The Tandem repeats element finds tandem repeats in a supplied sequence, stores found regions as annotations.
Parameters in GUI
Parameter | Description | Default value |
---|---|---|
Annotate As | Name of the result annotations. | repeate_unit |
Direction | See the description here. | Any |
Algorithm | The 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 period | Minimum acceptable repeat length measured in base symbols. | 1 n |
Max period | Maximum acceptable repeat length measured in base symbols. | 1000000 n |
Min tandem size | The 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 count | The minimum number of repeats of a searched tandem. | x3 |
Search for overlapped tandems | If this parameter is set to True then overlapped tandems should be included into the result. | |
Parallel threads | Number of parallel threads used for the task. | Auto |
Parameters in Schema File
Type: tandems
Parameter | Parameter in the GUI | Type |
---|---|---|
key | Annotate As | string |
algorithm | Algorithm | string Available values are:
|
min-period | Min period | numeric |
max-period | Max period | numeric |
min-tandem-size | Min tandem size | numeric |
min-repeat-count | Min repeat count | numeric |
show-overlapped-tandems | Search for overlapped tandems | boolean |
strand | Direction | string Available values are:
|
n-threads | Parallel threads | string |