Here is some more information about this plugin:
CpG Islands uses a well known Hidden Markov Model algorithm called the Forwards/Backwards algorithm to calculate the posterior probability of any residue being in a CpG Island, and uses state transition parameters from taken from p. 50 of R. Durbin, S. Eddy, A. Krogh, and G. Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.
The green bars are the best global reconstruction - green indicates CpG island regions in the most likely global assignment of CpG islands to the sequence.
The black/green line is the per-site log odds ratio, green indicates that the site is probably part of a CpG island, taking all possible reconstructions into account.