Each base has its own quality value. Assembly will allow only values between 1 and 99 inclusive. A quality value of 0 means that this base should be ignored. A quality value of 100 means that this base is definitely correct and the consensus will be forced to be the same base type and will be given a consensus confidence of 100. If two conflicting bases both have a quality of 100 the consensus will be a dash with a confidence of 0.
Newly added bases or replaced bases are assigned their own quality values. By default these are both 100. The "Set Default Confidence" option in the settings menu allows these values to be changed.
Several keyboard commands are available to edit the quality value of an individual base. The '[' and ']' keys set the quality to 0 and 100 repsectively. To increment or decrement the confidence of a base by 1 use Shift plus the Up and Down arrow keys. To increment or decrement by 10 use Control plus the Up and Down arrow keys. The editor will beep if you reach quality 0 or 100. Finally note that quality values can also be made visible by the use of grey scales for the sequence background colour. See section Show Reading and Consensus Quality.
The cutoff data is displayed by pressing the "Cutoffs" toggle at the top of the editor. The cutoff sequence will be displayed in grey. We call the boundary between the cutoff data and the used data the cutoff position. These positions can be shifted left or right for each end of the reading using the Meta Left-arrow and Meta Right-arrow keys respectively. As keyboards may not have a meta key, Control Left-arrow and Control Right-arrow also have the same effect. These key combinations adjust the cutoff positions by a single base at a time. They only work when the cursor is on the very first or very last "used" base, depending on which cutoff you wish to adjust.
If large changes are required the cutoffs can be "zapped" to new positions using the "<" and ">" keys. To use these, place the editing cursor to the position required (which may be within the cutoff data or the used data) and press the "<" key to set the left cutoff to the base between the cursor and the base leftwards of the cursor. Similarly ">" sets the right cutoff to the base between the cursor and the base leftwards of the cursor. Note that many keyboards have "<" and ">" above the "," and "." keys. In this case you will need to press Shift in conjunction with "," and "." to perform the operations.