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.