Table 1 Repeated sequences in Mercenaria mercenaria

Retroelements

9.68

339,509

179,875,339

9.74

305,795

174,196,718

 SINEs

1.98

213,809

36,728,732

1.54

179,455

27,466,966

 Penelope

0.50

11,273

9,261,821

0.36

7596

6,410,976

 LINEs:

3.33

51,152

61,848,151

3.20

47,180

57,211,122

  L2/CR1/Rex

1.56

26,146

28,997,539

1.41

22,581

25,216,806

  RTE-X

0.86

12,800

15,956,581

0.74

11,182

13,148,040

  R1/LOA/Jockey

0.57

7243

10,588,945

0.59

7013

10,529,781

  L1/CIN4

0.28

4000

5,126,704

0.32

4497

5,795,447

  R2/R4/NeSL

0.01

153

168,036

0.01

164

226,620

  RTE/Bov-B

0.01

119

113,581

0.01

185

172,540

  CRE/SLACS

0.00

112

80,085

0.00

0

0

  Others

0.03

579

573,523

0.10

1558

1,708,752

 LTR elements:

4.37

74,548

81,298,456

5.01

79,160

89,518,630

  Gypsy

3.87

63,016

71,828,997

4.27

66,510

76,423,586

  BEL/Pao

0.36

5102

6,644,022

0.55

9351

9,821,340

  Copia

0.07

1425

1,289,690

0.13

2022

2,285,303

  Retroviral

0.08

2128

1,535,747

0.06

1277

988,401

  Others

0.00

0

0

0.05

742

928,874

 YR elements:

0.22

2877

4,028,291

0.28

2883

5,084,062

  Ngaro

0.14

1741

2,664,318

0.18

1801

3,287,176

  DIRS

0.07

1136

1,363,973

0.10

1082

1,796,886

DNA transposons

5.74

105,943

106,712,868

6.28

109,894

112,397,883

 Maverick

1.69

7091

31,368,848

1.93

6453

34,529,082

 TcMar/Pogo

0.90

22,496

16,783,981

0.77

18,042

13,743,894

 hobo/Ac/Tam

0.62

13,852

11,531,215

0.71

15,005

12,617,816

 Zator

0.31

10,651

5,838,880

0.20

7691

3,611,369

 Crypton

0.28

9809

5,274,930

0.46

13,654

8,303,711

 Academ-1

0.27

2833

5,097,100

0.31

3377

5,558,034

 EnSpm

0.13

2744

2,455,561

0.15

4019

2,760,579

 MULE/MuDR/IS905

0.10

1838

1,822,048

0.04

895

662,200

 Harbinger/Tourist

0.08

2470

1,526,495

0.11

3294

1,934,619

 PiggyBac

0.00

0

0

0.01

228

181,113

 Others

1.35

32,159

25,013,810

1.59

37,236

28,495,466

Rolling-circles

4.81

389,027

89,393,728

4.06

374,505

72,579,061

Unclassified:

24.97

1,659,652

463,988,071

24.61

1,560,995

440,132,557

Total interspersed repeats:

45.20

839,970,006

44.69

799,306,219

Small RNA:

0.19

16,252

3,490,319

0.37

26,862

6,551,201

Satellites:

10.40

645,877

193,200,141

10.68

623,224

190,956,718

Simple repeats:

0.95

422,909

17,640,334

0.96

399,918

17,236,842

Low complexity:

0.17

65,697

3,083,823

0.16

58,512

2,789,745