Search for an Exact DNA Sequence

Open the DNA file to search.

To show or hide the Find controls, click the Find button in the bottom left corner of Map or Sequence view, then choose "Find DNA sequence:" via the drop down menu.

Alternatively, click menu Edit → Find → Find DNA Sequence.

1. Enter the DNA sequence you wish to search for in the search field, then click Next.  
2. If one or more matches are found then the number will be reported in the bar.
3. Use the Previous/Next buttons to step between multiple matches.
4. Matches will be highlighted on the Map or Sequence view. See more details below.
5. Information about the current selected "match" is shown in the bottom bar.

To allow multiple bases at a specific position in the query sequence, use parentheses to enclose the set of allowed bases.

In the example shown in the screenshot, either A or G will be allowed at the designated position. SnapGene will find matches to either GGTCTACTTC or GGTCTGCTTC.

Alternatively, to allow multiple bases at a position, use a degenerate DNA letter code such as R.

To view a list of all nucleotide ambiguity codes, click Tools → Letter Codes. For more information see View or Use IUPAC Ambiguity Codes.

To exclude bases at a particular position, use an exclamation point in front of the forbidden bases. For example, !R means not A, G, or R.

Alternatively, enclose the excluded bases in parentheses. For example, !(AG) also means not A, G, or R.  

To search for a degenerate base, enclose the query in quotes. For example, a search for R will find all matches to A or G or R, but a search for "R" will find only bases that are actually represented as R.

To review or reuse recent searches, use the drop down on the search box.

In Map view, the current selected matching DNA sequence region will be highlighted in blue.

In Sequence view, a matching DNA sequence on either strand will be highlighted in yellow (green if sequence motif is selected).

To view examples of DNA searches, click Help → Search Tips.