Table 2.
Characterization of the size, similarity, and nucleotide substitution patterns from pairwise comparison of tiger cymt (12.8 kb) and numt (12.5 kb) sequences. Stop codons within numt were determined after frame shift or indels.
| Pattern of substitutions
|
Pattern of gaps in numt |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Size (bp) | Changes between cymt and numt (bp)
|
Ts
|
Tv
|
||||||||||||
| Segments | cymt | numt | Subst. | Gaps | A-G | T-C | G-C | A-T | T-G | A-C | Ts/Tv ratio | Insertions (bp) | (bp) Deletions | Number of stop codons within numt | Percent differences of nucleotide |
| Protein Coding Genes | |||||||||||||||
| ND5 | 1530 | 1533 | 124 | 11 | 35 | 76 | 4 | 3 | 1 | 5 | 8,5 | 7(1bpx3+2bpx2) | 4(1bpx4) | 1 | 8,8 |
| ND6 | 528 | 527 | 38 | 5 | 14 | 19 | - | 1 | 3 | 1 | 6,6 | 2(1bpx2) | 3(1bpx1+2bpx1) | - | 8,1 |
| ND1 | 957 | 958 | 71 | 5 | 15 | 52 | 1 | 1 | 1 | 1 | 16,8 | 3(1bpx4) | 2(1bpx2) | 3 | 7,0 |
| ND2 | 1044 | 1044 | 84 | 4 | 26 | 46 | 4 | 4 | - | 4 | 6,0 | 2(1bpx2) | 2(1bpx2) | - | 8,4 |
| CytB | 1140 | 1143 | 94 | 15 | 29 | 59 | 1 | 2 | 1 | 2 | 14,7 | 9(1bpx9) | 6(1bpx6) | - | 10,5 |
| COI | 1545 | 1550 | 124 | 19 | 48 | 65 | 1 | 2 | 6 | 2 | 10,3 | 12(1bpx9+3bpx1) | 7(1bpx7) | 23 | 9,3 |
| COII | 684 | 684 | 62 | 8 | 27 | 33 | - | - | 1 | 1 | 30,0 | 4(1bpx2+2bpx1) | 4(1bpx4) | - | 10,2 |
| ATP8 | 182 | 183 | 23 | 9 | 10 | 9 | 1 | 2 | 1 | 1 | 3,8 | 5(1bpx3+2bpx1) | 4(1bpx2+2bpx1) | 5 | 17,6 |
| Total | 7610 | 7622 | 620 | 76 | 204 | 359 | 12 | 15 | 14 | 17 | 9,7 | 44 | 32 | 32 | 9,1 |
| rRNAs | |||||||||||||||
| 12S | 957 | 956 | 19 | 9 | 7 | 9 | - | - | - | 3 | 5,3 | 4(1bpx4) | 5(1bpx5) | - | 2,9 |
| 16S | 1575 | 1545 | 42 | 44 | 13 | 22 | 1 | 4 | - | 1 | 5,8 | 7(1bpx7) | 37(6bpx1+1bpx6+25bpx1) | - | 5,5 |
| Total | 2532 | 2501 | 61 | 53 | 20 | 31 | 1 | 4 | - | 4 | 5,7 | 11 | 42 | - | 4,5 |
| tRNAs | |||||||||||||||
| tRNA-Glu | 71 | 70 | - | 1 | - | - | - | - | - | - | - | - | 1(1bpx1) | - | 1,4 |
| tRNA-Thr | 70 | 70 | 4 | - | 1 | 2 | - | 1 | - | - | 3 | - | - | - | 5,7 |
| tRNA-Pro | 66 | 66 | - | - | - | - | - | - | - | - | - | - | - | - | 0 |
| tRNA-Phe | 71 | 75 | 6 | 6 | 3 | 1 | 1 | - | 1 | - | 2 | 5(2bpx1+1bpx3) | 1(1bpx1) | - | 16,9 |
| tRNA-Val | 68 | 68 | - | - | - | - | - | - | - | - | - | - | - | 0 | |
| tRNA-Leu | 75 | 75 | 4 | - | - | 2 | - | 1 | 1 | - | 1 | - | - | - | 5,3 |
| tRNA-Ile | 69 | 69 | 2 | - | 2 | - | - | - | - | - | 2 | - | - | - | 2,9 |
| tRNA-Gln | 74 | 74 | - | - | - | - | - | - | - | - | - | - | - | - | 0 |
| tRNA-Met | 69 | 69 | 1 | - | - | 1 | - | - | - | - | 1 | - | - | - | 1,4 |
| tRNA-Trp | 69 | 69 | 3 | 4 | - | 1 | - | 1 | 1 | - | 0,5 | 2(1bpx2) | 2(1bpx2) | - | 10,1 |
| tRNA-Ala | 69 | 69 | 3 | - | 1 | 2 | - | - | - | - | 3 | - | - | - | 4,3 |
| tRNA-Asn | 73 | 73 | 3 | - | 1 | 1 | - | - | 1 | - | 2 | - | - | - | 4,1 |
| tRNA-Cys | 66 | 66 | 2 | - | 1 | - | - | 1 | - | - | 1 | - | - | - | 3,0 |
| tRNA-Tyr | 68 | 66 | 4 | 4 | - | 2 | 1 | - | - | 1 | 1 | 1(1bpx1) | 3(1bpx3) | - | 11,8 |
| tRNA-Ser | 70 | 70 | 3 | - | 1 | 2 | - | - | - | - | 3 | - | - | - | 4,3 |
| tRNA-Asp | 69 | 70 | 4 | 1 | 2 | 2 | - | - | - | - | 4 | 1(1bpx1) | - | - | 7,2 |
| tRNA-Lys | 69 | 69 | 4 | - | 1 | 3 | - | - | - | - | 4 | - | - | - | 5,8 |
| Total | 1186 | 1188 | 43 | 16 | 13 | 19 | 2 | 4 | 4 | 1 | 2,9 | 9 | 7 | - | 5,0 |
| Control region | 1539 | 1181 | 79 | 378 | 25 | 39 | 2 | 6 | 2 | 5 | 4,3 | 10(1bpx7+3bpx1) | 368(1bpx5+23bpx1+340bpx1) | - | 30 |
| Total | 12867 | 12492 | 803 | 523 | 262 | 448 | 17 | 29 | 20 | 27 | 7,6 | 74 | 449 | 32 | 10,3 |