Visual Validation. a) The 1336 genes ("Gene Features"), 145 "Contigs", 26 "Scaffolds", and mapped BAC clones ("BAC Clone") are shown for the homologous chromosome pairs (the non-Esmeraldo-like haplotype are the "P" features and the Esmeraldo-like haplotype are the "S" features) of chromosome TcChr39. Where possible, contigs are aligned to place at least one pair of alleles in the same locus (red contigs). Lines between genes on the two homologous chromosomes indicate allelic synteny. BAC clones are color-coded according to the source library (blue = TARBAC, green = EPIFOS); note that only BAC clones that span scaffolds or whose ends map to opposite homologous chromosomes (light blue and light green) are shown. Black contigs are those that were not aligned with another on the opposite chromosome (either no homologous sequence present or the alignment could not be made). Finally, brown contigs indicate possible merged sequence from the two parental haplotypes, blue contigs denote sequences where one or more alleles exist on this chromosome but could not be aligned, and gray contigs indicate sequences where one or more alleles exist on a different chromosome altogether. b) The TriTryp synteny map of TcChr39 shows the regions of T. brucei ("Tb Chromosome Portion") and L. major ("Lm Chromosome Portion") for which at least 10 genes are syntenous with T. cruzi genes are shown. For each chromosome (i.e. Tc, Lm, Tb), the coding strand is shown ("Rev" for reverse strand and "For" for forward strand). Telomeric repeats were identified on the 3' end of this chromosome (yellow ellipses).