Fig. 2

Simages. Panel a The principle. A proviral sequence is divided into twentieths, each of which is BLASTed against a reference sequence collection. 1 A homogeneous, canonical, provirus. 2 A heterogeneous, noncanonical, provirus. Panel b A canonical chain. The chain id (“rvnr” in Additional file 1: Table S1), HERV classification, the chromosomal position and LTR divergence (if both LTRs were recognized by ReTe) are shown in the uppermost row. The subsequent three rows depict the RepeatMasker nucleic acids with the highest degree of identity, the next three rows which of the 39 consensus sequences determined in this paper (Additional file 3: List S3) has the highest degree of identity, all per twentieth of the chain. The lowest row depicts the ReTe putein interpretation per twentieth. 5 means 5′LTR, G Gag, R Pro, P Pol, E Env and 3 3′LTR. Panel c Three noncanonical chains containing secondary integrations which left a single LTR inside another retroviral chain. Annotation as in b. Colour is used here and in ensuing panels to distinguish components of mosaic chains. C1: HML4 LTR inside an HML2. LTR5 and HERVK refer to HML2. LTR13 is an HML4 LTR. C2: HERV9 LTR inside a HERVH. LTR12 and HylERV9-LTR are HERV9 LTR equivalents. A small pol piece most similar to HERVE is also present. C3: HML2 inside a HERVH. HylNERVH1 and HylNERVH2 are HERVH equivalents (see Additional file 2: List S2). LTR5 is an HML2 LTR. “0” depicts that no similarity was found with the respective query sequences. Panel d Noncanonical chains with signs of recombination. Annotation as in b. D1: HERV9 chain with a short piece similar to HERVIP at the end of pol and beginning of env. D2: a mosaic HERVE with HERVIP, HERVW and HML10 inside. ReTe recognized mainly one gene, env. As described in the text, this is a common pattern for chains labeled as “Harlequin”. D3: a complex HML3 chain where the RepeatMasker based Simage indicates contributions from six different HMLs. D4: An HML3 chain with short pieces of HML1, HML9/10 and HML8. D5: a complex chain which contains undetermined HML sequences in the end of pol, and whole of env. The differences between the consensus and RepeatMasker results in D3-5 indicate that the HML groups and HERVK families contain microheterogeneities, mainly in env, which sometimes can cause classification confusion. The HML10 consensus contains an HML9 like stretch in pol and an HML8 like stretch in env, which may explain some of the discrepancies between the RepeatMasker and Consensus Simages. HERVK14 = HML1, HERVK = HML2, LTR5 = HML2 LTR, HERVK9 = HML3, MER9 = HML3 LTR, HERVK14C = HML9, HERVK11D = HML7, HERVK11 = HML8