Clicking between sequence characters with the right button brings up the insert menu, allowing the addition of a base. If you click out side the vertical column defined by the sequence characters, an empty character box indicates a misplacement of the cursor.
Clipped regions (yellow bars above) may be opened to add more sequence
to the read by clicking on the down arrows head at the beginning of
the clipped segment as shown below. Similarly, the clipped region may
be extended by clicking on the opposite arrow head.
The suggested changes in the base calls
may be accepted by simply clicking on the highlighted character with
the left mouse button, this yields a single highlighted character
in the trace base call column.
A double highlight 
represents a
suggested insertion. After clicking on the highlighted character, the
display is updated to insert the base at the position of peak
intensity, as show in these before 
and after 
pictures.
Automatic Corrections
Automatic edits may be made using the items of the Fix button.The Fix Whole Contig item makes one pass through all the reads of the contig, making the suggested base call changes. This may produce additional suggested corrections for a second pass.
Realign recalculates the contig consensus sequences.
Auto Edit Base automatically makes suggested edits on the region in the current window.