Representative plots from 12 hybridizations for T. cruzi chromosome 39. Each dot represents an oligonucleotide probe. The CL-Brener strain, which was used as the reference strain for genome sequencing, is hybrid, thus probes were designed to non-Esmeraldo (non-Esm) sequences (blue spots), Esmeraldo-like (Esm) sequences (green spots), non-Esm gene family sequences (black spots), and Esm gene family sequences (gray spots). In each panel positive log2 ratios of signal intensities (test strain/reference strain) represent amplification in the test strain and negative log2 ratios represent deletion in the test strain, relative to CL-Brener, which was the reference strain in all hybridizations. Shown are examples of segmental aneuploidies of different sizes boxed in gray (>500 kbp amplification in Brazil strain relative to CL-Brener -arrow) and red (~40 kbp deletion in several strains). The Esmeraldo hybridization (boxed in orange) shows decreased log2ratios for the non-Esm probes (blue) and increased log2ratios for the Esm probes (green), as expected because Esmeraldo is homozygous for the Esm haplotype.