(A) All IAPLTR1 elements larger than 300 bps and the first 150bps of IAPEz-ints flanked by IAPLTR1 or IAPLTRs were clustered by sequence using PhyML with default settings. Major sequence variants for IAPLTR1s were separated into separate clades: clade1 (blue), clade 2 (Green), clade 3 (red), and clade 4 (orange). Major sequence variants for IAPEz-ints were separated into separate clades: clade α (dark blue), clade β (light blue), and clade γ (yellow). KZFP and KAP1 ChIP-seq signal was mapped across the consensus IAPLTR1 sequence as determined by MAFFT multiple sequence alignment. Gaps in the multiple sequence alignment for the IAPLTR1 sequence are displayed as grey. Heatmaps for KZFP and KAP1 ChIP-seq signals centered on the 5’ end of the IAPEz-int elements are show as well (B) Average KAP1 ChIP-seq signal across all IAPLTR1 and IAPEz-int clades. Each data point refers to the average KAP1 ChIP-seq signal at an individual IAPLTR1 element. Mean and standard deviation for each clade is shown as well. (C) Distribution of the IAPLTR1 elements clades (outer circle) and IAPEz-int clades (inner circle) for all IAP elements and VM-IAP elements. (D) Percent of VM-IAPLTR1s clade three elements and non VM-IAPLTR1 clade three elements that are within 50 kb of a constitutively expressed gene or 1 kb enhancer element, as a proxy for constitutive euchromatin environment. (E) Conservation of IAPLTR1 and IAPEz-int variants across mouse strains. Presence or absence of a IAP was determined using structural variants identified from the Sanger mouse genome project. Mouse KZFP and KAP1 ChIP-seq date are from GEO: GSE115291. VM-loci coordinates were obtained from Elmer et al., 2020.