In this example, the overlap pairs are divided into three groups, or overlap clusters , separated by blank lines. Each cluster consists of overlapping fragments that could be chained together into a single, continuous assembly. It also gives the orientation of each sequence. If Overlap rejects your nucleotide sequence, see Appendix VI for information on how to change or set the type of a sequence. WordSearch, however, accepts a single query sequence as input and finds regions of similarity rather than overlaps.
LineUp is a screen editor for editing and displaying overlapping sequences.
The total length of bases in any sequence set may not exceed 350,000. The word size must be between 1 and 30. The minimum overlap length must be between 1 and 1,000. The program cannot store more than 10,000 overlaps. If this number is exceeded, the program stops after suggesting that you increase the stringency to reduce the number of overlaps.