The lines for the read-pairs 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 creates a template display of the two contigs. The spanning template will be coloured bright yellow if the readings on the template are consistent with one another, 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 (see section The Join Editor) from the same menu will bring up the Join Editor with the two contigs shown end to end.