Table 2 Open in new tab Comparisons of...

Method	SE_CRs (%)	SE_SDs (%)	SE_ARs (%)	DEL (bp)	URL (bp)	PRL (bp)	FDR (%)	SP_Num	Time (min)	Mem (GB)
Arabidopsis thaliana
RepLoc	75.64	62.68	66.97	27 792 273	5 325 883	1 412 754	14.08	7761	1.62	0.73
Red	76.99	56.29	65.41	48 266 600	26 325 011	800 327	52.88	2728	2.78	0.91
Tallymer	63.79	38.14	49.13	21 002 177	4 520 842	503 480	19.13	8039	1.77	0.94
GRF	55.58	35.52	43.29	15 443 068	921 123	447 935	3.06	772	8.85	2.40
WinMask	38.07	23.60	30.48	25 335 171	15 108 496	128 506	59.13	7177	0.60	0.32
phRAIDER	7.82	3.31	5.36	1 810 768	11 108	5351	0.32	130	1.07	3.40
Drosophila melanogaster
RepLoc	86.05	95.16	86.11	30 406 825	3 624 759	286 476	10.98	19 411	1.75	0.73
Red	83.02	83.80	80.40	30 727 818	5 722 087	157 730	18.11	12 160	3.28	1.00
Tallymer	82.11	82.76	79.40	28 758 853	4 063 921	163 671	13.56	18 812	2.25	1.08
GRF	70.02	79.47	68.18	21 619 040	412 980	148 766	1.22	1720	8.88	2.80
WinMask	49.51	39.72	47.04	29 686 523	15 055 682	32 444	50.61	19 381	0.68	0.32
phRAIDER	37.23	44.81	36.74	11 491 245	64 107	46 170	0.16	1096	3.38	3.90
Oryza sativa
RepLoc	85.69	77.21	82.34	185 011 071	12 032 731	4 111 008	4.28	77 462	2.60	1.50
Tallymer	77.13	46.63	68.42	149 613 447	5 873 820	1 435 182	2.97	66 576	9.32	3.00
Red	73.05	41.49	64.08	137 634 418	2 999 845	1 071 069	1.40	55 536	9.18	2.40
GRF	72.95	50.71	66.15	143 570 275	4 592 364	1 807 796	1.94	22 613	11.92	8.30
WinMask	58.07	28.41	50.40	120 138 226	14 243 639	209 240	11.68	38 261	3.00	1.10
phRAIDER	34.42	14.81	29.31	61 742 598	160 949	76 377	0.14	7535	10.08	5.30
Danio rerio
RepLoc	88.32	91.41	87.98	814 834 122	60 910 450	8 919 596	6.38	416 859	13.48	6.20
Tallymer	87.27	84.12	86.33	802 714 830	62 891 311	6 284 038	7.05	373 038	44.67	11.50
Red	74.62	75.24	73.60	644 011 242	13 254 572	3 338 095	1.54	334 424	38.68	6.40
GRF	73.46	78.96	72.91	648 858 019	24 069 790	4 677 047	2.99	130 319	65.58	37.60
WinMask	67.41	52.17	65.75	646 304 388	82 840 510	1 870 446	12.53	203 965	15.52	1.30
phRAIDER	38.70	51.68	38.70	335 782 283	4 172 859	1 320 276	0.85	88 898	39.62	8.60
Zea mays
RepLoc	97.80	93.08	94.36	1 842 724 703	23 764 993	14 207 796	0.52	59 019	28.90	6.20
Tallymer	97.13	89.00	91.56	1 784 439 413	19 397 981	10 361 876	0.51	55 600	96.10	19.30
GRF	95.32	88.62	90.55	1 763 611 506	18 136 515	10 059 994	0.46	22 173	147.48	57.80
Red	93.66	82.41	85.89	1 662 061 491	6 330 715	5 000 258	0.08	36 219	40.47	9.10
WinMask	82.35	68.27	72.80	1 408 960 379	5 668 126	971 854	0.33	15 563	22.82	1.50
phRAIDER	84.66	70.34	74.98	1 447 164 002	1 868 048	1 396 725	0.03	13 123	115.95	21.40
Mus musculus
RepLoc	71.57	89.44	72.42	1 034 179 396	85 509 557	17 027 074	6.62	613 281	23.88	11.70
Tallymer	71.04	82.06	70.47	1 015 198 897	92 063 889	12 607 092	7.83	565 209	75.32	24.00
Red	66.60	76.73	65.57	918 070 891	59 121 015	10 459 466	5.30	527 817	78.53	8.80
GRF	60.81	79.94	61.38	900 984 319	48 454 914	10 742 424	4.42	270 293	149.22	64.00
WinMask	62.45	61.75	60.03	949 478 121	163 016 945	6 364 910	16.50	433 330	28.93	1.40
phRAIDER	43.76	61.26	44.04	591 931 802	14 963 277	6 768 816	1.38	295 621	82.30	21.80
Homo sapiens
RepLoc	67.30	85.57	67.89	1 190 032 803	102 056 428	28 757 056	6.16	716 463	24.22	11.70
Tallymer	65.93	63.74	64.85	1 144 451 245	105 103 160	16 578 923	7.74	648 553	149.47	25.70
Red	65.54	57.24	63.95	1 134 956 885	110 011 699	12 935 472	8.55	571 448	86.40	9.30
GRF	59.20	67.66	58.94	1 008 246 531	63 625 904	16 546 626	4.67	519 015	177.80	247.70
WinMask	58.29	38.50	56.02	1 104 198 589	206 414 002	3 464 958	18.38	569 385	32.47	1.50
phRAIDER	25.29	21.04	24.34	396 065 181	5 948 771	2 324 105	0.92	264 128	60.03	27.20

