mismatch到底只是一个碱基替换，还是也包括了插入缺失？

If two sequences in an alignment share a common ancestor, mismatches can be interpreted as and gaps as (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between occupying a particular position in the sequence can be interpreted as a rough measure of how a particular region or is among lineages. The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose have similar biochemical properties) in a particular region of the sequence, suggest that this region has structural or functional importance. Although DNA and RNA bases are more similar to each other than are amino acids, the conservation of base pairs can indicate a similar functional or structural role.

 

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