I'm trying to clone a particular gene (drosophilla melanogaster ntl) using PFLC vector.After restriction digestion I should get a band around 3500 bp but I'm consistently getting a baand of around 4500 bp.I really don't know how but the result is consistent for 8 experiments I performed.Any suggestion?

Try to sequence your plasmid

I have actually thought of that but sequencing a 4500 bp fragment is no easy job.Can anybody suggest me an alternate solution?

If you know the sequence of the vector and the insert you could do digestions with different enzymes to check if it is the right plasmid

do you use more than one enzyme? then you should check if all enzymes work!

yes, try to linearize your plasmid to see if you have right size all together and cut with different enzymes your plasmid and insert to obtain different bands.