Method

SE_CRs (%)

SE_SDs (%)

SE_ARs (%)

DEL (bp)

URL (bp)

PRL (bp)

FDR (%)

SP_Num

Time (min)

Mem (GB)

Arabidopsis thaliana

RepLoc

75.64

62.68

66.97

27 792 273

5 325 883

1 412 754

14.08

7761

1.62

0.73

Red

76.99

56.29

65.41

48 266 600

26 325 011

800 327

52.88

2728

2.78

0.91

Tallymer

63.79

38.14

49.13

21 002 177

4 520 842

503 480

19.13

8039

1.77

0.94

GRF

55.58

35.52

43.29

15 443 068

921 123

447 935

3.06

772

8.85

2.40

WinMask

38.07

23.60

30.48

25 335 171

15 108 496

128 506

59.13

7177

0.60

0.32

phRAIDER

7.82

3.31

5.36

1 810 768

11 108

5351

0.32

130

1.07

3.40

Drosophila melanogaster

RepLoc

86.05

95.16

86.11

30 406 825

3 624 759

286 476

10.98

19 411

1.75

0.73

Red

83.02

83.80

80.40

30 727 818

5 722 087

157 730

18.11

12 160

3.28

1.00

Tallymer

82.11

82.76

79.40

28 758 853

4 063 921

163 671

13.56

18 812

2.25

1.08

GRF

70.02

79.47

68.18

21 619 040

412 980

148 766

1.22

1720

8.88

2.80

WinMask

49.51

39.72

47.04

29 686 523

15 055 682

32 444

50.61

19 381

0.68

0.32

phRAIDER

37.23

44.81

36.74

11 491 245

64 107

46 170

0.16

1096

3.38

3.90

Oryza sativa

RepLoc

85.69

77.21

82.34

185 011 071

12 032 731

4 111 008

4.28

77 462

2.60

1.50

Tallymer

77.13

46.63

68.42

149 613 447

5 873 820

1 435 182

2.97

66 576

9.32

3.00

Red

73.05

41.49

64.08

137 634 418

2 999 845

1 071 069

1.40

55 536

9.18

2.40

GRF

72.95

50.71

66.15

143 570 275

4 592 364

1 807 796

1.94

22 613

11.92

8.30

WinMask

58.07

28.41

50.40

120 138 226

14 243 639

209 240

11.68

38 261

3.00

1.10

phRAIDER

34.42

14.81

29.31

61 742 598

160 949

76 377

0.14

7535

10.08

5.30

Danio rerio

RepLoc

88.32

91.41

87.98

814 834 122

60 910 450

8 919 596

6.38

416 859

13.48

6.20

Tallymer

87.27

84.12

86.33

802 714 830

62 891 311

6 284 038

7.05

373 038

44.67

11.50

Red

74.62

75.24

73.60

644 011 242

13 254 572

3 338 095

1.54

334 424

38.68

6.40

GRF

73.46

78.96

72.91

648 858 019

24 069 790

4 677 047

2.99

130 319

65.58

37.60

WinMask

67.41

52.17

65.75

646 304 388

82 840 510

1 870 446

12.53

203 965

15.52

1.30

phRAIDER

38.70

51.68

38.70

335 782 283

4 172 859

1 320 276

0.85

88 898

39.62

8.60

Zea mays

RepLoc

97.80

93.08

94.36

1 842 724 703

23 764 993

14 207 796

0.52

59 019

28.90

6.20

Tallymer

97.13

89.00

91.56

1 784 439 413

19 397 981

10 361 876

0.51

55 600

96.10

19.30

GRF

95.32

88.62

90.55

1 763 611 506

18 136 515

10 059 994

0.46

22 173

