PatternHunter utilizes numerous seeds (tiny search strings) with optimal intervals between them. Searches that employ seeds are extremely fast because they only determine homology in places where hits are established. The sensitivity of a search string is greatly influenced by the amount of space between adjacent strings. Large seeds are unable to find isolated homologies, whereas small ones generate numerous arbitrary hits that delay computation. PatternHunter strikes a delicate balance in this area by providing optimal spacing between search strings. It uses alternate k (k = 11) letters as seeds in contrast with BLAST, which utilizes successive k letters as seeds. The first stage in PatternHunter analysis entails a filtering phase where the program hunts for matches in k alternating points as denoted by the most advantageous pattern.[6]:11 The second stage is the alignment phase, which is identical to BLAST. In addition, it is possible to use more than one seed at a go with PatternHunter. This elevates the sensitivity of the tool without interfering with its speed.