Skip to end of metadata
Go to start of metadata

To find tandem repeats, select the Analyze ‣ Find tandems... context menu item in the Sequence View window.

In the opened dialog you can specify the tandem search parameters, the region to search in and the result parameters:

The dialog parameters:

Tandem preset — specify the tandem repeats parameters with predefined values by selecting the available preset:

Min periodMax period — the minimum and maximum acceptable repeat length measured in base symbols.

Region to process — specify the region to search in the whole sequence, a custom region or the region of the current selection (if any).

Save annotation(s) to — specify the existing or new annotations table file to save the resulting annotations into.

Annotation parameters — you can change the default group name and annotation(s) name values of the resulting annotation(s).

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.

  • No labels