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Finds repeats in each supplied sequence, stores found regions as annotations.

Parameters in GUI

ParameterDescriptionDefault value
Annotate as (required)Name of the result annotation to mark found repeats.repeat_unit
AlgorithmControl over variations of the algorithm.Auto
Filter nestedFilters nested repeats.True
IdentityRepeats identity in percents.100
InvertedSpecifies to search for inverted repeats.False
Max distanceMaximum distance between the repeats.5000
Min distanceMinimum distance between the repeats.0
Min lengthMinimum length of the repeats.5
Parallel threadsNumber of parallel threads used for the task.Auto

Parameters in Workflow File

Type: repeats-search

ParameterParameter in the GUIType
result-nameAnnotate asstring
algorithmAlgorithm

numeric

Available values are:

  • 0 - algorithm choosed automaticly
  • 1 - for diagonal algorithm
  • 2 - for suffix index algorithm
filter-nestedFilter nestedboolean
identityIdentitynumeric
max-distanceMax distancenumeric
min-distanceMin distancenumeric
min-lengthMin lengthnumeric
threadsParallel threads

numeric

0 - for using autodetected threads number

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequence

Name in Workflow File: in-sequence

Slots:

Slot In GUISlot in Workflow FileType
Sequencesequencesequence

And 1 output port:

Name in GUI: Repeat annotations

Name in Workflow File: out-annotations

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsannotationsannotation-table
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