I have searched and was able to find this forum discussion for achieving the effect of overlapping matches.
I also found the following SO question speaking of findin
As far as a workaround, this is what I have come up with to extract the overlapping matches.
> x <- 'ACCACCACCAC'
> m <- gregexpr('(?=([AC]C))', x, perl=T)
> mapply(function(X) substr(x, X, X+1), m[[1]])
[1] "AC" "CC" "AC" "CC" "AC" "CC" "AC"
Please feel free to add or comment on a better way to perform this task.