Short tandem repeats (STRs) are regions of genetic diversity occurring at thousands of loci throughout the human genome. They are composed of motifs 1-6 base pairs in length, which consecutively repeat a variable number of times depending on the individual and the genomic locus. STRs have previously been identified as the cause of some genetic diseases, such as Fragile X Syndrome and Huntington’s Disease, and more recently have been implicated to modulate the expression of nearby genes. In order to validate the claim that STRs impact and even regulate gene expression, we designed a framework in which thousands of potential regulatory sequences can be simultaneously assayed to quantitatively output their respective gene expression effects. Our design was able to efficiently analyze a large number of sequences containing STRs in parallel, with minimal dropout of input sequences and negligible effects resulting from process biases. While our design does involve dropout of a minority of input sequences, the output is able to retain ~62.8% of the total number of input sequences and ~90% of unique alleles found within the sequences. The retention enable researchers to continue further analysis and demonstrates the method efficacy.