When you use the Needleman-Wunsch or Smith-Waterman algorithms to find the maximum scoring alignment, you're playing by computational, not biological, rules. As a result, the maximum scoring alignment only approximates the truth. However, even if all the nuances of biology were clear and you could code this in a computer algorithm, you might still favor the approximation because the computational cost of the correct algorithm can be excessive. In any case, the fact that you can align the unrelated words pelican and coelacanth merits consideration. It's possible to align any sequence; finding proper meaning in alignments is up to the user, not the algorithm.