The main section of the template display is the large upper plot showing the templates and readings. Colour is used to illustrate information pertaining to the templates and readings. The reading colour is used to convey the primer information. The colours are:
When two template displays have been invoked from a find read pairs match two readings will be drawn in purple, regardless of their real primer types. These are the readings that the read pair match found.
For the templates, the colour is used to distinguish the number and location
of readings sequenced from this template (provided they have been entered into
the Gap database). Templates with readings sequenced from only one end of
the template are drawn in blue. Those with readings sequenced from both ends
are pink when both ends are contained within this contig and green when the
ends are in different contigs.
For each template Gap stores an expect length, as a range between two
values. From an assembly it is often possible to work out the actual length of
a template based upon the positions within a contig of readings sequenced
using the forward and reverse primers. If this observed distance is outside of
the range acceptable sizes then the template is drawn in black. Alternatively
it may be possible that both forward and reverse readings are assembled on the
same strand (in which case both arrows will point in the same direction). This
two represents a problem and hence the templates are drawn in black. A summary
of template colours follows.
Within the figure the contents of the View menu are visible. The "Ruler", "Templates", "Readings", "Quality Plot", "Restriction Enzyme Plot" commands control which portions of the template display to display. The graphics are always scale to fit the information within the window size, subject the the current zoom level. This means that turning off templates, but leaving readings displayed, will improve visibility of the reading only information.
The "ignore 'single' templates" toggle controls whether all templates or only those containing both forward and reverse readings are displayed. Hence when set the templates displayed are those with a known (observed) length.
The plot can be enlarged or reduced using the standard zooming mechanism (control right mouse button). The "back" button redraws the display at the previous zoom level. See section Zooming.
The crosshair toggle button controls whether the cursor is visible. This is shown as the black vertical line. The blue vertical line seen to the left of figure is the position of the editing cursor within a contig editor. If no contig editor is editing this contig then no editor cursor is visible. If several are editing then several editor cursors are visible, each with a different colour. Moving the editing cursor within the contig editor automatically moves this cursor within the template display. Similarly clicking and dragging the editor cursor with the middle mouse button within the template display scrolls the associated contig editor.