Dot plots are used to determine the percent similarity between two protein sequences. A short segment of one sequence also called window size, is compared with all possible segments of the same length in the second sequence. This generates a matrix of several alignments between the two sequences. For each pair of alignment, the similarity between the amino acid residues is scored based on the probability with which the various pairs of aligned residues replace each other and the similarity in five physical parameters of the amino acid residues. If the similarity between any two segments exceeds the threshold value then a positive score is registered which is displayed as a dot. Weak signals of homology could also be detected by manipulating this threshold value specifically by increasing the mismatch limit and the window size.