Why are there N's after Sanger sequencing?

I'll add on to this answer. A Sanger sequence is really only good for (at best) 800-900 bp. After this time, there is simply too little DNA left to have a reliable signal that you can confidently say is a specific nucleotide. A good habit to get into is always examine your chromatograms and trace, and reject everything after you start getting your first run of N's. I don't usually worry about my first N at the end of the read however because it can be attributed just to error, and the following bases are still confidently called.
– user560
Apr 16 '12 at 7:03