Table 1.

The four potential di-nucleotide RIP mutations detected by RIPCAL.

RIP mutation				Counted di-nucleotides
Forward		Reverse complement		Forward	Reverse complement
pre-RIP	post-RIP	pre-RIP	post-RIP
CpA	TpA	TpG	TpA	CpA, TpA	TpG, TpA
CpC	TpC	GpG	GpA	CpC, TpC	GpG, GpA
CpG	TpG	CpG	CpA	CpG, TpG	CpG, CpA
CpT	TpT	ApA	ApG	CpT, TpT	ApG, ApA

The deRIP process counts the occurrence of the contributing di-nucleotides incrementally across a multiple alignment of repeats and alters the consensus sequence at each position to the appropriate pre-RIP di-nucleotide sequence.