Search for Similar DNA Sequences

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 Similar DNA sequence:" via the drop down menu.

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

Enter the DNA sequence you wish to search for in the search field, then click Next.  

1. Use the drop-down menus to set whether to allow a "mismatch or gap/insertion" or a "mismatch only", and to specify the allowed frequency.
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 specify ambiguities in the query sequence, use ambiguity letter codes, for example W (specifies A or T), at degenerate positions.

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, !T means not T.

Alternatively, enclose the excluded bases in parentheses. For example, !(TA) means not T, A, or W.  

To review or reuse recent searches, click the arrow button at the end of the search box.

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

In Sequence view, a match will be highlighted in yellow (green if sequence motif is selected). Any mismatches will boxed red. 

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