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Sequence localizer/oligonucleotide and motif finder: find oligo in sequence

Find oligo in sequence! This application can be used to search for a sequence/oligonucleotide or motif within a target DNA sequence. It is great for localizing oligos within a target sequence, to "manually" look for restriction sites, and to locate binding sites for transcription factors or other DNA-binding proteins with a know binding consensus sequence.

The application fully supports ambiguous/degenerated sequences, both in the query and in the target sequence. Degeneration is managed through IUPAC code, that allows to specify ambiguous characters.

If several matches are found, details are provided for each match, with start and end points and the actual sequence matched.

Aug. 16 2013: Thanks to the feedback of Dr. Stefan Heinrichs @ Essen University, the application is now able to detect matches even if overlapping.

Input target sequence is limited to 100.000 base pairs to limit server load


Paste your DNA sequence below in any format including FASTA


Paste your search pattern/oligo here
You can use a 'degenerated' or ambiguous code to match different sequences that match the same pattern (see IUPAC code).
Example: AANNGAATTGK, will match any nucleotide (or ambiguous IUPAC nucleotide!!) in positions 3-4 and G or T in the last position

A web application written in Python by Andrea Cabibbo