1. A method of oligomer sequence mapping, the method comprising: receiving a data set including two or more related oligomer sequences obtained from a fragment of genetic material; receiving a key pattern corresponding to a reference index that was generated by applying the key pattern to a reference; assuming a first separation distance between two of the related oligomer sequences to create a first possible sequence; applying the key pattern to the first possible sequence to generate a first key, the key pattern selecting which bases of the first possible sequence are to be used in generating the first key; assuming a second separation distance between the two related oligomer sequences to create a second possible sequence, the second separation distance being different than the first separation distance; applying the key pattern to the second possible sequence to generate a second key, the second key including different bases than the first key; and comparing the first and second generated keys to the reference index to determine candidate locations of the two oligomer sequences in the reference, wherein the method is performed with a computer.