To study the relationship between the potential functional regions with the primary amino acid sequence, we introduced a new factor termed local degeneracy to analyze the degree of the degeneracy in a given segment of the protein. Using the defined local degeneracy, we have analyzed the human coagulation Factor IX (Christmas factor) which is an essential component of the clotting cascade. The mutational hotspots in Factor IX are primarily distributed in the high-degeneracy regions, suggesting a direct correlation of the functional regions with high degree of the degeneracy. This method may be useful to predict and to evaluate potential functional domains of a protein.