A method for preparing sample nucleic acid complements, which comprises: a. preparing a mixture comprising sample nucleic acid and a collection of solid supports under conditions in which a single molecule of the sample nucleic acid hybridizes to a nucleic acid molecule on a solid support in the collection, wherein: the nucleic acid molecules on each solid support in the collection comprise a single-stranded solid phase nucleic acid species including a primer sequence, an identifier sequence and a probe sequence orientated 5' - (primer sequence) - (identifier sequence) - (probe sequence) - 3'; the probe sequence of each solid phase nucleic acid species on a solid support in the collection hybridizes to a subsequence of the sample nucleic acid sequence when the probe sequence is complementary to a nucleotide subsequence in the sample nucleic acid sequence; the solid phase nucleic acid species of each solid support in the collection share a common probe sequence or the solid phase nucleic acid species do not share a common probe sequence with other solid phase nucleic acid species on the solid support; the solid phase nucleic acid species on each solid support in the collection share a common identifier sequence; and the sample nucleic acid is single-stranded nucleic acid; and b. contacting the mixture with extension reagents under conditions in which solid phase nucleic acid species hybridized to sample nucleic acid is extended by the reagents; whereby sample nucleic acid complements comprising the shared, unique identifier sequence of a solid support in the collection and comprising subsequences of the sample nucleic acid sequence are prepared. a. preparing a mixture comprising sample nucleic acid and a collection of solid supports under conditions in which a single molecule of the sample nucleic acid hybridizes to a nucleic acid molecule on a solid support in the collection, wherein: the nucleic acid molecules on each solid support in the collection comprise a single-stranded solid phase nucleic acid species including a primer sequence, an identifier sequence and a probe sequence orientated 5' - (primer sequence) - (identifier sequence) - (probe sequence) - 3'; the probe sequence of each solid phase nucleic acid species on a solid support in the collection hybridizes to a subsequence of the sample nucleic acid sequence when the probe sequence is complementary to a nucleotide subsequence in the sample nucleic acid sequence; the solid phase nucleic acid species of each solid support in the collection share a common probe sequence or the solid phase nucleic acid species do not share a common probe sequence with other solid phase nucleic acid species on the solid support; the solid phase nucleic acid species on each solid support in the collection share a common identifier sequence; and the sample nucleic acid is single-stranded nucleic acid; and the nucleic acid molecules on each solid support in the collection comprise a single-stranded solid phase nucleic acid species including a primer sequence, an identifier sequence and a probe sequence orientated 5' - (primer sequence) - (identifier sequence) - (probe sequence) - 3'; the probe sequence of each solid phase nucleic acid species on a solid support in the collection hybridizes to a subsequence of the sample nucleic acid sequence when the probe sequence is complementary to a nucleotide subsequence in the sample nucleic acid sequence; the solid phase nucleic acid species of each solid support in the collection share a common probe sequence or the solid phase nucleic acid species do not share a common probe sequence with other solid phase nucleic acid species on the solid support; the solid phase nucleic acid species on each solid support in the collection share a common identifier sequence; and the sample nucleic acid is single-stranded nucleic acid; and b. contacting the mixture with extension reagents under conditions in which solid phase nucleic acid species hybridized to sample nucleic acid is extended by the reagents; whereby sample nucleic acid complements comprising the shared, unique identifier sequence of a solid support in the collection and comprising subsequences of the sample nucleic acid sequence are prepared.