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Hi,
   I have heard similar effects from our collaborators who are working
with intensity based FRET. They had better results when they used
cerulean. It was also told that cerulean gave better ,realiable and
photostable rsults
   Flavin is also a concern for autofluorescnece since it has
excitation paeaks at 435nm. Flavin flourescence is also dependent on
environment.
               'Best
                       Deepak