Patent ID: 8563246

Claim:
A method of determining a nucleotide sequence of a polynucleotide, said method comprising the steps of: a) providing a substrate comprising a channel having a first subpopulation and a second subpopulation of captured nucleic acids distributed thereon, wherein captured nucleic acids of the first subpopulation and captured nucleic acids of the second subpopulation comprise an anchor sequence adjacent to a target sequence, the anchor sequence of the first subpopulation of captured nucleic acids having the same sequence as the anchor sequence of the second subpopulation of captured nucleic acids and the target sequence of the first subpopulation of captured nucleic acids being different from the target sequence of the second subpopulation of captured nucleic acids, wherein captured nucleic acids of the first subpopulation and captured nucleic acids of the second subpopulation are hybridized to a plurality of target probes comprising a variable region, said variable region comprising at least one detection nucleotide at a detection position, said detection nucleotide being able to basepair with a nucleotide of at least one of said different target sequences, wherein said plurality of target probes comprises different groups, and wherein target probes from different groups comprise a different detection nucleotide at the same detection position and a label that distinguishes the detection nucleotide; b) detecting the presence of said label; and c) associating the label with the identity of one or more nucleotides of the polynucleotide.