The T. cruzi maxicircle non-coding region contains a variable and a repetitive region. A) Dot plot analyses generated using Dottup comparing CL Brener maxicircle consensus vs. itself showing a repetitive region of short motifs (red) and a longer duplicated conserved element in the variable region (green). B) Expanded view of the repetitive non-coding region of the CL Brener dotplot. C) Dot plot comparison generated using Dotter software of CL Brener and Esmeraldo variable regions shows the presence of a conserved element (gray bars). For this analysis the CL Brener and Esmeraldo sequences of interest were joined for a combined comparison to self and to each other. Enlarged inset shows a conserved element with cross-structure indicative of a palindrome. D) The 39-bp imperfect palindrome within the variable region conserved element. E) Schematic representation of percent identity of variable region conserved element among all CL Brener and Esmeraldo assemblies.