DNA methylation is an important epigenetic mechanism in gene regulation and the detection of differentially methylated regions (DMRs) is enthralling for many disease studies. There are several aspects that we can improve over existing DMR detection methods: (i) methylation statuses of nearby CpG sites are highly correlated, but this fact has seldom been modelled rigorously due to the uneven spacing, (ii) it is practically important to be able to handle both paired and unpaired samples, and (iii) the capability to detect DMRs from a single pair of samples is demanded.