FIG. 3.

Neighbor-joining analysis of 134 reasonably intact HERV-K(HML-5) LTR sequences. Shown here is a consensus tree from 1,000 bootstraps replicates. Specific bootstrap values at major nodes are indicated. Consensus sequences, as given in Repbase (Rep) and as generated in this study (own), were also included in the analysis. LTR22 and LTR22A sequences are clearly distinguished, with the latter comprising the so-called LTR22A2 group. Other sequences belong to the LTR22B group with some ambiguous sequences remaining (Table 2). Note that the LTR22 Repbase sequence groups with LTR22B sequences, opposed to LTR22own. Numbers of LTR sequences refer to the proviruses listed in Table 1. The 5′ and 3′ LTRs of a particular provirus located at immediately neighboring terminal nodes are indicated as 5/3. Note in this context that 5′ and 3′ LTRs of particular proviruses do not always group together, reminiscent of recently suggested HERV-involving genomic rearrangement events (13).