It sounds like you are very new to molecular biology.  Go find an introductory textbook and read up on the basics of translation.

P.S. Is this a homework assignment?  No one does that sort of crappy old-school DNA sequencing anymore.

Well, I'm not new to this subject, just confused about the leftover base pairs. It's a small part of data analysis. :).. Can u help?

Since 3 nucleotides are required to code for an amino acid, if there are one or two nt left at the 3'-end, they cannot be translated. The same goes for the 5'-end if you start at nt 2 or 3.

Thank you so much! So should I leave nts from 5' or 3' end?

If you don't know which frame is the correct reading frame, you should try all three possibilities, starting at the first, second, and third nucleotides (counting from the 5' end). This will result in 3 different sequences of 6 residues, unless there is a stop codon.