Major Currently, "U2MsaRow::length" is calculated incorrectly. It is less than the expected value a little bit.
If a user inserts gaps into a Sanger read so that the length of the read is the same as the length of the reference, this causes the problem - additional gaps are inserted into the reference (at the right end). The number of additional gaps is equal to the difference between the expected length value and the actual length value.