Four output files of effold.lst, effold.txt, effold.greg and effold.reg are generated for each run of effold, except for the log file.
1. Output file: effold.lst It is a list file containing all thermodynamically favorable stems with the occurring frequency found in the simulation. 2. Output file: effold.txt The text file contains information about structure classification based on structure similarity. A set of predicted structures are also ranked by means of their energy distribution computed from those lowest free energy structures in the sample. 3. Output file: effold.greg The classified structures are grouped and each set of the grouped structures are represented by one whose folded energy is the most closed to the sample mean computed from this group. Those region tables included all base-pairing information of the represented structure are listed with annotation in the output file. Those represented structures are alternative prediction computed in the simulation. 4. Output file: effold.reg This output is a region table file that contains the base-pairing information of each computed structure. Each region table is consecutively listed in the file. That is the region table of one structure is followed by another region table, and so on. If the sample size of SER is 50, the file includes 50 region tables.
Examples for outputs computed from HCV-H77 RNA (AF011751) by using h77.csh and h77_988-1329.inp