The design and construction of intricate genetic circuits are fundamental to achieving specific cellular behaviors or functions. These alterations can generate a wide spectrum of genetic functionalities, providing a rich palette of genetic components for designing circuits with varying functions and behaviors1. Designing novel circuits enabled by synthetically assembling megabase scale inserts is now possible,2 but requires methods like genome mapping to ensure the correct structure is generated. Moreover, the inclusion of structural elements that resist rearrangements or disruptions can enhance the circuit’s stability over time, contributing to a more predictable and reliable performance3. Understanding these variations enables the selection and incorporation of specific genomic elements to diversify and enhance the functionality of the genetic circuit. Designers can strategically arrange genetic elements to optimize their interactions, reduce crosstalk, and ensure efficient circuit operation.