The frequency matrix for muscle gene tef sites...

  
  1.0  9.0  0.0 12.0  0.0  0.0  0.0  0.0  5.0  1.0  2.0  0.0
  6.0  0.0 12.0  0.0  0.0  0.0 12.0 11.0  0.0  7.0  4.0  2.0
  1.0  3.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  4.0  3.0  8.0
  4.0  0.0  0.0  0.0 12.0 12.0  0.0  1.0  7.0  0.0  3.0  2.0

    c    a    C    A    T    T    C    c    t    c    c    g



The resulting weight matrix...


 -1.05  1.35 -2.16  1.73 -2.16 -2.16 -2.16 -2.16  0.60 -1.05 -0.43 -2.16
  0.83 -2.16  1.73 -2.16 -2.16 -2.16  1.73  1.62 -2.16  1.02  0.33 -0.43
 -1.05  0.00 -2.16 -2.16 -2.16 -2.16 -2.16 -2.16 -2.16  0.33  0.00  1.20
  0.33 -2.16 -2.16 -2.16  1.73  1.73 -2.16 -1.05  1.02 -2.16  0.00 -0.43




The frequency matrix was generated by aligning the tef sites 
within the following list using a Gibbs sampling algorithim.  
Where possible two orthologous sites were obtained.  To 
maintain equal weighting for each gene, two copies of srf
sites were included if no orthologous gene was available.
 
 


> cardiac troponin T (cTnT) chicken promoter
TGCCAAAATAGCAGCTCACAAGTGTTGCATTCCTCTCTGGGCGCCGGGCACATTCCTGCTGCTCTGCCCGCCCCGGGGTGGGCGCCGGGGGGACCTT
> AChR beta, rat promoter/enhancer, (-101 to -1 relative to start)
ccggagggtggggcgggtgggctggcagctggtcccccgacaacaggtgcacattcctgggcgcctcgtcacttcccctggcctggcggcctcggcc
> AChR beta, mouse promoter/enhancer, (-101 to -1 reltive to start)
CCCGAGGGCGGGGCGGGTGGGCTGGCGTCTGGTCCCCCGACAACAGGTGCACATTCCTGGGCGCCTCGTCACTTCCCCTGGCCTGAGGCGCTATCCG
> Hamster beta-myosin heavy chain gene, 
GTCGTTGTCAGCTTACTCTGCAGTGAGCTGTGGAATGTAAGAGATATTTTCTGTTCGCTTTGAGCCACCCCACCCCTTGGAACTCAGACCCTGAACA
> Human gene for cardiac beta myosin heavy chain.
CCCTCTCCTGCCAGCTGTGGAATGTGAGGCCTGGCCTGGGAGATATTTTTGCTGCACTTTGAGCCACCCCGCCCCCTGGAACTCAGACCCTGCACAG
>  Human alpha-MHC gene for myosin heavy chain (N-terminus).
CCCAGCTATCTGCTCATCAGCCCTTTGAAGGGGAGGAATGTGCCCAAGGACTAAAAAAAGGCCGTGGAGCCAGAGAGGCTGGGGCAGCAGACCTTTC
>  Mus musculus cardiac myosin heavy chain gene, 5' end.
GACGCTCCTGTCTCTCCTCTATCTGCCCATCGGCCCTTTGGGGAGGAGGAATGTGCCCAAGGACTAAAAAAAGGCCATGGAGCCAGAGGGGCGAGGG
> Pig skeletal alpha actin gene, complete cds.
GCTCCAGTGCCAACACCCAAATATGGCTCGAGAAGGGGAGCGACATTCCAGTGAGGCGCTCGGGGGGAGAACCCGCGGGCTATATAAAACCTGAGCG
>  Mouse skeletal alpha-actin gene, complete cds.
ACTCTAGTGCCCGACACCCAAATATGGCTTGGGAAGGGCAGCAACATTCTTCGGGGCGGTGTGGGGAGAGCTCCCGGGACTATATAAAAACCTGTGC
>  Human alpha-actin (ACTA) gene, non-coding exon 1.
CCCACAGGCGGCTGAACCGCCTCCCGTTTCATGAGCAGACCAGTGGAATGCAGTGGAAGAGACCCAGGCCTCCGGCCACCCAGATTAGAGAGTTTTG
>  Chicken alpha-smooth muscle (aortic) actin gene, complete cds.
CTTACACAGCTGAAAGTCTCCTCCTGTTTCATGAGCTCTGCGTTGGAATGCAGTGGAAGGGACTGAGGGCCTGTCGACCCAGATTAGAGGTTTTTGT