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

From: Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum

BAC name BAC name Ss-75D04 So-57E04 So-96B11 So-99P01 So-146H19
(Length bp) Length (bp) 71,995 95,342 101,291 74,354 77,460
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
  1. Notes: A summary of gapless sequence comparison the haplotypes BACs among S.officinarum(LA Purple), S.spontaneum(AP85-441) and Saccarhum cultivar R570 was presented in table S. 4. SNP: single nucleotide polymorphism; MNP: Multiple nucleotide Polymorphisms