The DNA (deoxyribonucleic acid) segments sequenced are overlapped in order to obtain a genome sequence, because their sequences are identical.
Matching homologous sequences are shared by reads from overlapping clones. The sequence reads are associated into a consensus sequence covering the whole genome. The sequence contigs are units in which the overlapping reads are assembled. The order of the clones is found by finding the way in which they overlap.
There are many ways to identify the overlapping clones. One way of identifying is using a chemically labeled or radioactive probe containing sequence-tagged site. It can be hybridized onto a microarray. In the microarray the clones are printed. All the clones with a particular sequence in the genome are identified in this process.
Thus, once the overlap between the clones has been found, their order of relative to the genome is also known.