PairHMM state diagrams of Pairagon. (a) Alignment model and (b) Null model. RG1 and RG2 are unaligned genomic sequences in the 5' and 3' ends, respectively; RC1 and RC2 are unaligned cDNA sequences in the 5' and 3' ends, respectively; A, aligned; Entry corresponds to the first two bases of an intron; Exit corresponds to the last two bases of an intron; G, genomic insertion; C, cDNA insertion; RG and RC are random genomic and cDNA sequences, respectively. States that can start an alignment are marked with an asterisk and states that can end an alignment are marked with a dagger.
Arumugam et al. Genome Biology 2006 7(Suppl 1):S5 doi:10.1186/gb-2006-7-s1-s5