The large top section contains lines and arrows representing readings and templates. The template and reading section of the display is in two parts. The top part contains the templates which have been sequenced from both ends but which are in some way inconsistent - for example given the current relative positions of their readings, they may have a length that is larger or greater than that expected, or the two readings may, as it were, face away from one another. Colour coding is used to distinguish between different types of inconsistency, and whether or not the inconsistency involves readings within or between contigs. For example, most of the problems shown in the screendump above are coloured dark yellow, indicating an inconsistency between a pair of contigs.
Forward readings are light blue and reverse readings are orange.
The coloured blocks immediately above and below the ruler are tags. Those above the ruler can also be seen on their corresponding readings in the large top section. Zooming is available. The position of a crosshair is shown in the two left most boxes in the top right hand corner. The leftmost shows the distance in bases between the crosshair and the start of the contig underneath the crosshair.