During whole genome shotgun sequencing, generated terminal sequence reads of cloned inserts are assembled into a scaffold. This is facilitated by homologous sequences matching that are shared by reads from the overlapping clones.
Similarly, the central sequence of any single clone is obtained from the terminal sequences of overlapping clones.
The genomic fragments in clones from the shotgun library are partially sequenced. The sequencing reaction must start from a primer of known sequence.
As the sequence of a cloned insert is not known, primers are based on the sequence of adjacent vector DNA. These primers are used to guide the sequencing reaction into the insert.
Hence, short regions at one or both ends of the genomic inserts can be sequenced. After sequencing, the output is a large collection of random short sequences, some of them are found to be overlapping.