An example of a FAAST alignment dynamics programming matrix. Showing the calculated FAAST alignment where one peak (260, A) has been identified as a potential overcall (penalized with -1) and another peak (347, C) have been identified as a likely undercall (not penalized). In this example a nucleotide match score, M = [2, -3] and a gap penalty of G = [5,2] were used. The score of each cell C
is marked in the middle and the non-homopolymer score D
is marked in each upper right corner. Each flowpeak value is also indicated in each upper right corner of the query sequence (first row). Homopolymer corrections are marked in the produced alignment by lower-case characters, either inserted as with undercalls or aligned towards a database sequence gap as with overcalls. The corresponding Smith-Waterman-Gotoh alignment would result in an alignment of the non-gaped middle part of both queries ("AATTCCC").