Novel PEM patterns. (a) PEM pattern of a Del(s)+Inv (H5). We draw paired-end reads (black arrows) and how they map to the reference (Ref.) genome C57BL/6J (dashed grey lines). Blue boxes represent deletions and orange boxes inversions. Green arrows represent primers used for PCR amplification and sequencing reactions. (b) PEM pattern of an Inv+Ins (Q8), with PCR data across eight classical strains (A/J, AKR/J, BALB/cJ, C3H/HeJ, C57BL/6J, CBA/J, DBA/2J and LP/J). The pink box represents de novo sequence insertion. The amplicon size for BALB/cJ, C3H/HeJ, CBA/J and DBA/2J is about 500 bp larger than the other strains, indicative of the insertion.