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==Interpretation==
If two sequences in an alignment share a common ancestor, mismatches can be interpreted as [[point mutation]]s and gaps as [[indel]]s (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another[jeevan]. In sequence alignments of proteins, the degree of similarity between [[amino acid]]s occupying a particular position in the sequence can be interpreted as a rough measure of how [[conservation (genetics)|conserved]] a particular region or [[sequence motif]] is among lineages. The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose [[side chain]]s have similar biochemical properties) in a particular region of the sequence, suggest <ref name=predict>{{cite journal |author1=Ng PC |author2=Henikoff S |date=May 2001 | title = Predicting deleterious amino acid substitutions | journal = Genome Res | volume = 11 | issue = 5| pages = 863–74 | pmid = 11337480 | doi=10.1101/gr.176601 | pmc=311071}}</ref> that this region has structural or functional importance. Although DNA and RNA [[nucleotide]] bases are more similar to each other than are amino acids, the conservation of base pairs can indicate a similar functional or structural role.
==Alignment methods==
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