haplotype analysis

[Miss. V.M. Hodges]

Hi
I'm doing some haplotype analysis

Primers were obtained from the genome database to amplify dinucleotide
repeat sequences for chromosome 15 markers.  An annealing temp of 60
degrees was used in the PCR. When separated out on a 6% denaturing
polyacrylamide gel, with sequencing reactions as accurate markers, for
each patient there is an average of 4 bands, each 2 bases apart, all
within the size limits stated for the marker (size range 132-142 base
pairs).   Why are there 4 bands?  How do we know which bands represent our
patients alleles? Is this a common problem with assessing dinucleotide
repeats?  

thanks for your help

Vivien

Dr V.M. Hodges
Dept. Haematology
Imperial College School of Medicine
St. Mary's Hospital
Norfolk Place
London W2 1PG
UK

v.hodges at ic.ac.uk