Example of joining two HSPs. A single point on each HSP is chosen to be be included in the alignment. This is the centre of the HSP according to the scores, such that equivalenced bases on either side contribute to half of the HSP score. As shown in this example, if the centre of the HSPs according to their length had been chosen instead, it would not have been possible to join them to form an alignment.
Slater and Birney BMC Bioinformatics 2005 6:31 doi:10.1186/1471-2105-6-31