In silico digestion. A target sequence is digested in silico in a reaction consisting of a single enzyme cleaving in the middle of the recognition sequence ‘TA’. This reaction is certain to cleave the target sequence at two positions; between positions 2 and 3, and between positions 17 and 18. Cleavage between positions 5 and 6 is possible, but not certain, since it depends on the nucleotide actually present at position 5. This digestion thus generates one fragment, having a length, l, of 15, with the region of interest beginning at position rb = 7 and ending at position re = 11. A possible restriction enzyme cleavage position cp exists at position 3. Selection of structure-specific cleavage position. Finding an optimal cleavage position, p, using the parameters b = ‘T’, smax = 15, smin = 5 and fmax = 10 next proceeds as follows: the interval P is [4, 10] according to the definition of P. Since pmin + 1 < rb < pmax, we have an instance of case (iii). Thus, we start searching for a ‘T’ in the sub-interval [4, 6]. Positions are interrogated in the order 6, 5, 4. As no ‘T’ was found, we continue the search in the sub-interval [7, 10], starting from position 7. We find a ‘T’ at position 8, and thus set p = 8. This gives C(p) = C(8) = 3.