1. A method for detecting particular nucleotide sequences in a double-stranded oligonucleotide sample, comprising: amplifying segments of the sample with unlabeled primers in the presence of labeled nucleotides to generate labeled double stranded amplicons; cleaving the double-stranded amplicons at a multiplicity of sites which are randomly distributed along each strand to produce fragments which are not fully complementary to one another; mixing the fragments with a hybridization buffer; placing the fragments in contact with a set of single-stranded oligonucleotides under annealing conditions, wherein single-stranded oligonucleotides in the set are complementary to the fragments or to subsequences of the fragments; and detecting hybridization between said set of single-stranded oligonucleotides and the fragments.