I am trying to use BiBiServ-RNAHybrid but am encountering certain problems.KIndly help me asap.

I wish to obtain the following results using RNAHybrid (Objectives) - A) I wish to find the minimum free energies of the miRNA interacting with the 3'UTE/5'UTR or CDS of the gene (eg.APOE ) B)Structure
c)Alignment details

The problem I am having- a)If gene seq ( FASTA format )or mRNA seq (FASTA format ) is taken as target seq. (how is mRNA FASTA obtained if so)
b) what to fill in the options - helix constraint from helix constrain to max bulge loop length max internal bulge loop length

Would someone PLEASE explain me with an example like >ENSG00000130203|ENST00000252486|.It is APOE transcript and miRNA- hsa-mir-650