The contig comparator is used to plot all templates with readings that span contigs. That is, the lines drawn on the contig comparator are a visual representation of the relationship (orientation and overlap) between contigs. When a template spans more than two contigs, all the combinations of pairs of contigs are plotted. However such cases are normally rare.
The lines are by default shown in blue. The length of the line is the average length of the two readings within the pair. The slope of the line represents the relative orientation of the two readings. If they are both the same orientation (including both complemented) the line is drawn from top left to bottom right, otherwise the line is drawn from top right to botton left.
Clicking with the right mouse button on a read pair line display a menu containing amongst other things "Invoke template display".See section Template Display. This brings up two template displays, one to display of the two readings. The readings constituting the pair are marked as bold within the template displays.