I think this is a good write up, but I think the notation is still carrying some mental baggage. It's not necessary to have these open and closed brackets/parenthesis. They don't add anything, and if anything, they confuse the matter. An interval is just (1, 2) (or [1, 2] if preferred aesthetically). Since a base cannot be "on" either 1 or 2, it's not meaningful to have these open/closed interval notion. In other words, (1, 2) == [1, 2) == (1, 2] == [1, 2].

Open/closed intervals only come into play in continuous dimensions. DNA sequences, arrays in memory, et al are discrete.