This has been done many times.
See the literature in the '70s written by Doug Wallace, David Clayton
and Giuseppi Attardi and their collaborators. All had active groups
studying D-loop sequence at that time. Also see the work of Igor Dawid
on the Xenopus region and the guys in England at the John Innes Institute
(Flavell et al.) for the story on the plant mitochondrial genome.
Generally, it would be good to do a medline search before you do a
posting like this one.
Temple and Jefferson