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Table 4 Low stringency search and domains

From: Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

  roo rooA
Organism RT IN PR Total Trace archive RT IN PR Total Trace archive
D. simulans 5 4 5 6 + 1 4 1 7 +
D. sechellia 2 4 2 20 + 8 1 4 8 +
D. melanogaster 8 5 6 115 + - 1 2 2 +
D. yakuba 2 5 5 12 + 21 13 28 46 +
D. erecta 2 - 1 3 + 32 25 39 83 +
D. ananassae 3 3 6 11 + - - - - -
D. pseudoobscura - 3 - 3 NA - - - - NA
D. persimilis - 20 - 21 + - - - - -
D. willistoni 12 12 19 33 + - - - - -
D. mojavensis 7 5 5 19 + - 4 - 5 +
D. virilis - - - - - - - - - -
D. grimshawi - - - - - - - - - -
Total 41 61 49 243   62 44 74 151  
  1. For each genome, the number of identified sequence domains, which have a similarity of at least 90 percent and a length difference of less than 1 percent to a reverse transcriptase (RT), integrase (IN) or protease (PR) domain of the identified roo and rooA sequences, is shown, separated for roo (columns 2–4) and rooA (columns 7–9). All numbers are additional numbers meaning that domains corresponding to domains in the full length elements were excluded. The number of total elements (column 5 and 10 for roo and rooA, respectively) was calculated by adding the maximal number of the three domains to the number of elements of the high stringency search. A "+" in column 6 and 11 indicates that a fragment of an roo and rooA element, respectively, was found in the trace archive for that genome. Note: No trace archive was available for D. pseudoobscura