Provided is a method for characterising cDNA, which method comprises: (a) exposing a sample comprising a population of one or more cDNAs or fragments thereof to a cleavage agent which recognises a predetermined sequence and cuts at a reference site at a known displacement from the predetermined sequence proximal to an end of each cDNA or fragment thereof so as to generate a population of terminal fragments; (b) ligating to each reference site an adaptor oligonucleotide which comprises a recognition site for a sampling cleavage agent; (c) exposing the population of terminal fragments to a sampling cleavage agent which binds to the recognition site and cuts at a sampling site of known displacement from the recognition site so as to generate in each terminal fragment a sticky end sequence of a predetermined length of up to 6 bases, and of unknown sequence; (d) separating the population of terminal fragments into sub-populations according to sequence length; and (e) determining each sticky end sequence.
