Compositions, methods and kits are provided that are useful, for example, for determining activities of multiple cis-regulatory sequences, such as promoters and enhancers, and/or multiple trans-acting factors, such as transcription factors, in a cell. In particular, in certain embodiments, compositions are provided comprising a population of polynucleotide reporter transcription units (RTUs) in which each RTU comprises a reporter sequence, a processing tag located in the reporter sequence; and a cis-regulatory element operably linked to the reporter sequence, wherein the reporter sequences between any two RTUs in the population, outside of the processing tags, are substantially identical and wherein the positions of the processing tags within the reporter sequences distinguish between any two RTUs differing, for example, in their cis-regulatory elements. The compositions, methods and kits can further be used, for example, to identify a cell type or disease state, for example, in a biological organism.