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Table 1 Summary of the 85 Medicago truncatula LTR families

From: LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice

Family

Pre-existing name

Super-family

BAC

Location(bp)

LTR size(bp)

Element size(bp)

FL

Strong hit

Mtr1

-

Copia

AC150246.1

34464–46424

1309

11961

69

184

Mtr2

COPIA4

Copia

AC137553.45

99838–112535

2045

12698

11

29

Mtr3

-

Copia

CR931729.2

71151–77207

1287

6057

5

22

Mtr4

-

Copia

AC157648.18

22659–28446

627

5788

9

15

Mtr5

-

Copia

AC146866.6

121051–127748

602

6698

8

14

Mtr6

-

Copia

AC151725.26

4572–10226

797

5655

10

14

Mtr7

-

Copia

CT967304.4

59158–64899

639

5742

7

13

Mtr8

-

Copia

AC145027.17

30490–37188

676

6699

8

12

Mtr9

SHACOP3

Copia

AC159223.1

27730–32760

189

5031

6

11

Mtr10

-

Copia

AC144482.11

104300–109315

436

5016

10

11

Mtr11

-

Copia

AC165219.2

137152–141889

273

4738

7

10

Mtr12

-

Copia

AC149637.11

7608–18418

1344

10811

5

7

Mtr13

-

Copia

AC151956.5

65260–71649

203

6390

5

6

Mtr14

-

Copia

AC144538.23

111496–121985

1394

10490

5

6

Mtr15

COP20

Copia

AC121235.20

19414–24294

346

4881

5

6

Mtr16

-

Copia

CR931743.1

32761–38060

574

5300

4

6

Mtr17

SHACOP12

Copia

AC148291.22

18569–23612

213

5044

5

5

Mtr18

-

Copia

AC124217.21

65448–73850

1419

8403

2

4

Mtr19

-

Copia

AC149492.14

60016–72184

1822

12169

2

4

Mtr20

-

Copia

AC145330.19

54872–60067

190

5196

3

4

Mtr21

-

Copia

AC144760.27

99316–104667

597

5352

4

4

Mtr22

COP10

Copia

AC144618.7

69511–74634

324

5124

4

4

Mtr23

COP6

Copia

AC125476.30

52976–57511

212

4536

2

4

Mtr24

-

Copia

AC148470.14

69233–73561

250

4329

3

3

Mtr25

SHACOP4

Copia

AC152964.13

48071–52925

276

4855

2

3

Mtr26

-

Copia

CT573053.1

95022–106275

1608

11254

2

3

Mtr27

-

Copia

AC140916.17

54292–65468

1434

11177

1

3

Mtr28

-

Copia

AC174349.10

54241–58572

126

4332

3

3

Mtr29

COP12

Copia

AC165446.16

77640–82389

351

4750

2

3

Mtr30

MTCOPIA2

Copia

AC149471.1

84193–89268

186

5076

2

3

Mtr31

-

Copia

CT573028.11

32334–34027

204

3059

1

3

Mtr32

COP3

Copia

AC138465.22

17893–22580

181

4688

3

3

Mtr33

MTCOPIA1

Copia

CT963078.3

62740–67719

269

4980

2

3

Mtr34

SHACOP11

Copia

AC154867.1

30673–35442

189

4770

1

3

Mtr35

SHACOP20

Copia

AC149038.2

47760–52995

263

5236

2

3

Mtr36

-

Copia

AC174295.7

36459–41224

171

4766

2

2

Mtr37

-

Copia

AC157979.11

69871–74887

249

5017

1

2

Mtr38

-

Copia

AC171778.15

79794–84281

222

4488

2

2

Mtr39

-

Copia

AC148470.14

54043–59356

861

5314

2

2

Mtr40

SHACOP9

Copia

AC175047.2

122584–127374

190

4791

2

2

Mtr41

-

Copia

