Output of PAMPS for a set of 20 sequences, given l
= 17 and d
= 64 (gray background). In this case the output is a single sequence which is split just before a G nucleotide that is marked by 1 underneath it. Each nucleotide belongs to at least a sub-sequence of length at least 17 and degeneracy at most 64 which does not pass over the split point (the split point is indicated by the vertical dashed line; see Methods for description of split point). All sub-sequences that meet these criteria are indicated below the output. Obviously not all sub-sequences of length 17 nt have degeneracy less than 64. The possibility of choosing between several sub-sequences allows the user to design more compatible pairs of primers, e.g. primers with close annealing temperatures.