Abstract
Sequence alignment usually has two kinds of methods. The first kind of method is the dynamic programming. The second way is to set up index table. Dynamic programming is divided into a local method and global method. The principle of the index way can roughly be divided into two steps. The first step is to use index table to look for the proper range. The second step is to align sequence. The Unique Markers method is the second kind of method. The UM method will product the clustering. This phenomenon will cause the fault. If the query sequence belongs to this blank region, it can not be success for alignment. We propose a method solve the clustering problem. We use the Interval UM method to set up the second index table. This method keeps the concept of the original method. In our experiment, we show our method can improve the density of cover of the index.