AC174336.9

98223–102259

296

4704

1

2

Mtr42

-

Copia

AC157506.3

45694–50555

205

4862

1

2

Mtr43

-

Copia

AC175047.2

115144–119648

256

4505

1

2

Mtr44

-

Copia

AC183304.10

99523–104053

167

4531

2

2

Mtr45

-

Copia

CR955009.1

105072–109675

306

4604

2

2

Mtr46

COP14

Copia

AC170583.6

12146–16446

171

4301

2

2

Mtr47

COP21

Copia

AC182817.5

43694–48680

290

4987

2

2

Mtr48

SHACOP21

Copia

AC161106.13

30630–35152

232

4523

2

2

Mtr49

-

Copia

AC158377.1

75346–80903

131

5558

2

2

Mtr50

-

Copia

AC175047.2

83093–87466

242

4374

1

2

Mtr51

-

Copia

AC123573.41

60243–65229

213

4987

1

2

Mtr52

-

Copia

AC135798.31

10206–15241

330

5036

1

2

Mtr53

-

Copia

AC137831.27

31862–36604

218

4782

1

2

Mtr54

-

Copia

CT963132.5

16390–21157

239

5030

1

2

Mtr55

-

Copia

AC149634.8

14602–17988

206

3387

1

2

Mtr56

SHACOP2

Copia

AC146909.23

66018–71021

274

5004

2

2

Mtr57

Ogre1A,B,C,D

Gypsy

AC144405.30

85771–104542

3529

18772

114

137

Mtr58

-

Gypsy

AC162162.23

96896–105667

2127

8772

34

69

Mtr59

Ogre2,3,4

Gypsy

AC138465.22

43789–60338

2435

16550

31

37

Mtr60

-

Gypsy

AC123573.41

34307–46826

1335

12520

2

26

Mtr61

-

Gypsy

AC147430.9

69500–78131

2072

8632

1

10

Mtr62

-

Gypsy

AC160097.27

42464–45517

2076

8661

1

10

Mtr63

-

Gypsy

CU024896.3

74551–82251

2222

7701

3

6

Mtr64

-

Gypsy

AC146759.29

74288–85435

1218

11148

4

5

Mtr65

-

Gypsy

CT963073.3

80019–85667

313

5649

4

5

Mtr66

-

Gypsy

AC150705.16

77136–84299

1943

7164

2

4

Mtr67

-

Gypsy

AC140773.20

23404–37605

721

14202

3

4

Mtr68

-

Gypsy

AC125481.23

24806–33987

330

9182

2

3

Mtr69

-

Gypsy

AC157375.2

85556–93073

2125

7518

3

3

Mtr70

-

Gypsy

AC144591.10

13089–29661

2370

16573

1

3

Mtr71

-

Gypsy

CU024896.3

71754–86395

366

6936

1

2

Mtr72

GYPSHAN2

Gypsy

AC158209.13

42449–47637

409

5189

2

2

Mtr73

-

Gypsy

AC148657.1

69339–74484

394

5146

2

2

Mtr74

-

Gypsy

CU024896.3

86399–92950

819

6552

2

2

Mtr75

-

TRIM

AC147537.35

119057–119409

130

364

9

74

Mtr76

-

TRIM

CR954194.1

12806–16125

652

3320

17

38

Mtr77

-

LARD

AC155884.2

39928–44595

2191

4668

5

26

Mtr78

-

LARD

CT030253.10

41580–46389

921

5497

3

26

Mtr79

-

TRIM

AC158173.13

32092–32698

190

607

5

25

Mtr80

-

env-class

AC146719.32

60449–68395

1239

7947

5

20

Mtr81

-

LARD

CT025840.2

61376–73139

2414

11764

2

14

Mtr82

-

TRIM

CT009479.4

31485–34519

810

3035

7

10

Mtr83

-

LARD

AC140022.11

3262–11660

1440

8399

2

10

Mtr84

-

LARD

AC147201.16

18119–23949

259

5831

6

10

Mtr85

-

TRIM

AC145219.16

111276–112148

249

873

1

6

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