Even within a single program/algorithm, the length of the final alignment is critically dependent on the parameters for the gap insertion and gap extension penalty. Normally, you find in the final alignment blocks or regions where all sequences align reasonably well, while in other regions, gaps are concentrated but not placed in exactly the same position, although structurally they extend the same surface loop. It often makes sense to post-process the alignment to coalesce the gaps in these positions to get a more meaningful alignment. For an example, see:

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