how the miranda works ?

I am looking for the target sites of my MicroRNAs. So in miranda, i saw to inputs(Micro RNA sequence and Query sequence) and both formats are FASTA.
So can anyone tell me how can i put my data into them ? For example, should i put the reference genome into the Query sequence and turn my microRNA sequence into fasta file and then put it as MicroRNA sequence or else ?

Thank you