Local inversion on T. cruzi TcChr11. a) The region on left-hand side of homologous chromosome P appears inverted relative to S, as the orientation of scaffold CH473345-1 was reversed relative to CH473447 in order to close the BAC clones on both homologous chromosomes (i.e if CH473345-1 was oriented according to allelic synteny, then the BAC clones on the P chromosome would be unclosed). b) BAC clones and probes were chosen for Southern blot analysis to validate this inversion. The left-hand side shows a diagram of the design of the blot (see Figure 4 for more details). The chromosome inversion is confirmed if BAC clones 15L22, 14F9, 3J3, and 5D6 contains genes G1–G7 (but not G8), but BAC clones 17N21, 8P12, 6L16, and 10F10 contain genes G1–G3 and G5–G8 (but not G4). The right-hand side of the figure shows the result of the analysis where the hybridization results confirm the inversion.