This is a python reimplementation of the method designed by Walter N. Moss in the following publication:
Fang, R., Moss, W.N., Rutenberg-Schoenberg, M., and Simon, M.D. (2015). Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. PLOS Genetics 11, e1005668.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005668
See "In silico analysis of conformation regions in murine Xist" under Materials and Methods.
This program searches for regions in a long RNA sequence that demonstrate stronger predicted secondary structure than a random arrangement of nucleotides, controlling for nucleotide content.