147.48

57.80

Red

93.66

82.41

85.89

1 662 061 491

6 330 715

5 000 258

0.08

36 219

40.47

9.10

WinMask

82.35

68.27

72.80

1 408 960 379

5 668 126

971 854

0.33

15 563

22.82

1.50

phRAIDER

84.66

70.34

74.98

1 447 164 002

1 868 048

1 396 725

0.03

13 123

115.95

21.40

Mus musculus

RepLoc

71.57

89.44

72.42

1 034 179 396

85 509 557

17 027 074

6.62

613 281

23.88

11.70

Tallymer

71.04

82.06

70.47

1 015 198 897

92 063 889

12 607 092

7.83

565 209

75.32

24.00

Red

66.60

76.73

65.57

918 070 891

59 121 015

10 459 466

5.30

527 817

78.53

8.80

GRF

60.81

79.94

61.38

900 984 319

48 454 914

10 742 424

4.42

270 293

149.22

64.00

WinMask

62.45

61.75

60.03

949 478 121

163 016 945

6 364 910

16.50

433 330

28.93

1.40

phRAIDER

43.76

61.26

44.04

591 931 802

14 963 277

6 768 816

1.38

295 621

82.30

21.80

Homo sapiens

RepLoc

67.30

85.57

67.89

1 190 032 803

102 056 428

28 757 056

6.16

716 463

24.22

11.70

Tallymer

65.93

63.74

64.85

1 144 451 245

105 103 160

16 578 923

7.74

648 553

149.47

25.70

Red

65.54

57.24

63.95

1 134 956 885

110 011 699

12 935 472

8.55

571 448

86.40

9.30

GRF

59.20

67.66

58.94

1 008 246 531

63 625 904

16 546 626

4.67

519 015

177.80

247.70

WinMask

58.29

38.50

56.02

1 104 198 589

206 414 002

3 464 958

18.38

569 385

32.47

1.50

phRAIDER

25.29

21.04

24.34

396 065 181

5 948 771

2 324 105

0.92

264 128

60.03

27.20

Method	SE_CRs (%)	SE_SDs (%)	SE_ARs (%)	DEL (bp)	URL (bp)	PRL (bp)	FDR (%)	SP_Num	Time (min)	Mem (GB)
Arabidopsis thaliana
RepLoc	75.64	62.68	66.97	27 792 273	5 325 883	1 412 754	14.08	7761	1.62	0.73
Red	76.99	56.29	65.41	48 266 600	26 325 011	800 327	52.88	2728	2.78	0.91
Tallymer	63.79	38.14	49.13	21 002 177	4 520 842	503 480	19.13	8039	1.77	0.94
GRF	55.58	35.52	43.29	15 443 068	921 123	447 935	3.06	772	8.85	2.40
WinMask	38.07	23.60	30.48	25 335 171	15 108 496	128 506	59.13	7177	0.60	0.32
phRAIDER	7.82	3.31	5.36	1 810 768	11 108	5351	0.32	130	1.07	3.40
Drosophila melanogaster
RepLoc	86.05	95.16	86.11	30 406 825	3 624 759	286 476	10.98	19 411	1.75	0.73
Red	83.02	83.80	80.40	30 727 818	5 722 087	157 730	18.11	12 160	3.28	1.00
Tallymer	82.11	82.76	79.40	28 758 853	4 063 921	163 671	13.56	18 812	2.25	1.08
GRF	70.02	79.47	68.18	21 619 040	412 980	148 766	1.22	1720	8.88	2.80
WinMask	49.51	39.72	47.04	29 686 523	15 055 682	32 444	50.61	19 381	0.68	0.32
phRAIDER	37.23	44.81	36.74	11 491 245	64 107	46 170	0.16	1096	3.38	3.90
Oryza sativa
RepLoc	85.69	77.21	82.34	185 011 071	12 032 731	4 111 008	4.28	77 462	2.60	1.50
