Figure 7.

Autofinish checks each contig to see if either end is the clone end. Masked clone vector and subclone vector both appear as Xs, and Bs are high quality bases that do not match subclone or clone vector. Notice that vector-insert junctions of reads 1–4 are aligned. If read 5 were not present, this figure would suggest a typical clone end with the Xs clone vector. If only read 1 and read 2 were present, the Xs could instead be subclone vector, which just happens to align; but the presence of two additional reads (read 3 and read 4), or additional vector bases in one read, would make this less likely. However, if read 5 were present (all high quality bases surrounding the putative vector/insert junction), it would be unlikely that this is the clone end.