Process flow of PET data Analysis in PET-Tool. Experimental information for each PET library was entered into the system through the ProjectManager functions. High quality DNA sequences in the FASTA files of PET libraries were uploaded through Extractor. Extracted PETs and all related information were stored in a mySQL database. Virtually, PETs were organized in a hierarchical order from project to library, plate, well, and individual PTE. Each unique PET was assigned a unique ID and accorded with copy number (count). The quality of PET extraction was evaluated using Examiner. Errors that occurred in any steps in PET extraction or PET library construction and sequencing could be identified for correction. After PET extraction was validated, PET sequences were mapped to the genome sequences, and the mapping coordinates for each of the PETs were reported in table format.