## Pairwise comparison parameters

There are four kinds of comparison that can be made between the sequences in the alignment, as shown in figure 20.14.

Figure 20.14: Adjusting parameters for pairwise comparison.

• Gaps Calculates the number of alignment positions where one sequence has a gap and the other does not.
• Identities Calculates the number of identical alignment positions to overlapping alignment positions between the two sequences.
• Differences Calculates the number of alignment positions where one sequence is different from the other. This includes gap differences as in the Gaps comparison.
• Distance Calculates the Jukes-Cantor distance between the two sequences. This number is given as the Jukes-Cantor correction of the proportion between identical and overlapping alignment positions between the two sequences.
• Percent identity Calculates the percentage of identical residues in alignment positions to overlapping alignment positions between the two sequences.
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