How do I force a read to align to a specific repeat region?
When your reference sequence contains repeat elements that are longer than your ab1 trace sequences, and your ab1 trace match both repeats equally well, then SnapGene may align the read to the wrong repeat region.
This article explains how to realign individual reads with a specific repeat region.
Open the Reference Sequence
Open your reference sequence and toggle the "Show alignment" button in the side toolbar to show the "Align With" list box.
Import One or More Reads
Drag and drop reads into the List box, or alternatively, use the Aligned Sequences dropdown menu to import and align your reads to the reference. The aligned read will be displayed in the Map view.
In this example, a read that is known to cover the Repeat 2 region has incorrectly mapped to the Repeat 1 region.
Select the Incorrectly Aligned Read in the List
Click and select the read in the "Align With" list.
Select the Correct Repeat Region on the Reference Sequence
In Map View or Sequence View, select the region on the reference that you wish to "realign" the selected read/s to. You may click on a feature defining the repeat region (if present) or manually click and drag to define the sequence region.
Realign the Selected Read
Click Aligned Sequences → Realign Selected Sequence....
In the next dialog, check the option to "Restrict alignment to the selected region of the reference sequence" then click Realign.
Confirm the Read has Correctly Realigned
Confirm the read has realigned within the selected repeat region of the sequence.