Along the top of the editor window there is a row of labelled command buttons and menus which are activated by mouse clicks. The rightmost of these exits from the editor. To it's left are two menus, one of which is currently in use. To the left of this is a button that moves the editing cursor to the position of the next problem in the contig. The next left is the undo button: each time the user clicks on this box the program reverses the previous edit command. The next button, shown adjacent to a dark box and is hence active, is the reveal cutoffs button. The effect of this button is to toggle between showing or hiding the reading data that is of poor quality or is vector sequence. As can be seen, the ends of some of the aligned sequences are shown in lighter lettering. If reveal cutoffs was not activated these segments of the readings would not be displayed. The next command to the left is super edit. This mode of editing allows some more advanced, and hence potentially dangerous, commands to be performed. The next command toggles between insert and replace and so governs the effect of typing in the edit window.

Next are two pairs of repeater buttons for changing the consensus calculation thresholds. Clicking on a > box will increase the value to the left; clicking on a < will decrease the corresponding value. The left pair (labelled C) are for the overall consensus cutoff, and the right pair (labelled Q) control the quality threshold for including individual bases in the consensus calculation. Bases with numerical estimates of accuracy below this value will not be included in the consenus calculation.

In the strip below the row of labelled buttons is a horizontal scrollbar and four arrows (<<, <, >, >>) for movement along the contig. Along the top of the aligned sequences are numbers showing the position in the consensus. Below this are separate lines showing the readings that cover this segment of the contig. To the left are the reading numbers, negative numbers indicating those in the reverse orientation to their original readings. Next to these are the reading names. The bottom sequence is the consensus for the readings aligned above. Within the readings and on the consenus, annotated segments are shown in colour (here greyed in). One of the reading names has been highlighted by the user and the two others, whose names and numbers are slightly lighter, are the ones whose traces are being displayed (not shown in this picture). Some of nucleotides are shown in red. These all have quality values less than the quality cutoff, which is 65 in this figure.

Beneath the consensus line are several status lines. The topmost of these details the number of strands this sequence has been computed from. At the leftmost section of the screen we can see that the status line reflects that we only have one reading, in the reverse orientation, covering this region. Below the strand status line are the amino acid translations for each reading frame. Each translation can be shown or removed as wished.