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. 2014 Mar 26;6(4):776–791. doi: 10.1093/gbe/evu058

Table 5.

Percentage Distribution of Repeat Classes in the Olive Genome

Sequence type Order Superfamily Number of Contigs Number of Matched Reads Percentage
Retrotransposons Unclassified 42 34,017 0.025
(Class I) LTR Copia 54,110 24,725,640 17.821
Gypsy 47,920 28,884,342 20.819
Retrovirus 101 74,960 0.054
Endogenous retrovirus 4 6,314 0.005
Solo-LTR 52 18,355 0.013
Unknown 189 174,016 0.125
LINE L1 2384 1,739,119 1.253
RTE 453 123,845 0.089
Unknown 38 20,591 0.015
Short-interspersed elements tRNA 268 64,093 0.046
Total 40.265
DNA transposons Unclassified 67 32,668 0.024
(Class II, subclass I) TIR Tc1-Mariner 217 74,711 0.054
hAT 7,187 2,784,674 2.007
Mutator 5,790 3,335,678 2.404
PiggyBac 1 34 0.000
PIF-Harbinger 754 250,771 0.181
CACTA 1,212 496,957 0.358
Crypton Crypton 7 2,054 0.001
(ClassII, subclass II) Helitron Helitron 1,297 672,682 0.485
Total 5.514
Tandem repeats 11,260 43,233,770 31.161
rDNA 356 1,932,081 1.393
Unknown 308 179,225 0.129
No hits found 74,292 14,584,090 10.512
Total reads excluding organellar ones 138,741,954