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Table 2 Classification and distribution of known plant repeats in the BAC end sequences

From: Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato

  Tom. HBa Tom. Eco Tom. Mbo Pot. POT Pot. PPT
Class I retrotransposons 16.95 9.30 13.81 11.42 8.19
   LTR retrotransposons 16.81 9.19 13.72 11.16 7.92
Ty1/Copia 5.25 4.17 4.39 2.55 2.48
Ty3/Gypsy 11.56 5.02 9.33 8.60 5.43
Unclassified 0.00 0.00 0.00 0.01 0.01
   Non-LTR retrotransposons 0.14 0.11 0.09 0.26 0.27
LINE 0.09 0.06 0.05 0.15 0.13
SINE 0.05 0.05 0.04 0.11 0.14
Class II DNA transposons 0.64 0.66 0.49 1.03 1.23
En-Spm 0.26 0.26 0.21 0.27 0.27
Harbinger 0.00 0.00 0.00 0.00 0.00
Mariner 0.00 0.00 0.00 0.00 0.00
MuDR 0.07 0.09 0.05 0.10 0.11
Pogo 0.02 0.03 0.02 0.03 0.08
Stowaway 0.02 0.02 0.02 0.01 0.02
TcMar-Stowaway x x x 0.00 0.00
Tourist x x 0.00 0.00 x
hAT 0.02 0.04 0.02 0.05 0.19
hAT-Ac 0.01 0.00 0.01 0.01 0.01
hAT-Tip100 0.02 0.02 0.02 0.11 0.10
Unclassified 0.22 0.20 0.14 0.45 0.45
Satellites 0.00 0.00 0.00 0.04 0.03
Centromeric 0.00 x 0.00 0.00 0.00
Subtelomeric x x x 0.00 0.00
Unclassified 0.00 0.00 0.00 0.04 0.03
Ribosomal genes 0.04 2.98 8.58 0.03 0.53
rRNA 0.04 2.98 8.58 0.03 0.53
Unclassified 0.08 0.11 0.07 0.07 0.11
Centromeric x x x 0.00 x
Composite x x x x 0.00
RC/Helitron 0.08 0.11 0.07 0.06 0.11
Unknown 0.00 0.00 0.00 0.01 0.00
Total 17.66 13.01 22.91 12.54 10.02
  1. Numbers represent percentages of nucleotides that show similarity to a repeat of the indicated category. An 'x' represents the absence of a repeat family; '0.00' indicates that the repeat is present, but at a frequency lower than 0.005 % of the nucleotides in the BESs. Species names have been abbreviated as follows: Tom.: tomato; Pot.: potato.
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