Table 3 Summary of gapless sequence comparison the haplotypes BACs among S. officinarum(LA Purple) and S. spontaneum(AP85-441)

Ss-23 K06

range of aligned sequence

(287–88918)/(302–72582)

(39884–95090)/(17837–88219)

(168–81137)/(8608–80258)

(37335–85913)/(26–66382)

(6628–78055)/(5672–77310)

127,658

Span of aligned BAC

68512(77.30 %)/68716(95.07 %)

33316(60.35 %)/33467(47.55 %)

51174(63.20 %)/51331(71.64 %)

29192(60.09 %)/29187(43.99 %)

49413(69.18 %)/49502(69.10 %)

Aligned sequence

67783

32441

50240

28799

48249

Average identity (%)

98.37

95.92

96.08

96.72

94.53

SNP (%)

881(1.30 %)

620(1.91 %)

1035(2.06 %)

506(1.76 %)

1153(2.39 %)

MNP(%)

0.43

2.17

1.86

1.52

3.08

Ss-75D04

range of aligned sequence

(35029–72582)/(17837–83938)

(302–65299)/(8743–80258)

(32480–72726)/(26–74352)

(6303–62979)/(5672–77310)

71,995

Span of aligned BAC

29553(78.70 %)/29618(44.81 %)

49688(76.45 %)/49719(69.52 %)

29384(73.01 %)/29378(39.53 %)

46112(81.36 %)/46037(64.26 %)

Aligned sequence

28814

48973

28938

45233

Average identity (%)

95.80

96.48

97.00

96.36

SNP (%)

479(1.66 %)

984(2.01 %)

489(1.69 %)

1123(2.48 %)

2.54

1.51

1.31

1.16

So-57E04

range of aligned sequence

(9475–36844)/(39893–80175)

(17837–95341)/(6441–67799)

(10894–39851)/(28927–77310)

95,342

Span of aligned BAC

21851(79.84 %)/21895(54.35 %)

57223(73.83 %)/57303(93.39 %)

24491(84.58 %)/24304(50.23 %)

Aligned sequence

21601

56769

23815

Average identity (%)

95.99

97.28

95.44

SNP (%)

377(1.75 %)

993(1.75 %)

473(1.99 %)

MNP(%)

2.26

0.97

2.57

So-96B11

range of aligned sequence

(48130–80175)/(38–27603)

(14403–80175)/(5672–71165)

101,291

Span of aligned BAC

23235(72.51 %)/23221(84.24 %)

47909(72.84 %)/47707(72.84 %)

Aligned sequence

23083

46867

Average identity (%)

98.39

96.57

SNP (%)

364(1.58 %)

853(1.82 %)

MNP(%)

0.03

1.61

So-99P01

range of aligned sequence

(24–30055)/(34688–77310)

74,354

Span of aligned BAC

24568(81.81 %)/24554(57.61 %)

Aligned sequence

24266

Average identity (%)

96.98

SNP (%)

441(1.82 %)

MNP(%)

1.20