Many human diseases could be controlled by the knowledge of the gene’s structure and pattern. The human gene could be represented by four nucleotides. Each nucleotide is represented by a character - ‘J’, ’S’, ’M’, and ’F’. The string pattern of these nucleotides helps us understand the genes. The functions of the genes are based on these strings. Some biologists want to discover the medicine for the diseases, which could be controlled with the help of these genes. So they decided to compare the two genes and find the problem, so they could make the cure. Let’s have two genes JMFMJFM and MFFJM. One of the methods to get the problem of these two genes is called alignment comparison. In the alignment comparison, spaces are inserted (if necessary) in some positions of the genes. These spaces make them equally long and then we could score these resulting genes according to the scoring matrix