Example of repeat clusters at a syntenic break between E. histolytica and E. dispar. Black boxes, repetitive elements; blue boxes, E. histolytica genes; red boxes, E. dispar genes. GenBank accession numbers for each scaffold are shown above lines. Orthologous gene pairs between E. histolytica and E. dispar are connected by gray areas. Percent identity plots between nucleotide sequences DS571146 and DS550750 (positions 6 Kb – 19 Kb) and nucleotide sequences DS571146 and DS550750 (positions 32 Kb – 51 Kb) are shown above and below scaffolds respectively. Numbers indicate scaffold coordinates in Kb. Vertical gray lines depict the locations where synteny disappears.