RIPCAL analysis of the rDNA tandem repeat of Stagonospora nodorum. A) multiple alignment of the rDNA repeat family compared to highest G:C content model. Annotation is as for figure 3. Classical CpA↔TpA type RIP mutations are generally limited to full length rDNA-like repeats not located within the rDNA tandem array. One copy within the rDNA array exhibits RIP-like alterations. B) Overall RIP mutation frequency graph over a 50 bp scanning window, corresponding to the alignment above, demonstrating even dominance of CpA↔TpA changes in the non-array full-length repeats except near each end of the alignment.