Tallymer	77.13	46.63	68.42	149 613 447	5 873 820	1 435 182	2.97	66 576	9.32	3.00
Red	73.05	41.49	64.08	137 634 418	2 999 845	1 071 069	1.40	55 536	9.18	2.40
GRF	72.95	50.71	66.15	143 570 275	4 592 364	1 807 796	1.94	22 613	11.92	8.30
WinMask	58.07	28.41	50.40	120 138 226	14 243 639	209 240	11.68	38 261	3.00	1.10
phRAIDER	34.42	14.81	29.31	61 742 598	160 949	76 377	0.14	7535	10.08	5.30
Danio rerio
RepLoc	88.32	91.41	87.98	814 834 122	60 910 450	8 919 596	6.38	416 859	13.48	6.20
Tallymer	87.27	84.12	86.33	802 714 830	62 891 311	6 284 038	7.05	373 038	44.67	11.50
Red	74.62	75.24	73.60	644 011 242	13 254 572	3 338 095	1.54	334 424	38.68	6.40
GRF	73.46	78.96	72.91	648 858 019	24 069 790	4 677 047	2.99	130 319	65.58	37.60
WinMask	67.41	52.17	65.75	646 304 388	82 840 510	1 870 446	12.53	203 965	15.52	1.30
phRAIDER	38.70	51.68	38.70	335 782 283	4 172 859	1 320 276	0.85	88 898	39.62	8.60
Zea mays
RepLoc	97.80	93.08	94.36	1 842 724 703	23 764 993	14 207 796	0.52	59 019	28.90	6.20
Tallymer	97.13	89.00	91.56	1 784 439 413	19 397 981	10 361 876	0.51	55 600	96.10	19.30
GRF	95.32	88.62	90.55	1 763 611 506	18 136 515	10 059 994	0.46	22 173	147.48	57.80
Red	93.66	82.41	85.89	1 662 061 491	6 330 715	5 000 258	0.08	36 219	40.47	9.10
WinMask	82.35	68.27	72.80	1 408 960 379	5 668 126	971 854	0.33	15 563	22.82	1.50
phRAIDER	84.66	70.34	74.98	1 447 164 002	1 868 048	1 396 725	0.03	13 123	115.95	21.40
Mus musculus
RepLoc	71.57	89.44	72.42	1 034 179 396	85 509 557	17 027 074	6.62	613 281	23.88	11.70
Tallymer	71.04	82.06	70.47	1 015 198 897	92 063 889	12 607 092	7.83	565 209	75.32	24.00
Red	66.60	76.73	65.57	918 070 891	59 121 015	10 459 466	5.30	527 817	78.53	8.80
GRF	60.81	79.94	61.38	900 984 319	48 454 914	10 742 424	4.42	270 293	149.22	64.00
WinMask	62.45	61.75	60.03	949 478 121	163 016 945	6 364 910	16.50	433 330	28.93	1.40
phRAIDER	43.76	61.26	44.04	591 931 802	14 963 277	6 768 816	1.38	295 621	82.30	21.80
Homo sapiens
RepLoc	67.30	85.57	67.89	1 190 032 803	102 056 428	28 757 056	6.16	716 463	24.22	11.70
Tallymer	65.93	63.74	64.85	1 144 451 245	105 103 160	16 578 923	7.74	648 553	149.47	25.70
Red	65.54	57.24	63.95	1 134 956 885	110 011 699	12 935 472	8.55	571 448	86.40	9.30
GRF	59.20	67.66	58.94	1 008 246 531	63 625 904	16 546 626	4.67	519 015	177.80	247.70
WinMask	58.29	38.50	56.02	1 104 198 589	206 414 002	3 464 958	18.38	569 385	32.47	1.50
phRAIDER	25.29	21.04	24.34	396 065 181	5 948 771	2 324 105	0.92	264 128	60.03	27.20

Method

SE_CRs (%)

SE_SDs (%)

SE_ARs (%)

DEL (bp)

URL (bp)

PRL (bp)

FDR (%)

SP_Num

Time (min)

Mem (GB)

