PCRTags are alterations incorporated into most open reading frames (ORFs) (on average one per ORF, as some ORFs are too small and others contain multiple PCRTags). These are made by recoding a ~20bp segments of the coding region of an ORF to a different DNA sequence encoding the same amino acid sequence. PCR primer pairs can then be designed that will selectively amplify only the synthetic or wild type sequences. In this way, transformants that have incorporated a synthetic segment can be quickly scanned to ascertain that a complete substitution of the segment has occurred. PCRTags can also be used to monitor for the deletion of non-essential segments post-SCRaMbLE induction.