RIPCAL analysis of the X0 repeat family of Stagonospora nodorum , representative of a repeat family exhibiting strongly dominant classical CpA→TpA type RIP mutation. A) multiple alignment of the putative transposon repeat family X0 compared to highest G:C content model. Incomplete repeated regions are typical for repeat family alignments illustrated by the blocks in white in panel A. Black = match; grey = mismatch; white = gap. Mismatches corresponding to selected di-nucleotide changes are coloured as indicated. B) Overall RIP mutation frequency graph over a 50 bp scanning window, corresponding to the alignment above, demonstrating the overall dominance of the CpA↔TpA mutation over other CpN↔TpN mutations for the X0 repeat family.