Synthesis of Pools of Probes by Primer Extension

A composition of matter comprising:

• a population of duplexes, wherein said duplexes comprise:
• a first population of oligonucleotides comprising a top strand sequence having the following formula:
• V1-B-3′;
• and
• a second population of oligonucleotides comprising a bottom strand sequence having the following formula:
• V2′-B′-3′;
• wherein:
• the nucleotide sequences of B and B′ are complementary and are at least 15 nucleotides in length;
• the nucleotide sequence of B is the same for each oligonucleotide of said first population;
• the nucleotide sequence of B′ is the same for each oligonucleotide of said second population;
• the nucleotide sequence of V1 is variable between the oligonucleotides of the first population
• the nucleotide sequence of V2′ is variable between the oligonucleotides of the second population, and
• V1 and V2′ hybridize to different sites in a reference genome.

A kit comprising

• a) a first population of oligonucleotides comprising a top strand sequence having the following formula:
• V1-B-3′;
• and
• b) a second population of oligonucleotides comprising a bottom strand sequence having the following formula:
• V2′-B′-3′;
• wherein:
• the nucleotide sequences of B and B′ are complementary and are at least 15 nucleotides in length;
• the nucleotide sequence of B is the same for each oligonucleotide of said first population;
• the nucleotide sequence of B′ is the same for each oligonucleotide of said second population;
• the nucleotide sequence of V1 is variable between the oligonucleotides of the first population
• the nucleotide sequence of V2′ is variable between the oligonucleotides of the second population, and
• V1 and V2′ hybridize to different sites in a reference genome.