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Once a sequence containing the desired polymorphism was selected (usually 400-700 bp in length), it was run through the Repeat Masker program http://ftp.genome.washington.edu/cgi-bin/RepeatMaskerin order to avoid selecting PCR primers within Alu, L1, or other repeats.
The gene was located in the approximate interval both cytologically and on the Santa Cruz map http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg10, but was located on chromosome 16p on the NCBI map (builds 25 to 28).
The full report, including GAO's objectives, scope, methodology, and analysis is available at www.gao.gov/cgi-bin/getrpt?GAO-02-966.
A web-interfaced program, Primer3 http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi, was used.
Primers used for amplification of BMP-5 cDNA were designed to unique sequences of rat BMP-5 using the Primer3 program http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi.