Fig. 1

Overview of the PCIP-seq method. a Simplified outline of the method. Only 5′ LTR-containing circles and fragments are represented. Detailed outline available in Supplementary Methods. b A pool of CRISPR guide-RNAs targets each region, the region is flanked by PCR primers. Guides and primers adjacent to 5′ and 3′ LTRs are multiplexed. c As the region between the PCR primers is not sequenced, we created two sets of guides and primers (sets A and B). Following circularization, the sample is split, with CRISPR-mediated cleavage and PCR occurring separately for each set. After PCR, the products of the two sets of guides and primers are combined for sequencing. d Distribution of coverage across a BLV provirus (red line) and host DNA (blue line) in an expanded clone. Gray boxes: LTRs. The large drops in coverage adjacent to the LTRs correspond to the region between the PCR primers. The colored lines represent SNPs in the host genome