Annotation anomalies identified by Mugsy-Annotator. Four classes of anomalies are shown (a-d). On the right, examples of aligned genes are drawn with the boxed region indicating the location of the anomaly. On the left, a multiple alignment is depicted across the highlighted region with sequence identity indicated by dots. In (c), a gap indicated by a dash introduces a shift in reading frame that results in use of a termination codon that is inconsistent with the annotations in the other genomes. Translation initiation sites are marked as "start" and termination codons are marked as "stop" with an arrow indicating the direction of translation.