Supplementary Table 1. Proportion of mutated targets (target saturation) for each of the 32 Emx1.6 target variants, sampled at different developmental stages (embryos, L3 larvae, adults) and in the absence of Cas9 (untargeted). Targets 13, 17, 18, 21 and 23 were not analysed further because there were no good quality reads in the untargeted condition or because the targets showed a high proportion of sequencing errors. Supplementary Table 2. Proportion of mutated targets (target saturation) in the embryo after correcting for sequencing errors and estimated mutation rates per cell division, for the target variants showing the highest mutation rates. Supplementary Table 3. PCR primers used for preparation of the sequencing libraries. Forward primers (F) carry adapter sequences (uppercase), barcodes specific for each condition (underlined, BC1 to BC6), and sequences annealing to the spacers of the repeat construct (lowercase). Reverse primers (R) carry adapters (uppercase) and sequences annealing to the spacers of the repeat construct (lowercase); see Figure 3B and Materials and methods.