Extension traces of an ε -core. Alignment matrix with two possible traces of the extension of an ε-core. Depending on the length of the extension (red numbers), we obtain the lowest error rates by aligning different sequence positions to each other. For an extension length of 5, 7, and 9 it is better to follow the upper trace, whereas for a length of 11 the lower trace has fewer errors. For all other lengths there is a longer trace with the same number of errors, and therefore it is not necessary to consider those lengths while looking for maximal ε-matches.