Search order and scoring matrix for DiagHunter. As the program walks through a matrix of similarity hits, each hit (represented by a red X) initiates a search for a diagonal. Candidates for extension of the diagonal are picked first from those closest to the present hit, and closest to either a forward or reverse diagonal. The search order and scores are represented by the area of the circles in the figure. Once either a forward or a reverse diagonal is initiated, only the reverse (a) or forward (b) version of the search order/score matrix is used for extension of the candidate diagonal, and the diagonal is recursively extended while candidate hits are available and the accumulated diagonal quality score remains above the quality threshold parameter. The sensitivity and selectivity of the search is increased if coding-strand information is included, as this reduces the number of 'random' hits that might be considered at any step.