Arabidopsis thaliana

RepLoc

75.64

62.68

66.97

27 792 273

5 325 883

1 412 754

14.08

7761

1.62

0.73

Red

76.99

56.29

65.41

48 266 600

26 325 011

800 327

52.88

2728

2.78

0.91

Tallymer

63.79

38.14

49.13

21 002 177

4 520 842

503 480

19.13

8039

1.77

0.94

GRF

55.58

35.52

43.29

15 443 068

921 123

447 935

3.06

772

8.85

2.40

WinMask

38.07

23.60

30.48

25 335 171

15 108 496

128 506

59.13

7177

0.60

0.32

phRAIDER

7.82

3.31

5.36

1 810 768

11 108

5351

0.32

130

1.07

3.40

Drosophila melanogaster

RepLoc

86.05

95.16

86.11

30 406 825

3 624 759

286 476

10.98

19 411

1.75

0.73

Red

83.02

83.80

80.40

30 727 818

5 722 087

157 730

18.11

12 160

3.28

1.00

Tallymer

82.11

82.76

79.40

28 758 853

4 063 921

163 671

13.56

18 812

2.25

1.08

GRF

70.02

79.47

68.18

21 619 040

412 980

148 766

1.22

1720

8.88

2.80

WinMask

49.51

39.72

47.04

29 686 523

15 055 682

32 444

50.61

19 381

0.68

0.32

phRAIDER

37.23

44.81

36.74

11 491 245

64 107

46 170

0.16

1096

3.38

3.90

Oryza sativa

RepLoc

85.69

77.21

82.34

185 011 071

12 032 731

4 111 008

4.28

77 462

2.60

1.50

Tallymer

77.13

46.63

68.42

149 613 447

5 873 820

1 435 182

2.97

66 576

9.32

3.00

Red

73.05

41.49

64.08

137 634 418

2 999 845

1 071 069

1.40

55 536

9.18

2.40

GRF

72.95

50.71

66.15

143 570 275

4 592 364

1 807 796

1.94

22 613

11.92

8.30

WinMask

58.07

28.41

50.40

120 138 226

14 243 639

209 240

11.68

38 261

3.00

1.10

phRAIDER

34.42

14.81

29.31

61 742 598

160 949

76 377

0.14

7535

10.08

5.30

Danio rerio

RepLoc

88.32

91.41

87.98

814 834 122

60 910 450

8 919 596

6.38

416 859

13.48

6.20

Tallymer

87.27

84.12

86.33

802 714 830

62 891 311

6 284 038

7.05

373 038

44.67

11.50

Red

74.62

75.24

73.60

644 011 242

13 254 572

3 338 095

1.54

334 424

38.68

6.40

GRF

73.46

78.96

72.91

648 858 019

24 069 790

4 677 047

2.99

130 319

65.58

37.60

WinMask

67.41

52.17

65.75

646 304 388

82 840 510

1 870 446

12.53

203 965

15.52

1.30

phRAIDER

38.70

51.68

38.70

335 782 283

4 172 859

1 320 276

0.85

88 898

39.62

8.60

Zea mays

RepLoc

97.80

93.08

94.36

1 842 724 703

23 764 993

14 207 796

0.52

59 019

28.90

6.20

Tallymer

97.13

89.00

91.56

1 784 439 413

19 397 981

10 361 876

0.51

55 600

96.10

19.30

GRF

95.32

88.62

90.55

1 763 611 506

18 136 515

10 059 994

0.46

22 173

147.48

57.80

Red

93.66

82.41

85.89

1 662 061 491

6 330 715

5 000 258

0.08

36 219

40.47

