Figure 2.

(Top left): binding rules for canonical DNA base pairs interactions. (Top right): given a strand 1 of length $L=11$ and a strand 2 of length $l=8$, schematization of the MCO and TMO between them. In this peculiar $r_{1,2}$, there is a total of three matching base pairs, but only two of them are consecutive (hence, MCO = 2 and TMO = 3). (Bottom): representation of the calculation of $\omega$ for strand 1 and strand 2. An MCO${|}_{r_{1,2}}$ is determined for each relative position $r_{1,2}$ between them, and then the largest is selected.