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C. elegans/C. briggsae Transcription Factor Binding Site Search
Introduction Methods Download Prediction

Transcription Factor Binding Site Prediction using Position Weight Matrices and C. elegans / C. briggsae Ortholog-based Filtering (Phylogenetic Footprinting)

Output name (optional):
Maximum number of retrieved hit-pairs desired
Maximum number of hits retrieved per species before phylogenetic filtering
Maximum number of next-highest hits reported for each gene
Input file type:
Search Type (CisOrtho or Individual Site Scores):

or Paste TF binding site alignment or PWM here:
File containing list of putative hits to score:

Please submit an ungapped TF Alignment or a position weight matrix.   Alignment must have lines all the same length, containing only [acgtnACGTN]. Position weight matrix must at least six lines, with each line containing four integers separated by whitespace. Results will appear on a randomly named webpage which will be deleted after two hours.

Note:    Binding Site Alignment must have at least 6 conserved columns (as judged by HMMER) or the search cannot be run. Please read the CisOrtho manual for further details.