A method of identifying a nucleotide in a candidate sequence, said method comprising: a) providing an array substrate comprising a surface having at least a first subpopulation and a second subpopulation of identifier probes attached to beads distributed thereon, wherein identifier probes of the first subpopulation and identifier probes of the second subpopulation comprise a first sequence adjacent to a candidate sequence, the first sequence of the first subpopulation of identifier probes having the same sequence as the first sequence of the second subpopulation of identifier probes and the candidate sequence of the first subpopulation of identifier probes being different from the candidate sequence of the second subpopulation of identifier probes; b) adding a set of decoding probes, said decoding probes comprising a second sequence complementary to a portion of the first sequence and a variable region adjacent to said second sequence, wherein said variable region comprises at least one detection nucleotide at a detection position, wherein said set of decoding probes comprises different subsets, and wherein decoding probes from different subsets comprise a different detection nucleotide at the same detection position and a label wherein the decoding probes of at least one subset have a detection nucleotide at the detection position that correctly base pairs to a nucleotide of at least one of said different candidate sequences, and wherein a decoding probe having a detection nucleotide that correctly base pairs to the nucleotide of the candidate sequence hybridizes more efficiently to an identifier probe comprising said candidate sequence than a decoding probe having a mismatch at the detection position; and c) detecting the presence of said label. a) providing an array substrate comprising a surface having at least a first subpopulation and a second subpopulation of identifier probes attached to beads distributed thereon, wherein identifier probes of the first subpopulation and identifier probes of the second subpopulation comprise a first sequence adjacent to a candidate sequence, the first sequence of the first subpopulation of identifier probes having the same sequence as the first sequence of the second subpopulation of identifier probes and the candidate sequence of the first subpopulation of identifier probes being different from the candidate sequence of the second subpopulation of identifier probes; b) adding a set of decoding probes, said decoding probes comprising a second sequence complementary to a portion of the first sequence and a variable region adjacent to said second sequence, wherein said variable region comprises at least one detection nucleotide at a detection position, wherein said set of decoding probes comprises different subsets, and wherein decoding probes from different subsets comprise a different detection nucleotide at the same detection position and a label wherein the decoding probes of at least one subset have a detection nucleotide at the detection position that correctly base pairs to a nucleotide of at least one of said different candidate sequences, and wherein a decoding probe having a detection nucleotide that correctly base pairs to the nucleotide of the candidate sequence hybridizes more efficiently to an identifier probe comprising said candidate sequence than a decoding probe having a mismatch at the detection position; and c) detecting the presence of said label.