A target region with an internal section of known sequence and unknown flanking regions is identified
Genomic DNA is digested into fragments of a few kilobases by a usually low-moderate frequency (6-8 base) cutting restriction enzyme.
Under low DNA concentrations, self-ligation is induced to give a circular DNA product.
PCR is carried out as usual, with primers complementary to sections of the known internal sequence.*
Finally the sequence is compared with the sequence available in the data base.