Additional file 5. Fasta alignment of ERV-W proviral sequences retrieved from marmoset and squirrel monkey genome assemblies. A total of 59 and 71 reasonably complete ERV-W proviruses, i.e. having intact LTRs and internal portions, were retrieved from marmoset and squirrel monkey genome assemblies, respectively, and aligned with respect to the corresponding proviral consensus sequences [15].

Additional file 5. Fasta alignment of ERV-W proviral sequences retrieved from marmoset and squirrel monkey genome assemblies. A total of 59 and 71 reasonably complete ERV-W proviruses, i.e. having intact LTRs and internal portions, were retrieved from marmoset and squirrel monkey genome assemblies, respectively, and aligned with respect to the corresponding proviral consensus sequences [15].

HERV-W loci in the human reference genome sequence and ERV-W orthologous sequences in non-human Catarrhini primates reference genome sequences. Table S2: ERV-W loci in non-human Catarrhini primate reference genome sequences with a solitary HERV-W LTR at the orthologous human genome position. Table S3: ERV-W loci in non-human Catarrhini primates corresponding to HERV-W-like elements with lesser similarities to HERV17. Table S4: ERV-W loci in non-human Catarrhini primate genome sequences lacking an ortholog in the human reference genome sequence. (XLSX 85Â kb)

HERV-W loci in the human reference genome sequence and ERV-W orthologous sequences in non-human Catarrhini primates reference genome sequences. Table S2: ERV-W loci in non-human Catarrhini primate reference genome sequences with a solitary HERV-W LTR at the orthologous human genome position. Table S3: ERV-W loci in non-human Catarrhini primates corresponding to HERV-W-like elements with lesser similarities to HERV17. Table S4: ERV-W loci in non-human Catarrhini primate genome sequences lacking an ortholog in the human reference genome sequence. (XLSX 85Â kb)

HML10 multiple alignment. FASTA multiple alignment of the 9 HML10 proviral sequences with respect to LTR14-HERV-K(C4)-LTR14 RepBase reference. (FASTA 149Â kb)

HML10 multiple alignment. FASTA multiple alignment of the 9 HML10 proviral sequences with respect to LTR14-HERV-K(C4)-LTR14 RepBase reference. (FASTA 149Â kb)

Additional file 5: Table S5. HERV group Excel table with 1. Nucleotide frequencies and marked biases, 2. LTR divergence and 3. Consensus statistics.

Additional file 4: List S4. HERV Env subgroup consensus sequences. The FASTA names contain 1. taxorder, 2. subgroup, 3. number of members in the subgroup, 4. 23-amino acid consensus immunosuppressive domain, 5. if present, the most highly related envelope protein from maximum likelihood (Fig. 6, 7) phylograms, and 6. the bootstrap value of the common branch of these envelope proteins.

Additional file 1: Table S1. Excel table generated from the master.dbf table. Field names that need an explanation, and are not explained in the main text, are; “Subgenes”: Presence of motif hits belonging to portions of LTRs and the four major genes (from ReTe); “Chainscore”: Weighted sum of motif hits calculated by ReTe, ranging from 300 to 2500; “Breaks”: ReTe detected two proviral portions seemingly belonging together but separated by a longer than normal distance, therefore disregarded the intervening sequence, its start and stop shown in this field; the PBS fields are described in the main text; “Gagscore” (as well as scores for the other three major genes) shows the degree of fit of the putein to the reference proteins in the best fitting genus-specific alignment included in ReTe; “Tperc”, “Aperc” etc.: percentage of each nucleotide in the chain (from ReTe); “Bestrefrv”: Best fitting nucleotide sequence out of a set of reference retroviral nucleic acid sequences, together with % identity and total length of the reference sequence (from ReTe); “Polclass”: best fitting reference Pol amino acid sequence, with the score of the reference sequence to itself/score of the query sequence to the reference sequence (from ReTe); The five “idpc” fields show the % identity to group consensus for dna and the four major proteins; the “Envidpc2” field shows % identity to the Env subgroup2 consensus; “Repantist” shows antisense portions of a repeatmasker Simage; the five Simage field collections show nucleic acid Simages for repeatmasker (rep), HML (hml), reference sequence collection (ref), first (con1) and second [con2, this paper (Additional file 3: list S3), including best representative (bre) noncanonical or single canonical sequences] consensus collections, respectively. For each Simage are also shown a quantification (-simgst), a list (-simgls) explaining the letter symbols, and the sense relative to the chain sense (-simgse); The con2 set also contains the field “con2simgtg”, which depicts the presence of LTR (5 and 3), Gag (G), Pro (R), Pol (P) and Env (E) in each chain twentieth; The “twomost” fields show the two most frequent (with number of hits out of twenty) AutoFrame hits per the four major genes; The ensuing Simages show the distribution of AutoFrame hits per putein for each gene followed by a hit list and a quantification like for the nucleotide Simages; “Isd” is the “immunosuppressive domain” calculated from the envelope evaluation program henzyscore or identified manually; “Envhpoints” is the score from henzyscore; “Envgroup2” shows the envelope subgroup (like “HERVT_A”, in the main text often shown as “hervta”); “Envqscore” is the output from the envelope quality control program EnvQual.

Additional file 5: Table S5. HERV group Excel table with 1. Nucleotide frequencies and marked biases, 2. LTR divergence and 3. Consensus statistics.