Pseudoknot

In the top left panel in the figure above is a window that is following the development of the number of pseudoknots in each structure.  Black stands for 0 pseudoknots, red 1,  orange 2, yellow 3, green 4, cyan 5  blue 6, violet 7, and white is greater then seven.  In the top right panel there is a Stem Trace window that is following the 2 stems that make the pseudoknots.  There is a color designated for each of the stems.  Processors that contain one of the stems will show up in the designated color in the window.  When a processor contains both stems it shows up as white and when the processor contains neither of the stems it appears black.  In the bottom right panel there is a population fitness window.  Red denotes poor fitness.  The colors move through green to blue, which indicates good fitness.  In the bottom left panel is a window showing the 2D and 3D structure of a particular stem drawn by H. Martinez's rna_2d3d program.

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