The Blast program developed by National Center for Biotechnology Information (NCBI) is one of the powerful tools for sequence analysis including both nucleotide and amino acid sequences. Although it could be used for multiple sequences alignment, the result is not always available. After analysis of the blast result, a new algorithm was designed to optimize the multiple alignment of Blast. A program named "Mblast" was then developed for application. Result demonstrated that the program is useful in identifying conserved region of multiple sequences.