Notice u/s 139(9) - interest u/s 234 a

Hi,

I had filed my ITR for AY 2013-14 on 27th July 2013 and paid the self-assessment tax on 28th July 2013. The error was that I paid the tax after filing my return and hence the return does not have the BSR Code and Challan No. Now I have got a notice under 139(9) for a re-filing. When I try to refile under 139(9) online, the utility is calculating interest u/S 234A.  My Questions are:

1) Am I supposed to pay this interest? since my filing and payment both were before the due date.

2) If yes, Should I pay this first, include it in the return and then do the re-filing?

Please guide.

Thanks a lot,

Disha