Table 2 Cross-species results of Look4LTRs compared to other tools. The tools used are Look4LTRs-SS (Single-Species), Look4LTRs-CS (Cross-Species), LTRharvest, and LtrDetector on the following five rice species: (i) Oryza sativa japonica, (ii) Oryza glaberrima, (iii) Oryza sativa indica, (iv) Oryza longistaminata, and (v) Oryza rufipogon. Look4LTRs-SS is applied to each species separately, i.e., it only trains and predicts on one given genome at a time. Look4LTRs-CS is applied to the five species together, i.e., it learns the repeat content of the five species and predicts on all of them. ^aThe memory and time for Look4LTRs-CS is the same for every genome and the Overall because Look4LTRs-CS was run on all genomes at once. Thus, they all come from the same exact run

Oryza sativa japonica

     Look4LTRs-SS

90.80

92.78

91.78

1,500

1,362

106

10,462

12.94

00:01:51

     Look4LTRs-CS

91.80

92.48

92.14

1,500

1,377

112

10,315

–

–

     LTRharvest

72.67

91.37

80.95

1,500

1,090

103

6,684

0.34

00:05:54

     LtrDetector

86.87

85.67

86.26

1,500

1,303

218

10,659

15.61

00:05:44

Oryza glaberrima

     Look4LTRs-SS

79.15

83.17

81.11

331

262

53

5,128

7.25

00:01:13

     Look4LTRs-CS

87.61

83.82

85.67

331

290

56

5,297

–

–

     LTRharvest

83.69

81.71

82.69

331

277

62

3,942

0.26

00:02:45

     LtrDetector

91.24

69.43

78.85

331

302

133

5,192

13.02

00:02:00

Oryza sativa indica

     Look4LTRs-SS

81.71

70.38

75.62

410

335

141

13,845

8.16

00:02:03

     Look4LTRs-CS

83.17

69.31

75.61

410

341

151

13,829

–

–

     LTRharvest

74.39

71.93

73.14

410

305

119

8,543

0.36

00:04:20

     LtrDetector

77.56

54.83

64.24

410

318

262

15,865

15.51

00:13:35

Oryza longistaminata

     Look4LTRs-SS

63.49

26.76

37.65

126

80

219

13,132

7.49

00:03:08

     Look4LTRs-CS

65.08

26.45

37.61

126

82

228

12,678

–

–

     LTRharvest

52.38

23.57

32.51

126

66

214

12,226

0.36

00:04:37

     LtrDetector

57.94

16.70

25.93

126

73

364

18,802

15.00

00:14:38

Oryza rufipogon

     Look4LTRs-SS

79.39

60.94

68.95

228

181

116

8,281

7.79

00:01:50

     Look4LTRs-CS

86.40

62.15

72.29

228

197

120

8,330

–

–

     LTRharvest

85.96

59.39

70.25

228

196

134

6,436

0.31

00:03:39

     LtrDetector

85.53

41.85

56.20

228

195

271

11,373

13.64

00:03:40

Overall

     Look4LTRs-SS

85.55

77.76

81.47

2,595

2,220

635

50,848

12.94

00:10:05

     Look4LTRs-CS

88.13

77.42

82.43

2,595

2,287

667

50,449

18.54^a

00:08:51^a

     LTRharvest

74.53

75.37

74.95

2,595

1,934

632

37,831

0.36

00:21:15

     LtrDetector

84.43

63.71

72.62

2,595

2,191

1,248

61,891

15.61

00:39:37