Variable nucleotide sites in a 476 bp alignment of orthologous HERV-K(HML-2) 1p31.1a LTRs. A consensus sequence is shown at the top. Topology of the 1p31.1a LTRs within the phylogeny of GAPS loci is shown on the right. Singleton substitutions have a white background and parsimoniously informative sites are shaded in grey. Sequence of the 526 bp truncated 5′ LTR within gorilla is shown at the bottom. Black arrows show parsimonious differences in the human lineage and grey arrows highlight parsimonious species differences.