Patent ID: 8298767

Claim:
A method of sample analysis, comprising: a) annealing a reflex sequence in a polynucleotide strand in a sample with a complement of the reflex sequence present in the polynucleotide strand, wherein the polynucleotide strand comprises the following in a 5′ to 3′ orientation: a first domain comprising i. a primer site and ii. a multiplex identifier (MID) comprising a unique nucleotide sequence that distinguishes said polynucleotide strand from other polynucleotide strands in said sample; the reflex sequence; a polynucleotide of interest that is from 100 bases to 30 kilobases in length, wherein said polynucleotide of interest has a desired site that is distal to the first domain; and the complement of the reflex sequence, wherein the complement of the reflex sequence is present at the 3′ end of the polynucleotide strand; b) extending from the 3′ end of the complement of the reflex sequence through the first domain to produce a double stranded region comprising a complement of the first domain at the 3′ end of the extended polynucleotide strand, thereby moving the first domain into proximity with the desired site; and c) sequencing the MID and the desired site using a primer that is complementary to the primer site in the complement of the first domain.