About DNA sequencing

[kou]

Hello everybody,

 I am PhD stdent and working on circadian rhythms in Drsophila.

I am planning to do sequencing of period locus for detecting
polymorphism.

I have a very basic question about sequencing :

After sequencing, entire sequence is not accurate. stretch of sequence
immediately after primers is not accurate.
So my question is

How to choose accurate sequence ?
 I mean what should be the start  point and end point  of accurate
sequence with respect to primer position?

Kou