Table 1

Summary of the number of peaks per profile, homoplasy rate and maximum number of co-migrating fragments obtained in silico with different numbers of selective bases for each species.

    Primer combinations

    No. of peaks

    Homoplasy rate (%)

Species

No. of sba

GC contb

No tested

Mean

Range

Mean

Range

Max fragmc


Bacillus thuringiensis ser. Konkukian

1

AT

2

260

260 - 260

68.5

67.7 - 69.2

18

GC

2

184

162 - 206

45.4

45.2 - 45.7

18

2

AT

4

140

122 - 165

37.2

28.4 - 41.8

16

m

8

98

47 - 136

22.8

8.5 - 42.8

6

GC

4

60

42 - 76

13.9

8.2 - 22.3

14

3

AT

32

46

18 - 96

8.9

0 - 24.6

14

GC

32

21

5 - 47

7.8

0 - 15.4

14

Arabidopsis thaliana

4

AT

27

207

139 - 283

46.6

27.3 - 58.5

64

m

17

129

56 - 185

29.3

21.9 - 45.1

21

GC

9

62

28 - 94

13.3

3.6 - 21.3

5

5

AT

12

77

32 - 115

18.5

8.8 - 30.4

8

GC

9

35

18 - 50

12.1

2.8 - 22

38

6

AT

5

26

12 - 54

8.8

0 - 20.4

3

m

11

12

4 - 21

4.3

0 - 15.4

3

GC

10

7

2 - 12

6.6

0 - 28.5

33

Aedes aegypti

5

AT

6

266

232 - 294

58.4

47.8 - 66.6

61

GC

8

253

209 - 293

53.2

41.6 - 62.4

582

6

AT

17

156

94 - 234

36.7

27.5 - 59.8

400

m

22

109

61 - 148

27.8

18.1 - 40.2

284

GC

14

58

33 - 97

15.8

7 - 32

180

7

AT

8

44

27 - 62

13.6

6.5 - 22.6

7

GC

5

25

17 - 39

11.6

0 - 18

6

8

AT

10

10

3 - 28

7.0

0 - 33.3

2

m

5

8

5 - 12

1.7

0 - 8.3

3

GC

5

6

3 - 11

6.7

0 - 33.3

2


a Total number of selective bases added for the 2 primers.

b "GC cont" is composed of three classes of selective bases differing according to the proportion of their GC content: "AT" corresponds to selective bases containing a larger number of A or T, "GC" to selective bases containing a larger number of C or G, "m" to selective bases containing same number of A or T and C or G.

c Maximum number of co-migrating fragments in one single peak.

Paris et al. BMC Genomics 2010 11:287   doi:10.1186/1471-2164-11-287

Open Data