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 bottom left.
Clicking with the right mouse button on a read pair line brings up a menu containing amongst other things "Invoke template display".See section Template Display. This brings up a template display of the two contigs. The spanning template will be coloured either bright yellow if the readings on the template are consistent with each other or dark yellow if they are not. The ordering of the contigs may need to be altered or one contig may need complementing before the readings on the template become consistent. Using the "Invoke join editor" command from the same menu will bring up the join editor with the two contigs shown end to end. No attempt is made to automatically align the contigs as in some cases an overlap may not even exist.