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Sequence identity

See also
-id option

  Definition of sequence identity
  Identity and clustering
  Accept options
  Alignment parameters 

Sequence identity is a measure of the similarity (or differences) between two sequences. It is the fraction of columns containing matching letters in a pair-wise alignment of the sequences. See definition of sequence identity for details.

Since identity is calculated from an alignment, in general the identity of a pair of sequences varies with the alignment parameters as well as the definition of identity. This means that different programs may report a different identity for the same pair of sequences, even if the same definition is used. The concept of sequence identity is therefore not biologically well-defined and should not be taken too seriously.