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Consensus site finder

Purpose of this page

This page is designed to identify sequences that match or are similar to a consensus sequence. This sequence may contain invariant positions which are entered as uppercase characters. The program is not designed to deal with ambiguous nucleotide codes when scoring the level of homology between the consensus site and a possible match.

Since it is possible to find numerous matches to a simple consensus sequence only the first 500 matches will be returned.

insilicase icon A Windows program that duplicates this page can be downloaded here.

Enter the consensus sequence with invariants positions entered as uppercase letters.


Enter the minimum number of positions that must match the consensus site. 


Enter the sequence to be searched in the text box below (maximum length is 50,000bp)


Instructions and test data

To screen a sequence for a consensus site enter its sequence in the first text box. Invariant positions should be entered as capital letters, e.g. the splice site consensus sequence is entered as GTaagt since the first GT is invariant, but the last four bases may be any nucleotide. To reduce the number of matches you can specify that some of the variable positions must also matches the consensus site. For example entering the number 2 in the second text box will ignore matches which do not contain the invariant GT and at least 2 of the other residues.

Finally, copy the target sequence into the first large text box and then press 'Submit' The location of any consensus sites in the sequence will be shown in the lower text box.

While the consensus sequence is case sensitive the test sequence is not case sensitive but spaces, numbers and end off line characters will be screened as well as the 'normal' sequence. Therefore the sequence will have all formatting removed before been screened.

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