Why is my sequence not auto-reindexing when I realign?

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DNA sequences do not appear to be auto-reindexing when realigning.


Alignments in the Molecular Biology application 


Auto-reindexing functionality is for circular DNA sequences. If sequences are set as linear on Benchling, the sequences will fail to auto-reindex.

Resolution steps

  1. Confirm if the sequence is set as linear by opening the sequence entity and clicking the i icon in the right-side menu bar.
  2. Set the topology to Circular and click Update information.
  3. Create a new alignment using the updated sequences.
  4. Click Realign and ensure Automatically reindex alignment if needed is checked in the Parameters tab.
  5. Click Realign.


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