Nucleotide composition analysis of the mt genome of R. similis. A. Based on a cumulative GC-skew (G-C/G+C) graph, the offset (vertical bar) from the fitted model (dashed line) corresponds to the location of the origin of replication of the light strand (OriL) . B. A linear representation of the circular mt genome, with rRNA and PCGs as indicated. Black bars and checkers represent tRNAs and repeat regions, respectively. The predicted OriL is located near the sextuple C motif. The prediction of OriH is explained in C and D. C. Due to deaminations preferably occurring during single-strandness, the ratios T/C (right y-axis), G/A (left y-axis) and T+G/C+A (left y-axis) differ. From these curves, in which 1 is the mean value, predictions about OriL and OriH can be made. The minimum of the T/C curve corresponds to the OriL, while for G/A the minimum is located in the tRNAs preceding nad4. These differences could be explained by different kinetics for both deamination processes . The T+G/C+A measure (covering both processes) reaches a maximum at the start of cox2 and a minimum at the predicted OriL. From this, two replication origins could be concluded, with OriH located at the start of cox2. If OriL is at 11,000 and OriH at 4,000, both replicases meet around 1,000 (assuming similar speeds), leaving this region single-stranded for a short period, causing a local minimum (star). D. The average T+G/A+C (left y-axis) and G/A (right y-axis) of the nucleotides at third codon positions. From cox2 on, both measures decrease with a minimum at nad6. The G/A ratio shows a pattern corresponding to that of T+G/A+C, as opposed to graph C, where the kinetics of the A to G mutations  and the natural variation cause a high level of noise in the G/A ratio.