MicroRNAs (miRNAs) are a type of short non-coding RNA sequences involved in crucial biological processes. In fact, multiple studies show that they can be used as biomarkers for human diseases such as cancer and Parkinson's as well as phylogenetic markers for species evolution. Thanks to the huge amount of high-quality RNA reads that Next Generation Sequencing is able to produce, the analysis of miRNA has improved over the years, with computer science playing an increasingly important role in this bioinformatics field. miRNAs are characterized by a mechanism that mostly relies on a specific nucleotide region to bind to messenger RNA, so when performing miRNA alignment it is crucial to prioritize the conservation of this so-called seed sequence.