I have Illumina data of 1 x50bp from small RNA library. I am interested in identifying known and novel miRNAs in my plant, whose reference genome is not available. However, first I want to count the reads aligning Exon sense, Exon antisense, Intron sense, Intron antisense. Basically, I want to replicate the information shown in table below. I have gone through the complete publication and they have mentioned the use of Rfam database in "Experimental procedures" section for identifying mRNA. So my question is how can I classify reads as Exon sense, Exon antisense, Intron sense, Intron antisense using Rfam or any other databases?