I m sequencing Dna by Genetic Analyzer 31/30 system and i m usiing Applay Biosystem size standart kit. but in my electropherogram after my peak I always found another peak what does it show?
It's difficult to say anything without seeing an image of your electropherograms, but it might be that you have more than one sequence being sequenced. Some extra information would help, like what type of marker are you trying to sequence, from the mithochondria, chloroplast or nucleus? Is your species diploid or polyploid?
If I understood right, you perform fragment analysis and each peak of commercial size standard is represented with two peaks? Are the observed peaks of the same dye?
I am not sure, but it could be also settings problem, for example dye set selection in analysis protocol. Check all settings, see previous analysis settings on your instrument.