Table 3.
Paralog identification based on sequence homology between the mtDNA segments that showed homology to the same ctDNA region
| Ct segment No. | Ct-coordinates | Mt segments compareda) | Size comp’d (bp) | No. matched nucleotides | % Homologyb) | Originc) |
|---|---|---|---|---|---|---|
| 1 | 6,696–6,749 | 1a/1b | 54 | 54 | 100.0 | Paralog |
| ″ | ″ | 1a, b/1c | 54 | 53 | 98.1 | Paralog |
| 7,8 | 34,262–34,366 | 7/8 | 58 | 8 | 13.8 | - |
| 10–13 | 34,918–36,108 | 10/11a,b | 328 | 327 | 99.7 | Paralogd) |
| ″ | ″ | 10/12 | 147 | 88 | 59.9 | - |
| ″ | ″ | 11a/11b | 1,110 | 1,110 | 100.0 | Paralog |
| ″ | ″ | 11a,b/12 | 766 | 518 | 67.6 | - |
| ″ | ″ | 11a,b/13 | 496 | 348 | 70.2 | - |
| ″ | ″ | 12/13 | 323 | 81 | 25.1 | - |
| 18–20 | 48,013–48,128 | 18/19a,b,c | 27 | 26 | 96.3 | - |
| ″ | ″ | 18/20 | 47 | 38 | 80.9 | - |
| ″ | ″ | 19a/19b/19c | 27 | 27 | 100.0 | Paralog |
| ″ | ″ | 19a,b,c/20 | 26 | 17 | 65.4 | - |
| 29,30 | 64,017–64,131 | 29/30a,b | 16 | 15 | 87.5 | - |
| ″ | 64,069–64,131 | 30a/30b | 64 | 64 | 100.0 | Paralog |
| 36,37 | 82,945–82,976 | 36/37 | 30 | 21 | 70.0 | - |
| 39,40 | 84,711–89,049 | 39/40 | 177 | 45 | 25.4 | - |
| 41 | 91,016–92,532 | 41a/41b/41c | 1,932 | 1,932 | 100.0 | Paralog |
| 43–45 | 94,995–97,615 | 43a/43b | 3,145 | 3,145 | 100.0 | Paralog |
| ″ | ″ | 43a,b/44 | 69 | 69e) | 100.0 | Paralog |
| ″ | ″ | 43a,b/45 | 65 | 50e) | 76.9 | - |
| ″ | ″ | 44/45 | 65 | 50 | 76.9 | - |
| 46,47 | 98,811–98,896 | 46/47a,b,c | 58 | 47 | 81.0 | - |
| ″ | ″ | 47a/47b/47c | 59 | 59 | 100.0 | Paralog |
| 50–53 | 110,973–111,387 | 50/51 | 39 | 15 | 38.5 | - |
| ″ | ″ | 50/52 | 43 | 34 | 79.1 | - |
| ″ | ″ | 50/53a,b | 32 | 26 | 81.3 | - |
| ″ | ″ | 52/53a,b | 32 | 20 | 65.2 | - |
| ″ | ″ | 53a/53b | 32 | 32 | 100.0 | Paralog |
a) MtDNA segment numbers are taken from Table 2. Numerator and denominator indicate the DNA segments compared.
b) [No. of matched nucleotides]/[Number of nucleotides compared] × 100.
c) Definition of paralog is given in the text.
d) Segment no. 10 (size 328 bp) is 99.7% homologous to the 328 bp 5′-end of segments no. 11a and 11b, indicating paralogy of the former to the 5′-end of the latter two segments.
e) The 69 bp 5′-end of segments no. 43a and 43b is completely homologous to segment no. 44 and the 65 bp 5′-end of 43a and 43b is partially homologous to segment no. 45.