It is not clear what you need to do. However, assuming that you manage to clone two identical sequences few hundred bp long after inserting, for example, a unique restriction site in one of them, I would expect them to recombine through HR.

If you are still waiting for more answer you should explain in more detail what you plan. Otherwise one can only start to guess.

Sorry for the delay in response, i am relocating. I have a reporter gene construct. Aiming for integrating it into host genome. 

Referring to your first answer, Just taking few hundreds bp flanking sequence (at site of integration) would suffice the need of HR? Why do we need to have restriction site in one of them - guessing thats for stand aligning and facilitating HR. 

If you want to do homologous recombination, you design a construct with flanking homologous arms, sequences of the locus you want to target with your reporter construct. These should not be rich in repetitive elements. They usually have a length in the kb range. To verify homologous recombination you should plan a Southern blot. To identify clones with correct integration you need a flanking probe and a restriction enzyme that detects a fragment in case of integration that differs from the endogenous pattern. A restriction site in your reporter may be helpful.

Hi Pranali,

You did not mention that which host (species) genome you are working on. For plants, the frequency of simply using HR alone to integrate a transgene into their genome is extremely low. Nowadays, people seek to use Genome editing tools (such as TALEN, CRISPR..) to create a DSB at the target locus first, then doing HR. This will increase the frequency of HR to many magnitude. Besides, generally, you need some kind of sequence information to design your HR vector (such as the homologous arms.).