Remove magic numbers

[rkretsch]

Lot's of magic number in current code that need to be moved to variables, verbosity, or specified for readability.

• Number of sequences per punpaired figure
• Figures variables, dpi, figsize ratio, fontsize, frequency of plotting nuc number on sequence
• verbosity of padding code

[rkretsch]

• Number of selected sequences to confirm structure of pads for

[rkretsch]

• minimum length of a helices in stem-loop pads

[rkretsch]

Sufficiently updated in utils. Not all options available in main prepare_library script, will plan to add upon request.