Why are the example output sequences truncated?
In this assignment, the policy is to have no end-gap penalties imposed, on either end. (This differs from what Prof. Altman said in class.) Thus the ends of the sequences that do not participate in the alignment do not count towards the score. The example output in the project description has truncated the end gaps in the output. E.g., the first alignment shown is ATGC AGGC with the leading A in sequence 1 excluded because it is aligned with an end gap. This is still a global alignment! An alternative representation of that alignment is AATGC _AGGC which is equivalent. Either type of output is fine.
