Evolutionary Path Table

Legend

A .... index of the shape along the path (0=start, 44=target) B .... time at which a sequence folding into shape i-1 gave rise to a sequence folding into shape i. We will short-cut this phrase by simply saying that shape i-1 is an "ancestor shape" of shape i. We only record shape innovations. Hence, shape i was not realized in the reactor at this time. This time corresponds to the transition from step i-1 to step i in the green trace of Figure 1A.

C .... Number of point mutations at the sequence level which caused the shape transition.

D .... Hamming distance between the current shape on the path and the target. (That's the number of positions in which two shapes - represented as in column G - differ.)

E .... total number of instances of shape i-1 at the time shape i was generated. (The average number of sequences sustainable in the reactor is 1000.) This number gives an indication of whether the ancestor shape was a dominant one.

F .... number of alternative ancestor shapes of shape i. (Shape i may have been present in the reactor on and off. Thus it may have been "rediscovered" several times. Column E gives the total number of different ancestor shapes which innovated the reactor with shape i over the entire history of the simulation.)

G .... shape. The shape is represented in a "balanced parentheses" notation, in which a dot indicates an unpaired position and a matching pair of parentheses stands for a base pair. For example in ..(((((...))).)) the red pair of matching parentheses represents a base pair between positions 4 and 15 in the sequence. Click on the number in column A to see a graphical representation of the secondary structure.

Colors have the same meaning as in the shape path plate (see the corresponding readme).