Published base frequency tables and weight matrices:

Promoter element HMMs derived from EPD release 68 (September 2001):

  • TATA-box HMM trained from 900 unrelated general promoter sequences:
  • Position 1 2 3 4 5 6 7 8 9 10 11 12
    % A 21.4 15.9 3.7 91.1 0.0 94.5 67.3 97.3 52.1 40.7 16.5 23.6
    % C 22.7 39.3 9.8 0.0 0.0 0.0 0.0 0.0 0.0 9.1 34.8 37.1
    % G 28.2 35.2 2.9 0.0 0.0 0.0 0.0 2.7 12.0 40.2 38.0 30.4
    % T 27.7 9.6 83.6 8.9 100.0 5.5 32.7 0.0 35.9 10.0 10.7 8.9
    Consensus
     
     
    T
    A
    T
    A
    W
    A
    W
    R
       

     
  • TATA-box HMM trained from 600 unrelated vertebrate promoter sequences:
  • Position 1 2 3 4 5 6 7 8 9 10 11 12
    % A 17.7 19.3 6.6 83.4 0.0 95.0 72.3 94.2 53.3 29.3 17.7 22.7
    % C 21.1 36.1 14.8 0.0 0.0 0.0 0.0 0.0 0.0 9.0 32.5 33.0
    % G 29.0 36.4 6.8 0.0 0.0 0.0 0.0 5.8 20.1 51.2 37.7 33.2
    % T 32.2 8.2 71.8 16.6 100.0 5.0 27.7 0.0 26.6 10.5 12.1 11.1
    Consensus  
     
    T
    A
    T
    A
    W
    A
    D
    R
       

     
  • TATA-box HMM trained from 134 unrelated plant promoter sequences:
  • Position 1 2 3 4 5 6 7 8 9 10 11 12
    % A 31.6 16.3 2.0 90.8 0.0 94.9 57.1 100.0 27.6 69.4 11.2 24.5
    % C 24.5 60.2 3.0 2.1 0.0 0.0 0.0 0.0 0.0 3.1 39.8 52.0
    % G 15.3 10.2 0.0 2.0 1.0 0.0 0.0 0.0 2.0 13.3 37.8 21.4
    % T 28.6 13.3 94.9 5.1 99.0 5.1 42.9 0.0 70.4 14.3 11.2 2.1
    Consensus  
     
    T
    A
    T
    A
    W
    A
    W
    A
       

     

    Previous HMMs derived from release 60 (September 1999)

    Previous HMMs derived from release 54 (March 1998)

Methods: models were trained with MEME software version 3.0.3 (release 68) or with SAM software using a Baum-Welch (EM) algorithm (release 60 and 54). 
Last update May 2017