Gap4 has two functions for clipping the sequences so hide the poor quality regions. This has two main purposes. Firstly it tidies up the alignments and it helps the user to only look at the better data. Secondly it improves the reliability of the consensus sequence. It is important to note that in no case is the clipped sequence thrown away. The contig editor can show this "cutoff" data and the clip points may be manually adjusted to recover any clipped sequence.