Table 2 Assembly-based quantification of repeats. Copy number, total base pair, and density of different classes of repeats annotated by RepeatMasker using a combined library of the RepeatModeler de novo library from each race (manual curation of the P24X0 library, used for reclassification of the three other de novo libraries), the Arthropod library from Repbase, and libraries from each race from HelitronScanner and RepeatExplorer2, across males of four chromosomal races of the viatica species group. TR tandem repeats, GP genome proportion (% assembly)

SINE

355,321

57,777,060

1.45

476,672

84,209,572

2.31

498,884

86,588,794

2.16

331,980

55,473,057

1.45

LINE

1,630,136

751,701,393

18.88

1,544,315

715,290,166

19.6

1,603,310

792,142,166

19.79

1,780,161

819,481,256

21.40

LTR

270,520

191,052,819

4.80

298,156

160,264,290

4.39

316,814

207,702,027

5.19

303,192

169,275,629

4.42

DNA

2,269,382

712,386,285

17.89

2,136,964

678,964,713

18.61

2,179,781

734,004,927

18.34

2,165,693

714,794,492

18.66

Helitron

3,194,220

663,607,802

16.72

8,654,890

708,282,512

19.45

3,887,696

878,010,926

21.88

3,569,564

782,636,309

20.45

TR

5269

790,157

0.02

3294

506,934

0.01

10,988

1,403,691

0.04

232

12,409

0.01

Unclassified

889,785

237,465,164

5.98

795,764

240,830,299

6.62

946,725

290,976,813

7.29

8,992,548

237,984,790

6.24

Total

8,614,633

2,614,780,680

65.74

13,910,055

2,588,348,486

70.99

9,444,198

2,989,425,653

74.69

17,143,370

2,779,657,942

72.62