Abstract: A method for characterizing cDNA, which comprises: (a) cutting a sample comprising a population of one or more cDNAs or isolated fragments thereof, each having a strand complementary to the 3′ poly-A terminus of an mRNA and bearing a tail, with a first sampling endonuclease at a first sampling site of known displacement from a reference site proximal to the tail to generate from each cDNA or isolated fragment thereof a first and second sub-fragment, each comprising a sticky end sequence of predetermined length and unknown sequence, the first sub-fragment bearing the tail; (b) sorting either the first or second sub-fragments into sub-populations according to their sticky end sequence and recording the sticky end sequence of each sub-population as the first sticky end; (c) cutting the sub-fragments of each sub-population with a second sampling endonuclease, which is the same as or different from the first sampling endonuclease, at second sampling site of known displacement from the first sampling site to