does kc-align handle start/stop correctly?

[wm75]

I have trouble understanding the purpose of % 3 in lines like:

kc-align/kcalign/__init__.py

Line 604 in 52fd2a1

seq = (record.seq[start[0] % 3:].translate(table=tab)[start[0]//3:end[0]//3],

Isn't the user supposed to enter start/stop as 1-based nucleotide positions. Why do you not stick with start-1, stop-1?

Another thing is that you seem to allow exactly one or two start/stop intervals. From a brief look it does not seem complicated to allow an arbitrary number of intervals. This might even simplify the code.

What do you think?