Scroll down below the table and look at the calculated alignment. This is known as a traceback, which is indicated here by the green cells in the table. Notice that the similarity score for this alignment is the value found in the bottom-right cell of the table, which is also where the traceback began. This is not a coincidence, but it is how the final similarity score for an alignment is defined in dynamic programming. Usually, however, simple conventions in how the algorithm is used allow computer programs to select one single alignment for display.
Global alignments are excellent for sequences that are known to be very similar.
If the sequences being compared are not similar over their entire lengths, but have short stretches within them that have high levels of similarity, a global alignment may miss the alignment of these important regions. A new table and alignment should be displayed in the DP results window. This is done by definition of local DP comparisons. Next, notice that the alignment displayed does not include all of the characters in both sequences, but includes only those residues involved in the best local alignment. The final difference is in the traceback, where we don't begin in the last cell of the table, but start in the cell having the highest value over the entire table.