Table 1

Copy numbers and conservation degrees of 12 transposable elements based on the BLAST analyses

TE

Accession or reference (1)

Size (Pb)

Total count of Blast (A) (2)

Highest score (bit) (3)

Count over 80% of the highest score (B) (4)

80% of highest score

Conservation degree (B/A%) (5)

noaCRR1

AY827986

794

479

1467

29

1173

6.05

RIRE5

AB105803LTR

995

270

1674

14

1339

5.19

RIRE7

AB033234LTR

858

119

1541

30

1232

25.21

p-SINE1

Mochizuki et al. (1992) p-SINE1 consensus

123

207

209

66

167

31.88

Akan

AB077838

486

110

784

47

627

42.73

Kiddo

AF484680

269

42

459

37

367

88.1

Kiserul

AB077834

259

835

453

390

362

46.71

mPing

BK000588

430

50

795

48

636

96

Mashu

AB077839

263

563

457

441

360

78.33

Tabitoll

AB077831

146

563

226

339

180

60.21

Toya

AB077842

176

11

287

8

229

72.73

Basho

Inukai and Sano (2002) MS399

201

396

359

29

287

7.32

1: Representatives of the 12 TEs were selected from these accessions or references, which were used as the queries for the BLAST analyses.

2: These correspond to numbers of the sequences hit by the rice BLAST analyses at NCBI as described in Materials and Methods.

3: The scores are those of the most homologous sequences hit by the BLAST analyses.

4: The numbers of the sequences with more than 80% of the highest scores.

5: Conservation degrees of the TEs are estimated by percentages of the counts with more than 80% of the highest scores(B) in the total counts (A).

Takata et al. BMC Genomics 2007 8:469   doi:10.1186/1471-2164-8-469