Table 1.
Analysis of test sequences with Locus-Assigner and RECCO.
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
| artifical sequence | Locus-Assigner | # diff's | # recom's | loci involved | recom region | # diff's to locus | p value | # diff's after recom |
| B86_B107 | 22_012 | 37 | 1 | 22_012 7_450 |
282 – 307 | 4 0 |
0,001 | 4 |
| B112_B131 | 7_450 | 34 | 1 | 7_450 6_324/3_496 |
282 – 307 | 1 0 |
0,001 | 1 |
| B2_B15_B2 | 4_742 | 26 | 2 | 4_742 10_019 4_742 |
317 – 384 583 – 603 |
0 0 0 |
0,003 0,001 |
0 |
| B443_B474 | 10_019 | 18 | 2 | 10_019 3_385 |
388 – 436 | 3 2 |
0,001 | 5 |
| B86_B44 | 22_012 | 8 | 1 | 10_310 1_504 |
59 – 191 503 – 639 |
0 4 |
4 | |
| B86_B44 | 22_012 | 8 | 0 | 22_012 | 8 | 8 | ||
| B44_B45_B187 | 11_424/3_610/5 544/7_345 |
6 | 0 | 11_424/3_610/5_544/7_345 | 6 | 6 | ||
Test sequences were created in silico by combining sequence regions of assignable HML-2 cDNA sequences, with the aim to construct recombination events between transcripts from corresponding HML-2 loci. Pairwise comparisons, using the in-house Bio-Python script Locus-Assigner, were then performed for test and reference sequences. Column 1 denotes the cDNA sequence name. Column 2: best matching HML-2 proviral locus according to pairwise sequence comparisons with Locus-Assigner. The numbers given here disregard the PCR primer binding regions, and therefore are, for HERV-KX sequences B262, B12 and 93, below the <18 nt differences-threshold initially set for HERV-KX (see text). Due to the lack of a HERV taxonomy, and for the sake of simplicity, HML-2 proviral loci have been numbered artificially in this paper, with the first number indicating chromosomal location of the locus, and the second number being a consecutive number without further connotation. Column 3: nucleotide differences to best match. Column 4: number of recombinations according to RECCO. Column 5: proviral loci involved in recombination(s). More than one locus is given when different loci displayed identical (dis)similarities. Column 6: regions where recombination(s) occured, with the 5' end of the RT-PCR product being defined as nucleotide +1. Column 7: nucleotide differences to individual HML-2 loci. Column 8: p-values of particular predicted recombinations. Column 9: nucleotide differences remaining after considering recombination(s) (see text).