A method of employing a nanopore (20) structure in a manner that allows the detection of the positions (relative and/or absolute) of nucleic acid probes (12) that are hybridized onto a single- stranded nucleic acid molecule (14) . In accordance with the method the strand (14) of interest is hybridized with a probe (12) having a known sequence. The strand (14) and hybridized probes (12) are translocated through a nanopore (20) . The fluctuations in current measured across the nanopore (20) will vary as a function of time corresponding to the passing of a probe (12) attachment point along the strand (14) . These fluctuations in current are then used to determine the attachment positions of the probes (12) along the strand (14) of interest. This probe (12) position data is then fed into a computer algorithm that returns the sequence of the strand (14) of interest.
