The accurate mapping of clones derived from genomic regions containing comp
lex arrangements of repeated elements presents special problems for DNA seq
uencers. Recent advances in the automation of optical mapping have enabled
us to map a set of 16 BAC clones derived from the DAZ locus of the human Y
chromosome long arm, a locus in which the entire DAZ gene as well as subsec
tions within the gene copies have been duplicated. High-resolution optical
mapping employing seven enzymes places these clones into two contigs repres
enting four distinct copies of the DAZ gene and highlights a number of diff
erences between individual copies of DAZ.