The largest repetitive region and structural polymorphism surrounding orf288 in the hau CMS mitochondrial genome. (A) The largest repeats in the hau CMS mitochondrial genome are 7369 bp and 7404 bp, both of which showed 8 bp indel SNPs. There was also three small direct repeats named sR1, sR2 and sR3 in the largest repeats. A detailed nucleotide sequence of the three repeats is given above. (B) Three large repeats of more than 100 bp were located downstream of the CMS-associated orf288 gene.