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The Tandem repeats element finds tandem repeats in a supplied sequence, stores found regions as annotations.

Parameters in GUI

ParameterDescriptionDefault value
Annotate AsName of the result annotations.repeate_unit
DirectionSee the description here.Any
AlgorithmThe algorithm parameter allows one to select the search algorithm. The default and a fast one is the optimized suffix array algorithm.Suffix index(optimized)
Min periodMinimum acceptable repeat length measured in base symbols.1 n
Max periodMaximum acceptable repeat length measured in base symbols.1000000 n
Min tandem sizeThe minimum tandem size sets the limit on minimum acceptable length of the tandem, i.e. the minimum total repeats length of the searched tandem.9
Min repeat countThe minimum number of repeats of a searched tandem.x3
Search for overlapped tandemsIf this parameter is set to True then overlapped tandems should be included into the result. 
Parallel threadsNumber of parallel threads used for the task.Auto

 

Parameters in Schema File

Type: tandems

ParameterParameter in the GUIType
keyAnnotate Asstring
algorithmAlgorithm

string

Available values are:

  • Suffix index
  • Suffix index (optimized)
min-periodMin periodnumeric
max-periodMax periodnumeric
min-tandem-sizeMin tandem sizenumeric
min-repeat-countMin repeat countnumeric
show-overlapped-tandemsSearch for overlapped tandemsboolean
strandDirection

string

Available values are:

  • complement
  • direct
  • both
n-threadsParallel threadsstring
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