Pseudoknots differ from real knots in the sense that the strand does not pass completely through the loop but only becomes potentially entangled with it. Anyone who has tried to untangle a pair of earphones or tried to untangle a recently, neatly wound up cord can realize that knots naturally occur on long flexible cords. Indeed, great effort seems to be required to avoid tangling a heap of cords. Figure S5a shows a common pseudoknot known as an H-type pseudoknot. This is also known as an ABAB pseudoknot. The structure is notated below with the standard parenthesis notation for the basic secondary structure (here shown in blue) and square brackets for the pseudoknot linkage (here shown in red). Green indicates the regions of free strand that are not forming base pairs (bps).