Table 1

Frequencies of BAC end sequences and Sanger shot gun sequences matching sequences in Repbase

Type

Absolute number in BESs

Percentage BESs

Percentage repeats in BESs

Absolute number in SGSs

Percentage SGSs

Percentage repeats in SGSs


DNA TEs

hAT

642 (1,671)

0.92 (2.41)

6.84 (4.61)

20 (41)

0.74 (1.52)

5.73 (2.94)

MuDR

343 (724)

0.49 (1.04)

3.65 (2.00)

7 (30)

0.26 (1.11)

2.00 (2.15)

CACTA

27 (75)

0.04 (0.11)

0.29 (0.21)

0 (4)

0 (0.15)

0 (0.29)

Helitrons

12 (69)

0.02 (0.10)

0.13 (0.19)

0 (3)

0 (0.11)

0 (0.22)

Other

108 (595)

0.15 (0.86)

1.15 (1.64)

1 (24)

0.04 (0.89)

0.29 (1.72)

Total

1,132 (3,134)

1.63 (4.51)

12.06 (8.64)

28 (102)

1.04 (3.78)

8.02 (7.31)

Retrotransposons

LTR Ty1-copia

2,162 (9,578)

3.11 (13.79)

23.02 (26.42)

64 (314)

2.37 (11.65)

18.34 (22.51)

LTR Ty3-gypsy

2,431 (8,395)

3.50 (12.09)

25.89 (23.15)

129 (377)

4.78 (13.98)

36.96 (27.03)

LTR not classified

720 (2,868)

1.04 (4.13)

7.67 (7.91)

51 (139)

1.89 (5.16)

14.61 (0.96)

LINEs

1,876 (8,055)

2.70 (11.60)

19.98 (22.22)

55 (294)

2.04 (10.91)

15.76 (21.08)

SINEs

11 (183)

0.02 (0.26)

0.12 (0.50)

0 (4)

0 (0.15)

0 (0.29)

Retro not classified

1,058 (4,046)

1.52 (5.82)

11.27 (11.16)

23 (165)

0.85 (6.12)

6.59 (11.83)

Total

8,258 (33,125)

11.89 (47.69)

87.94 (91.36)

321 (1,293)

11.91 (47.96)

91.98 (92.69)

Total

9,390 (36,259)

13.52 (52.20)

100 (100)

349 (1,395)

12.95 (51.74)

100 (100)


Results in parentheses include Internal BlastN searches. Repbase v.15.08 was used [38]. SINE, short interspersed element; SGS, Sanger shot gun sequence.

Zuccolo et al. Genome Biology 2011 12:R48   doi:10.1186/gb-2011-12-5-r48

Open Data