So, you take some blood from the patient, put it in your table sequencer, and you see that this patient has two mutations in her ensiemase sequence. You see that one of the two mutations falls in an area where pillenolol is supposed to bind. So, after about 20 minutes, you know that pillenolol is unlikely to cure the patient, and you can look up in the bensiekus disease database what other medicins you can try. So lets align sequences. Nevertheless, I think that this alignment is the best that can be achieved for these two sequences.
Lets think about an alignment.
An alignment is a representation of a whole series of events that took place during evolution and that left their traces in the sequence. Once nature decided on an indel, its length is less important, but longer indels are more difficult to make than shorter ones. Residues mutate more easily to residues encoded by similar codons. Surface residues mutate more easily than core residues. Core residues mutate more easily when they make fewer contacts.