This plugin identifies likely CpG islands in a DNA sequence. The most likely reconstruction is drawn as the background colour, with light green indicating CpG islands (likely genes) and white indicating an inter-island region. Thus, the background colour gives the most plausible answer to the question: "Where are the CpG islands in this sequence?".

Additionally, for sequences under 1 million bases in length, the log odds ratio of each residue to belong to a CpG island or inter-island region is drawn as a graph. For each residue individually, this graph answers the question: "Is this residue part of a CpG island? How much more plausible is it that it is part of a CpG island, rather than an inter-island region?".

More specifically, the Y axis indicates the log odds ratio, i.e. the logarithm of the ratio between the likelihood of the residue being inside and outside of a CpG island. The Y axis is scaled so that the center represents an odds ratio of 1.0 (log odds ratio of log(1.0) = 0.0), indicating that it is equally plausible that the residue is part of a CpG island or an inter-island region. Values above this center line are coloured green. The higher up a value is, the more likeliy is it that it is part of a CpG island.

Implementation detail: The parameterisation of the Hidden Markov Model for this implementation was adapted 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.