Both stems in Fig. S5c contain 14 base pairs (bp). Since the helical axis makes a rotation of 360 o every 10 bps, this means that the structure in Fig. S5c is tangled in a knot. There is no reason why such a structure cannot form. Indeed, knots are known to form in some rare proteins [2, 3] . However, it is not a pseudoknot and the current approach is not designed to estimate its existence or the likelihood of its formation. One important feature of a pseudoknot is, therefore, that the linkage stem (here shown in red) must be shorter than 10 contiguous bps. Figure S5e shows two stem-hairpins-loops (blue and purple) that are joined by a linkage stem (red). The stems are all short as in Fig. S5a . This is a pseudoknot, sometimes referred to as a kissing loop. It is also known as an ABACBC pseudoknot. It is also observed in a number of places, although less frequently than H-type pseudoknots. The corresponding bracket notation for this structure is shown below (Fig. S5f) . Belvedere knot secondary structure Supplement Figure S6 . A special type of knot (right hand side) that becomes entangled due to the way the structure folds up. The two dimensional nature of the RNA schematics tends to hide curious possibilities as this. The knot is seen in equilibrium between the unknotted structure (left hand side) and the "Belvedere knot" (right hand side).