INITIAL RECRUITMENT OF FOSMID READS

Align all fosmid end sequences using NCBI megablast

(-p 80 -s 90 .v 7 .b 7 .w 12 .t 21) to Build35, July 2004,400kb segments
A score cutoff allowed for the flexibility to detect shorter alignments with higher similarity or longer alignments with lower sequence identity, such as those due to base-calling errors in poor quality traces

Additional Threshold

an 80% identity threshold (-p 80) was set to avoid recruiting numerous pairwise representing related transposable/repetitive elements