Try the new updated ConTra V3 - update 2017 Or use old ConTra (V1) »
Please cite - ConTra is described in
Broos S, Hulpiau P, Galle J, Hooghe B, Van Roy F, De Bleser P
ConTra v2: a tool to identify transcription factor binding sites across species, update 2011.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W74-8. Epub 2011 May 16.

Step 1 (out of 4):

select the type of analysis and specify the gene/transcript to be subjected to analysis

Type of analysis
  Visualization: Identify binding sites for 1 or several transcription factors (TFs) in the cross-species alignment of my promoter(s). help
  Exploration: Identify which transcription factors (TFs) can regulate my gene(s)/transcript(s). This can take a long time... help

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Reference organism
Select the organism you're working on.

Gene or transcript
Gene or transcript help

valid input: gene name or symbol, Ensembl gene ID (ENSG), entrez gene ID, RefSeq (NM_|NR_) or Ensembl transcript ID (ENST)

Example: ATOH7 (Try example)
more examples...
alignment file [multifasta, maf or CLUSTAL format] help
(skip step 2/3)

Use your own PWM collection [optional]
upload file with your own PWMs (format) OR upload a multifasta file (max sequence length 50nt)
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