. The orientation of the first fosmid end sequence must be "+" and the orientation of the second fosmid end sequence must be "-".
End sequences were trimmed at the NCBI using ssahaCLIP written by Jim Mullikin. Trimmed fosmid end sequences are placed on the assembled sequence using Jim Kent's blat program.
Sequencing of the fosmid ends was done at the Whitehead Institute. Sequences and quality scores are available in the NCBI Trace Respository.