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The expected sequence file:

The expected sequence file is a simple text-format file that indicates the location and possible genotypes of the analyzed variations. The indel should be indicated between {} brackets. It is possible to phase only biallelic SNPs that follow the indel. The two possible genotypes of these SNPs should be indicated between [] brackets. It is necessary to include at least 20 bases upstream of the indel site, which are important for identification of this site by the program. Bases upstream this stretch and bases that are downstream the site of the last SNP have no significance for the operation of TraceHaplotyper and they can be removed. Examples for expected sequence files can be viewed and downloaded at TraceHaplotyper Example Data Set webpage. 

To analyze cases of multiallelic indels (microsatellites) for each trace a suitable file of the expected sequence should be prepared. This requires either previous genotyping of the microsatellite for obtaining the sizes of the two alleles or detecting the specific size of shift using Shift Detector.  The file should contain the sequence of the longer allele with the indel indicated between brackets {} around the repeats according to the size difference between these two alleles.