Patent ID: 8518640

Claim:
A method of determining a first nucleotide at a detection position of a target sequence comprising a plurality of detection positions, said method comprising: a) providing an array comprising a plurality of concatemers randomly disposed on a surface, wherein each concatemer comprises a plurality of monomers and each monomer comprises: i) a target domain of said target sequence comprising a set of target detection positions; ii) an adaptor comprising a first anchor site; b) hybridizing a first anchor probe to said first anchor site; c) hybridizing a fully degenerate second anchor probe to the target sequence, adjacent to said first anchor site, or, hybridizing a partially degenerate second anchor probe to a second anchor site in the adaptor adjacent to the first anchor site, wherein said partially degenerate second anchor probe also hybridizes to the target sequence; d) hybridizing a sequencing probe to said target domain, wherein said sequencing probe comprises: i) a first probe domain complementary to said target domain; ii) a unique nucleotide at a first interrogation position; and iii) a label; under conditions wherein if said unique nucleotide is complementary to said first nucleotide, said sequencing probe hybridizes to said target domain; e) ligating said anchor probes and said sequencing probe; and f) identifying said first nucleotide wherein said ligating step (e) is driven to between about 20 percent and about 90 percent completion.