The sequence arrangement is an important tool in molecular biology, sequence multiple sort (MSA).The arrangement of three or more biological sequence by general protein DNA or an amplified to identify regions of similarity may result from the function and relationship of structure or evolution between ships. Respectively.A high order between the molecule shows the similarity of structural and functional significance in the position. MSAs using more complicated because they are more complex, hidden Markov model computer (HMM) is a state machine Ltd. Is widely used in biological sequence analysis HMMs. HMM used in biological sequence analysis. In this article, we show that personal information is useful for HMMs sequence arrangement. We will test their applicability to the tasks of alignment and find that they work well.