Attached, find the program I used to do the respective calculations (info.pl), a document answering the 2 questions (ExplanationSKM.pdf), and the picture of my plotted entropy values. A discussion of this plot can be found below:
From the graph, it is clear to see which positions and/or areas of the sequence have the lowest and highest entropies. This is particularly informative in this case of the conservation at each location. As one might expect for a specialized 2d structure such as tRNA possess, there are certain areas (likely stem regions) where the entropy is quite low, indicating that across the sequences they are fairly conserved (and thus would require less information to encode). The opposite is true for the high entropy sections, which could represent the anti-codon loop or any of the unpaired loop regions.
-- SeanMcFarland - 10 Nov 2010