This week I have finished the 1 million iteration run (shown below) and have been working to install and run a program with similar functions to mine so that I can examine my results.
I also read a paper called "Designing RNA Secondary Structure in Coding Regions" by Rukhsana Yeasmin and Steven Skiena that is about optimizing the maximum or minimum folding energies based on local modification. This research is very similar to mine, however, their program is not available for testing. I downloaded and installed a program called D-Tailor to compare my results but am still working on learning Python so that I can design a script that can run it, as you can not run it simply after downloading it.