Polynucleotide-array assay and methods

A method of analyzing a polynucleotide analyte sequence, comprising

• (i) contacting the analyte with a position-addressable array of oligonucleotides formed in an array of capillary tubes, where each capillary tube in the tube array includes a different-sequence oligonucleotide attached to an inner wall portion of that tube and having a 5'-proximal and 3'-distal orientation,
• said contacting being carried out under conditions that allow hybridization of the analyte, wherein said analyte is in single-stranded form, to array oligonucleotides whose sequences are complementary to sequences within the analyte,
• (ii) extending analyte-hybridized array oligonucleotides by strand-directed polymerization, along analyte segments extending distal to the 3' ends of the hybridized array oligonucleotides, to produce extended oligonucleotides,
• (iii) during or after said extending, labeling the extended oligonucleotides with a detectable reporter, and
• (iv) analyzing the analyte sequence from the observed pattern of labeled, extended oligonucleotides in the array.