1.24.2 Using the Alignment Settings Dialog

Step 3 - Uploading Sequences to Align

  • The Alignment Settings dialog allows you to upload sequences and then hide, display or trim them in the project.
  • The first step is to upload sequences to align to the template.
  • You can upload as many sequences to align as you like, whether they are in overlapping regions or on opposite ends of the sequence.
  • You can either:
    • Drag and drop a file from the Materials box
    • "Choose a file" (.AB1, .SCF, text, fasta/multisequence fasta, genebank) from your computer
    • Or type/paste a raw DNA sequence, enter a name and select "Add".
  • The files will be added to the "Selected Sequences" list (Figures and

    Figure QC settings.


    Figure QC settings - Upload sequences.


Step 4 - Hiding and deleting Alignments

  • In order to hide specific alignments in the project, deselect the sequence checkboxes from the "Selected Sequences" list.
  • To remove sequences click the "Delete" icon (Figure

    Figure Hiding and deleting Alignments.


Step 5 - Automatic trimming

  • You can choose to automatically trim the ends of your sequence by selecting the checkbox and setting your desired confidence score threshold.
  • The default is set to 30%. Regions of the sequence which fall below the set threshold will be automatically trimmed.
  • In addition you can manually trim your sequences through the project (coming soon) (Figure

    Figure Auto Trimming.


Select "Apply" to run your alignments.