9.10

WinMask

82.35

68.27

72.80

1 408 960 379

5 668 126

971 854

0.33

15 563

22.82

1.50

phRAIDER

84.66

70.34

74.98

1 447 164 002

1 868 048

1 396 725

0.03

13 123

115.95

21.40

Mus musculus

RepLoc

71.57

89.44

72.42

1 034 179 396

85 509 557

17 027 074

6.62

613 281

23.88

11.70

Tallymer

71.04

82.06

70.47

1 015 198 897

92 063 889

12 607 092

7.83

565 209

75.32

24.00

Red

66.60

76.73

65.57

918 070 891

59 121 015

10 459 466

5.30

527 817

78.53

8.80

GRF

60.81

79.94

61.38

900 984 319

48 454 914

10 742 424

4.42

270 293

149.22

64.00

WinMask

62.45

61.75

60.03

949 478 121

163 016 945

6 364 910

16.50

433 330

28.93

1.40

phRAIDER

43.76

61.26

44.04

591 931 802

14 963 277

6 768 816

1.38

295 621

82.30

21.80

Homo sapiens

RepLoc

67.30

85.57

67.89

1 190 032 803

102 056 428

28 757 056

6.16

716 463

24.22

11.70

Tallymer

65.93

63.74

64.85

1 144 451 245

105 103 160

16 578 923

7.74

648 553

149.47

25.70

Red

65.54

57.24

63.95

1 134 956 885

110 011 699

12 935 472

8.55

571 448

86.40

9.30

GRF

59.20

67.66

58.94

1 008 246 531

63 625 904

16 546 626

4.67

519 015

177.80

247.70

WinMask

58.29

38.50

56.02

1 104 198 589

206 414 002

3 464 958

18.38

569 385

32.47

1.50

phRAIDER

25.29

21.04

24.34

396 065 181

5 948 771

2 324 105

0.92

264 128

60.03

27.20

Table 2

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Comparisons of the performance of Red, Tallymer, WindowMasker, phRAIDER, GRF and RepLoc in de novo repeat detection

Method	SE_CRs (%)	SE_SDs (%)	SE_ARs (%)	DEL (bp)	URL (bp)	PRL (bp)	FDR (%)	SP_Num	Time (min)	Mem (GB)
Arabidopsis thaliana
RepLoc	75.64	62.68	66.97	27 792 273	5 325 883	1 412 754	14.08	7761	1.62	0.73
Red	76.99	56.29	65.41	48 266 600	26 325 011	800 327	52.88	2728	2.78	0.91
Tallymer	63.79	38.14	49.13	21 002 177	4 520 842	503 480	19.13	8039	1.77	0.94
GRF	55.58	35.52	43.29	15 443 068	921 123	447 935	3.06	772	8.85	2.40
WinMask	38.07	23.60	30.48	25 335 171	15 108 496	128 506	59.13	7177	0.60	0.32
phRAIDER	7.82	3.31	5.36	1 810 768	11 108	5351	0.32	130	1.07	3.40
Drosophila melanogaster
RepLoc	86.05	95.16	86.11	30 406 825	3 624 759	286 476	10.98	19 411	1.75	0.73
Red	83.02	83.80	80.40	30 727 818	5 722 087	157 730	18.11	12 160	3.28	1.00
Tallymer	82.11	82.76	79.40	28 758 853	4 063 921	163 671	13.56	18 812	2.25	1.08
GRF	70.02	79.47	68.18	21 619 040	412 980	148 766	1.22	1720	8.88	2.80
WinMask	49.51	39.72	47.04	29 686 523	15 055 682	32 444	50.61	19 381	0.68	0.32
phRAIDER	37.23	44.81	36.74	11 491 245	64 107	46 170	0.16	1096	3.38	3.90
