|
Classification and distribution of known plant repeats in the BAC end sequences |
|||||
| Tom. HBa |
Tom. Eco |
Tom. Mbo |
Pot. POT |
Pot. PPT |
|
|
|
|||||
| Class I retrotransposons |
16.95 |
9.30 |
13.81 |
11.42 |
8.19 |
| LTR retrotransposons |
16.81 |
9.19 |
13.72 |
11.16 |
7.92 |
| Ty1/Copia |
5.25 |
4.17 |
4.39 |
2.55 |
2.48 |
| Ty3/Gypsy |
11.56 |
5.02 |
9.33 |
8.60 |
5.43 |
| Unclassified |
0.00 |
0.00 |
0.00 |
0.01 |
0.01 |
| Non-LTR retrotransposons |
0.14 |
0.11 |
0.09 |
0.26 |
0.27 |
| LINE |
0.09 |
0.06 |
0.05 |
0.15 |
0.13 |
| SINE |
0.05 |
0.05 |
0.04 |
0.11 |
0.14 |
| Class II DNA transposons |
0.64 |
0.66 |
0.49 |
1.03 |
1.23 |
| En-Spm |
0.26 |
0.26 |
0.21 |
0.27 |
0.27 |
| Harbinger |
0.00 |
0.00 |
0.00 |
0.00 |
0.00 |
| Mariner |
0.00 |
0.00 |
0.00 |
0.00 |
0.00 |
| MuDR |
0.07 |
0.09 |
0.05 |
0.10 |
0.11 |
| Pogo |
0.02 |
0.03 |
0.02 |
0.03 |
0.08 |
| Stowaway |
0.02 |
0.02 |
0.02 |
0.01 |
0.02 |
| TcMar-Stowaway |
x |
x |
x |
0.00 |
0.00 |
| Tourist |
x |
x |
0.00 |
0.00 |
x |
| hAT |
0.02 |
0.04 |
0.02 |
0.05 |
0.19 |
| hAT-Ac |
0.01 |
0.00 |
0.01 |
0.01 |
0.01 |
| hAT-Tip100 |
0.02 |
0.02 |
0.02 |
0.11 |
0.10 |
| Unclassified |
0.22 |
0.20 |
0.14 |
0.45 |
0.45 |
| Satellites |
0.00 |
0.00 |
0.00 |
0.04 |
0.03 |
| Centromeric |
0.00 |
x |
0.00 |
0.00 |
0.00 |
| Subtelomeric |
x |
x |
x |
0.00 |
0.00 |
| Unclassified |
0.00 |
0.00 |
0.00 |
0.04 |
0.03 |
| Ribosomal genes |
0.04 |
2.98 |
8.58 |
0.03 |
0.53 |
| rRNA |
0.04 |
2.98 |
8.58 |
0.03 |
0.53 |
| Unclassified |
0.08 |
0.11 |
0.07 |
0.07 |
0.11 |
| Centromeric |
x |
x |
x |
0.00 |
x |
| Composite |
x |
x |
x |
x |
0.00 |
| RC/Helitron |
0.08 |
0.11 |
0.07 |
0.06 |
0.11 |
| Unknown |
0.00 |
0.00 |
0.00 |
0.01 |
0.00 |
| Total |
17.66 |
13.01 |
22.91 |
12.54 |
10.02 |
|
Numbers represent percentages of nucleotides that show similarity to a repeat of the indicated category. An 'x' represents the absence of a repeat family; '0.00' indicates that the repeat is present, but at a frequency lower than 0.005 % of the nucleotides in the BESs. Species names have been abbreviated as follows: Tom.: tomato; Pot.: potato. | |||||
Datema et al. BMC Plant Biology 2008 8:34 doi:10.1186/1471-2229-8-34 |
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