The present invention relate to methods and compositions for simultaneously analyzing multiple different polynucleotides of a
nucleic acid sample. The subject methods and compositions may also be applied to analyze or identify single
polynucleotide; however, the subject methods and compositions are particularly useful for analyzing large diverse populations of polynucleotides. Methods of the invention involve hybridizing guide oligonucleotides to target polynucleotides for analysis, subsequently digesting double-stranded or partially double-stranded guide
oligonucleotide intermediates, and isolating and analyzing digested part. The guide
oligonucleotide is marked in identifier sequence and
constant region so as to facilitate the simultaneous testing of
multiple target polynucleotides. The identity or expression of a particular
polynucleotide of interest may be ascertained by producing and quantifying a short identifier sequence derived from combining guide oligonucleotides and target polynucleotides.