Oryza sativa
RepLoc	85.69	77.21	82.34	185 011 071	12 032 731	4 111 008	4.28	77 462	2.60	1.50
Tallymer	77.13	46.63	68.42	149 613 447	5 873 820	1 435 182	2.97	66 576	9.32	3.00
Red	73.05	41.49	64.08	137 634 418	2 999 845	1 071 069	1.40	55 536	9.18	2.40
GRF	72.95	50.71	66.15	143 570 275	4 592 364	1 807 796	1.94	22 613	11.92	8.30
WinMask	58.07	28.41	50.40	120 138 226	14 243 639	209 240	11.68	38 261	3.00	1.10
phRAIDER	34.42	14.81	29.31	61 742 598	160 949	76 377	0.14	7535	10.08	5.30
Danio rerio
RepLoc	88.32	91.41	87.98	814 834 122	60 910 450	8 919 596	6.38	416 859	13.48	6.20
Tallymer	87.27	84.12	86.33	802 714 830	62 891 311	6 284 038	7.05	373 038	44.67	11.50
Red	74.62	75.24	73.60	644 011 242	13 254 572	3 338 095	1.54	334 424	38.68	6.40
GRF	73.46	78.96	72.91	648 858 019	24 069 790	4 677 047	2.99	130 319	65.58	37.60
WinMask	67.41	52.17	65.75	646 304 388	82 840 510	1 870 446	12.53	203 965	15.52	1.30
phRAIDER	38.70	51.68	38.70	335 782 283	4 172 859	1 320 276	0.85	88 898	39.62	8.60
Zea mays
RepLoc	97.80	93.08	94.36	1 842 724 703	23 764 993	14 207 796	0.52	59 019	28.90	6.20
Tallymer	97.13	89.00	91.56	1 784 439 413	19 397 981	10 361 876	0.51	55 600	96.10	19.30
GRF	95.32	88.62	90.55	1 763 611 506	18 136 515	10 059 994	0.46	22 173	147.48	57.80
Red	93.66	82.41	85.89	1 662 061 491	6 330 715	5 000 258	0.08	36 219	40.47	9.10
WinMask	82.35	68.27	72.80	1 408 960 379	5 668 126	971 854	0.33	15 563	22.82	1.50
phRAIDER	84.66	70.34	74.98	1 447 164 002	1 868 048	1 396 725	0.03	13 123	115.95	21.40
Mus musculus
RepLoc	71.57	89.44	72.42	1 034 179 396	85 509 557	17 027 074	6.62	613 281	23.88	11.70
Tallymer	71.04	82.06	70.47	1 015 198 897	92 063 889	12 607 092	7.83	565 209	75.32	24.00
Red	66.60	76.73	65.57	918 070 891	59 121 015	10 459 466	5.30	527 817	78.53	8.80
GRF	60.81	79.94	61.38	900 984 319	48 454 914	10 742 424	4.42	270 293	149.22	64.00
WinMask	62.45	61.75	60.03	949 478 121	163 016 945	6 364 910	16.50	433 330	28.93	1.40
phRAIDER	43.76	61.26	44.04	591 931 802	14 963 277	6 768 816	1.38	295 621	82.30	21.80
Homo sapiens
RepLoc	67.30	85.57	67.89	1 190 032 803	102 056 428	28 757 056	6.16	716 463	24.22	11.70
Tallymer	65.93	63.74	64.85	1 144 451 245	105 103 160	16 578 923	7.74	648 553	149.47	25.70
Red	65.54	57.24	63.95	1 134 956 885	110 011 699	12 935 472	8.55	571 448	86.40	9.30
GRF	59.20	67.66	58.94	1 008 246 531	63 625 904	16 546 626	4.67	519 015	177.80	247.70
WinMask	58.29	38.50	56.02	1 104 198 589	206 414 002	3 464 958	18.38	569 385	32.47	1.50
phRAIDER	25.29	21.04	24.34	396 065 181	5 948 771	2 324 105	0.92	264 128	60.03	27.20

