The algorithm starts by searching for perfectly matching hexa-, hepta-, octa-and nonamers, as potential nucleation sites (the 'Nuc' part). Every matching oligomer is given the number of matching nt as its NucScore. If the oligomer contains dInosine, the number of dInosines is subtracted from the score but the segment is still counted as uninterrupted, regardless of the dInosines. The NucScore is then used to select the two highest scoring potential nucleation sites which will undergoing zipping, up and downstream.