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 whose identity can be used to differentiate polynucleotides in the sample; the reflex sequence; a polynucleotide of interest having 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; c) replicating the polynucleotide strand of Step b) with a first nucleic acid synthesis primer that anneals at the 3' end of the complement of the first domain to produce a first extension product; d) annealing a second nucleic acid synthesis primer to the first extension product, wherein the second nucleic acid synthesis primer comprises a 3' priming domain that is complementary to a site within the polynucleotide of interest in the first extension product, the site being 3' of the desired site; e) extending the second synthesis primer to produce a second extension product; and f) sequencing the MID and the desired site using a primer complementary to the primer site in the complement of the first domain. 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 whose identity can be used to differentiate polynucleotides in the sample; the reflex sequence; a polynucleotide of interest having 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; a first domain comprising: i) a primer site; and ii) a multiplex identifier whose identity can be used to differentiate polynucleotides in the sample; i) a primer site; and ii) a multiplex identifier whose identity can be used to differentiate polynucleotides in the sample; the reflex sequence; a polynucleotide of interest having 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; c) replicating the polynucleotide strand of Step b) with a first nucleic acid synthesis primer that anneals at the 3' end of the complement of the first domain to produce a first extension product; d) annealing a second nucleic acid synthesis primer to the first extension product, wherein the second nucleic acid synthesis primer comprises a 3' priming domain that is complementary to a site within the polynucleotide of interest in the first extension product, the site being 3' of the desired site; e) extending the second synthesis primer to produce a second extension product; and f) sequencing the MID and the desired site using a primer complementary to the primer site in the complement of the first domain.