Table 1 Nature, frequency and relative distribution of microsatellites in the four non-coding and coding sequence components of rice genes distributed over 12 chromosomes

Number of sequences examined

14308

18935

70083

18935

122261

5799 (Chr 10) to 18954 (Chr 1)

18935

Size (bp) of examined sequences

15481256

4230243

27485418

7506247

54703164

2786342 (Chr 9) to 8429186 (Chr 1)

25733724

Number (%) of identified perfect microsatellites

8366 (58.5)

5780 (30.5)

25495 (36.4)

2817 (14.8)

42458

5920 (31.2, Chr 1) to 2475 (42.4, Chr 11)

4828 (25.5)

Number (%) of mononucleotides

3709 (26)

937 (4.9)

16499 (23.5)

1797 (9.5)

22942

2263 (12, Chr 1) to 1348 (23, Chr 11)

134 (0.7)

Number (%) of dinucleotides

2187 (46.9)

1508 (31)

5805 (64.5)

507 (49.7)

10007

1299 (21.9, Chr 1) to 742 (27.6, Chr 12)

139 (3)

Number (%) of trinucleotides

2351 (50.5)

3171 (65.5)

2586 (28.7)

437 (42.8)

8545

298 (12.8, Chr 10) to 625 (21.5, Chr 8)

4514 (96.2)

Number (%) of tetranucleotides

82 (1.7)

100 (2)

494 (5.5)

68 (6.7)

744

38 (1, Chr 4) to 70 (2.4, Chr 8)

21 (0.4)

Number (%) of pentanucleotides

34 (0.7)

52 (1.1)

81 (0.9)

8 (0.8)

175

9 (0.24, Chr 4) to 16 (0.59, Chr 12)

10 (0.2)

Number (%) of hexanucleotides

3 (0.06)

12 (0.25)

30 (0.33)

1 (0.09)

46

1 (0.04, Chr 1) to 10 (0.2, Chr 2)

10 (0.2)

Number (%) of perfect microsatellites excluding mononucleotides

4657 (32.5)

4843 (25.6)

8996 (12.8)

1020 (5.4)

19516 (16)

1087 (18, Chr 9) to 2585 (13.6, Chr 1)

4694 (24.8)

Number (%) of primer-pairs for perfect microsatellites

4278 (91.8)

4484 (92.6)

8370 (93)

834 (81.7)

17966 (92)

938 (86.3, Chr 9) to 2395 (92.6, Chr 1)

4411 (94)

Perfect microsatellite counts per Mb sequences

300.8

1144.8

327.3

135.9

356.7

450 (Chr 12) to 306.7 (Chr 1)

182.4

Number (%) of compound microsatellites

948 (6.6)

746 (3.9)

2421 (3.4)

169 (0.9)

4284 (3.5)

217 (3.6, Chr 9) to 585 (3, Chr 1)

510 (2.7)

Compound microsatellite counts per Mb sequences

61.2

176.3

88.0

22.5

78.3

99.8 (Chr 12) to 68.5 (Chr 4)

19.8

Number (%) of perfect class I microsatellites

877 (18.8)

1031 (21.3)

2394 (26.6)

257 (25.2)

4559 (23.3)

229 (21, Chr 10) to 598 (24.4, Chr 3)

743 (15.8)

Number (%) of primer-pairs for perfect class I microsatellites

829 (94.5)

953 (92.4)

2275 (95)

231 (89.8)

4288 (94)

216 (94.3, Chr 10) to 571 (95.5, Chr 3)

714 (96%)

Perfect class I microsatellite counts per Mb sequences

56.6

243.7

87.1

34.2

83.8

101.4 (Chr 12) to 67.7 (Chr 1)

28.8