DNA fragment separation is done by:

Nucleic acids may be separated in an electrophoretic field in an agarose (highly purified agar) gel. The speed of migration depends on size, with the smaller molecules moving faster and appearing at the bottom (end) of the gel. This method is able to separate DNA fragments in the range of 0.1 to 50 kilobases, which is far below the size of bacterial genomes but includes some naturally occurring genetic elements such as bacterial plasmids. Ref: Ray C.G., Ryan K.J. (2010). Chapter 4. Principles of Laboratory Diagnosis of Infectious Diseases. In C.G. Ray, K.J. Ryan (Eds), Sherris Medical Microbiology, 5e.