Following advice, I redesigned the whole lattice to accommodate a seam in the middle of the origami structure. It is argued that a circular scaffold (M13) is easier to staple together with crossovers "pinching" rather than end to end. This can be changed using the preferences menu of cadnano
(should be on by default). Alternatively, the midseam can be placed by moving the crossovers to the desired place along the helices (in this case, the middle) by dragging them manually.
This was the first generation of the lattice. It was built on a raster scaffold type, pictured on the right. This was modelled through CanDo
and showed overall right-handed twist. This is due to the assumed 10.67bp / turn in the Square CADNano lattice.