A method of automated reconstruction of a genotype, comprising a. providing a nucleic acid isolated from a patient sample, wherein the nucleic acid has at least one GC-rich nucleotide repeat region comprising one or more interruptions; b. determining parameter information for the nucleic acid, wherein determining parameter information comprises measuring the total length of the at least one GC-rich nucleotide repeat region, the distance from the start of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region, and the distance from the end of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region; and c. using an apparatus to conduct automated exhaustive enumeration on the parameter information to generate a reconstructed genotype, wherein exhaustive enumeration comprises i) using the total length of the at least one GC-rich nucleotide repeat region and either the distance from the start of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region or the distance from the end of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region to generate a set of potential genotypes comprising all possible arrangements of the one or more interruptions in the region; and ii) evaluating the set of potential genotypes to determine a solution genotype that satisfies all the parameter information. a. providing a nucleic acid isolated from a patient sample, wherein the nucleic acid has at least one GC-rich nucleotide repeat region comprising one or more interruptions; b. determining parameter information for the nucleic acid, wherein determining parameter information comprises measuring the total length of the at least one GC-rich nucleotide repeat region, the distance from the start of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region, and the distance from the end of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region; and c. using an apparatus to conduct automated exhaustive enumeration on the parameter information to generate a reconstructed genotype, wherein exhaustive enumeration comprises i) using the total length of the at least one GC-rich nucleotide repeat region and either the distance from the start of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region or the distance from the end of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region to generate a set of potential genotypes comprising all possible arrangements of the one or more interruptions in the region; and ii) evaluating the set of potential genotypes to determine a solution genotype that satisfies all the parameter information. i) using the total length of the at least one GC-rich nucleotide repeat region and either the distance from the start of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region or the distance from the end of the at least one GC-rich nucleotide repeat region to the one or more interruptions in the region to generate a set of potential genotypes comprising all possible arrangements of the one or more interruptions in the region; and ii) evaluating the set of potential genotypes to determine a solution genotype that satisfies all the parameter information.