Method	SE_CRs (%)	SE_SDs (%)	SE_ARs (%)	DEL (bp)	URL (bp)	PRL (bp)	FDR (%)	SP_Num	Time (min)	Mem (GB)
Arabidopsis thaliana
RepLoc	75.64	62.68	66.97	27 792 273	5 325 883	1 412 754	14.08	7761	1.62	0.73
Red	76.99	56.29	65.41	48 266 600	26 325 011	800 327	52.88	2728	2.78	0.91
Tallymer	63.79	38.14	49.13	21 002 177	4 520 842	503 480	19.13	8039	1.77	0.94
GRF	55.58	35.52	43.29	15 443 068	921 123	447 935	3.06	772	8.85	2.40
WinMask	38.07	23.60	30.48	25 335 171	15 108 496	128 506	59.13	7177	0.60	0.32
phRAIDER	7.82	3.31	5.36	1 810 768	11 108	5351	0.32	130	1.07	3.40
Drosophila melanogaster
RepLoc	86.05	95.16	86.11	30 406 825	3 624 759	286 476	10.98	19 411	1.75	0.73
Red	83.02	83.80	80.40	30 727 818	5 722 087	157 730	18.11	12 160	3.28	1.00
Tallymer	82.11	82.76	79.40	28 758 853	4 063 921	163 671	13.56	18 812	2.25	1.08
GRF	70.02	79.47	68.18	21 619 040	412 980	148 766	1.22	1720	8.88	2.80
WinMask	49.51	39.72	47.04	29 686 523	15 055 682	32 444	50.61	19 381	0.68	0.32
phRAIDER	37.23	44.81	36.74	11 491 245	64 107	46 170	0.16	1096	3.38	3.90
Oryza sativa
RepLoc	85.69	77.21	82.34	185 011 071	12 032 731	4 111 008	4.28	77 462	2.60	1.50
Tallymer	77.13	46.63	68.42	149 613 447	5 873 820	1 435 182	2.97	66 576	9.32	3.00
Red	73.05	41.49	64.08	137 634 418	2 999 845	1 071 069	1.40	55 536	9.18	2.40
GRF	72.95	50.71	66.15	143 570 275	4 592 364	1 807 796	1.94	22 613	11.92	8.30
WinMask	58.07	28.41	50.40	120 138 226	14 243 639	209 240	11.68	38 261	3.00	1.10
phRAIDER	34.42	14.81	29.31	61 742 598	160 949	76 377	0.14	7535	10.08	5.30
Danio rerio
RepLoc	88.32	91.41	87.98	814 834 122	60 910 450	8 919 596	6.38	416 859	13.48	6.20
Tallymer	87.27	84.12	86.33	802 714 830	62 891 311	6 284 038	7.05	373 038	44.67	11.50
Red	74.62	75.24	73.60	644 011 242	13 254 572	3 338 095	1.54	334 424	38.68	6.40
GRF	73.46	78.96	72.91	648 858 019	24 069 790	4 677 047	2.99	130 319	65.58	37.60
WinMask	67.41	52.17	65.75	646 304 388	82 840 510	1 870 446	12.53	203 965	15.52	1.30
phRAIDER	38.70	51.68	38.70	335 782 283	4 172 859	1 320 276	0.85	88 898	39.62	8.60
Zea mays
RepLoc	97.80	93.08	94.36	1 842 724 703	23 764 993	14 207 796	0.52	59 019	28.90	6.20
Tallymer	97.13	89.00	91.56	1 784 439 413	19 397 981	10 361 876	0.51	55 600	96.10	19.30
GRF	95.32	88.62	90.55	1 763 611 506	18 136 515	10 059 994	0.46	22 173	147.48	57.80
Red	93.66	82.41	85.89	1 662 061 491	6 330 715	5 000 258	0.08	36 219	40.47	9.10
WinMask	82.35	68.27	72.80	1 408 960 379	5 668 126	971 854	0.33	15 563	22.82	1.50
phRAIDER	84.66	70.34	74.98	1 447 164 002	1 868 048	1 396 725	0.03	13 123	115.95	21.40
Mus musculus
RepLoc	71.57	89.44	72.42	1 034 179 396	85 509 557	17 027 074	6.62	613 281	23.88	11.70
Tallymer	71.04	82.06	70.47	1 015 198 897	92 063 889	12 607 092	7.83	565 209	75.32	24.00
Red	66.60	76.73	65.57	918 070 891	59 121 015	10 459 466	5.30	527 817	78.53	8.80
GRF	60.81	79.94	61.38	900 984 319	48 454 914	10 742 424	4.42	270 293	149.22	64.00
WinMask	62.45	61.75	60.03	949 478 121	163 016 945	6 364 910	16.50	433 330	28.93	1.40
phRAIDER	43.76	61.26	44.04	591 931 802	14 963 277	6 768 816	1.38	295 621	82.30	21.80
Homo sapiens
RepLoc	67.30	85.57	67.89	1 190 032 803	102 056 428	28 757 056	6.16	716 463	24.22	11.70
Tallymer	65.93	63.74	64.85	1 144 451 245	105 103 160	16 578 923	7.74	648 553	149.47	25.70
Red	65.54	57.24	63.95	1 134 956 885	110 011 699	12 935 472	8.55	571 448	86.40	9.30
GRF	59.20	67.66	58.94	1 008 246 531	63 625 904	16 546 626	4.67	519 015	177.80	247.70
WinMask	58.29	38.50	56.02	1 104 198 589	206 414 002	3 464 958	18.38	569 385	32.47	1.50
phRAIDER	25.29	21.04	24.34	396 065 181	5 948 771	2 324 105	0.92	264 128	60.03	27.20

SE_CRs is the sensitivity to common repeats annotated by RepeatMasker. SE_SDs is the sensitivity to segmental duplications identified by SEDEF. SE_ARs is the sensitivity to all repeats merged from CRs and SDs. DEL is the total length of repeats detected by every tool in the table. URL is the total length of repeats detected by de novo tools but are unannotated by RepeatMasker or SEDEF. PRL is the total length of PRs that are not annotated but validated by BLAST. FDR is the false discovery rate. SP_Num is the number of specifically detected repeats. WinMask is short for WindowMasker. The symbol ‘bp’ means base pair. ‘min’ is minute. ‘GB’ is gigabyte. The CPU cores used by RepLoc and GRF for A. thaliana, D. melanogaster, O. sativa, D. rerio, Z. mays, M. musculus and H. sapiens are 5, 7, 12, 20, 10, 20 and 20, respectively.

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