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The dialog parameters:
Tandem presetPresent Settings — specify the tandem repeats parameters with predefined values by selecting the available preset:
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Min period, Max period — the minimum and maximum .
Algorithm — the algorithm parameter allows to select the search algorithm. The default and a fast one is optimized suffix array algorithm.
Min length of repeated sequence - the minimum acceptable repeat length measured in base symbols.
Max length of repeated sequence - the mzximum acceptable repeat length measured in base symbols.Region to process — .
Min length of tandem repeat - the minimum tandem size sets the limit on the minimum acceptable length of the tandem, i.e. the minimum total repeats length of the searched tandem.
Min number of repeats - the minimum number of repeats of a searched tandem.
Show overlapped tandems - check if the plugin should search for the overlapped tandems, otherwise keep unchecked.
Search in - specify the region to search in the whole sequence, a custom region or the region of the current selection (if any).
The output settings can be found in the Output tab:
In the Save annotation(s) to group you group, you can set up a file to store annotations. It could be either an existing annotation table object, a new annotation table or auto-annotations table (if it is available).
In the Annotation parameters group you , you can specify the name of the group and the name of the annotation. If the group name is set to <auto> UGENE will <auto> UGENE will use the group name as the name for the group. You can use the ‘/’ characters in this field as a group name separator to create subgroups. If the annotation name is set to by type UGENE will UGENE will use the annotation type from the Annotation type: table as the name for the annotation. Also you Also, you can add a description in the corresponding text field.
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Additional search options can be found in the Advanced tab:
Algorithm — the algorithm parameter allows to select the search algorithm. The default and a fast one is optimized suffix array algorithm.
Minimum 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.
Minimum repeat count — the minimum number of repeats of a searched tandem.
Show overlapped tandems — check if the plugin should search for the overlapped tandems, otherwise keep unchecked.
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