The Align button aligns the overlapping consensus sequences and adds pads The alignment routine assumes that the two contigs are already in approximately the right relative position (as they are immediately after the Join Editor has been invoked from Find Internal Joins, or Find Repeats). If they are not they must be positioned manually before using the Align button.

It should be noted that each of the pair of editors comprising the Contig Editor maintains its own undo history, and using Align is likely to add to both undo histories. Hence, to undo the results of the Align command the Undo button in both editors must be used.

Note also that storing the undo information takes up a great deal of computer memory and slows down the alignment process. For this reason the settings menu contains an option to turn off (or on) the saving of undo information. When aligning very long overlaps it is advisable to turn off the undo saving.

When "Join/Quit" is pressed a dialogue box is displayed containing the percentage mismatch of the overlap, and asking if the join should be made. For joins above a certain level of mismatch (20 percent by default) a second confirmation is required.