A scientist can change the alignment by assuming that an insertion or deletion, of one of the bases has occurred. They could make such a change, called an indel for short, to see if it improves the alignment

Scientists measure how closely related a species is by looking at the DNA sequences for key proteins and seeing how similar/dissimilar they are. If the two sequences of DNA are essentially the same, the two species are considered to be evolutionarily closer since there is a relationship between changes and time. This process is called sequence alignment.