Notes on reference sequence quality:

The reference sequence (used for the CDS annotation) mustn't have sequencing-error indels within CDSs, as these will throw the software out of read-frame and cause global problems. However indels are tolerated in the other sequences: there'll be a local incorrect codon identification, but no long-range problems. Bad alignments or local (paired) frameshifts (gaps not in threes) will mean that nucleotides within the 'mis-aligned' region may get wrong codon position identifications - leading to wrong codon identifications - but the problems should be local. It is up to the user to check for alignment problems. In non-coding regions, of course, gaps not in threes are allowed and don't cause problems.