Search for sequences with the potential to form H-DNA or Z-DNA
1. Select species and gene to search OR select a sequence file to upload and search.
Use the popup list to select to search by gene description, gene name (i.e. symbol), or Entrez Gene ID
and then enter search criterion in the text box. You can use an asterisk (*) as a wildcard if you wish
to perform a non-exact search on gene name. Gene description searches are always non-exact
and the criterion is treated as a phrase.
Gene name (symbol)
Entrez Gene ID
Alternatively, select a sequence file to upload and search. The sequence file may have a definition line (e.g. FASTA).
The file must be plain text, though it may be zipped if you like. The search is limited to 3 M bases.
2. Select the types of repeat sequences for which you wish to search and set search parameters.
Mirror repeats (propensity to form H-DNA)
Minimum arm length:
Minimum spacer length:
Maximum spacer length:
one mismatch if arms are ≥
Minimum %G in arms:
Omit mirror repeats where:
The arms are simple repeats of A with or without a G at the extremities
The entire mirror repeat sequence is a simple GA repeat
Alternating purine/pyrimidine repeats (propensity to form Z-DNA)
3. Set the size of the putative promoter sequence to be searched. (This option is not applicable to uploaded files.)
Putative promoter region length: