% Seq Identity - How?

[Shiao Y. Wang]

How does one calculate % sequence identity for multiple clones? We have 4
cDNA clones sequenced and we need to report some measure of sequence
identity. Is it the number of nucleotides shared divided by total number
of nucleotides?
For example:

Clone 1     GGG CCC TTT A
Clone 2     GGG TCC TTT A
Clone 3     TGG CCC TTT A

Are these three clones (28/30) 93% identical or (8/10) 80% identical or ??

Thanks for your help.

Shiao Wang
University of Southern Mississippi
sywang at whale.st.usm.edu