Fig. 2.
The optimum search scheme for two mismatches consists of three searches with four pieces each. The arrows indicate in which order the pieces are searched. The error bounds below each part are cumulative bounds, i.e. the minimum number of errors that must, respectively, the maximum number of errors that can be spent until searching the end of the corresponding piece. Illustrated for searching the 8-mer CGTACAAG. The forward search covers the error distributions 0010, 0011, 0020, the backward search covers 2000, 1100, 0200, 1010, 0110 and the bidirectional search 0000, 0001, 0002, 1000, 1001, 0100, 0101. (a) Forward search: Sfwd=(1234, 0011, 0022); (b) backward search: Sbwd=(4321, 0002, 0122) and (c) bidirectional search: Sbi=(3214, 0000, 0112)