Universal variable fragments

A method of analyzing genomic DNA comprising a repeat sequence in a sample, said method comprising:

• providing first and second oligonucleotide primers for performance of a first polymerase chain reaction amplification on said genomic DNA, said first oligonucleotide primer comprising a repeat sequence and at least one non-repeat nucleotide on the first oligonucleotide primer's 5′ end, wherein said non-repeat nucleotide localizes the first oligonucleotide primer to the 5′ end of a repeat sequence in the genomic DNA sample, and said second oligonucleotide primer on the 3′ side of the repeat sequence in the genomic DNA sample comprising at least one a-selective base;
• conducting said first amplification of said genomic DNA at a first temperature permitting both the first and second oligonucleotide primers to anneal to the genomic DNA, thus producing DNA fragments based on repeat sequences on one end of the genomic DNA, and other sequences based on the opposite end of the genomic DNA;
• optionally diluting the reaction products of the first amplification;
• conducting a second amplification on the reaction products of the first amplification, said second amplification being conducted using third and fourth oligonucleotide primers, said third and fourth oligonucleotide primers being elongated versions of said first and second oligonucleotide primers, respectively, enabling amplification at a second temperature permitting annealing of the primers, where the second annealing temperature is higher than the first annealing temperatures, and enabling a selection of a sub-set of the DNA fragments amplified in the first amplification;
• and
• analyzing the sub-set of amplified products.