The frequency matrix for muscle gene myf sites...

  
  7.0  9.0  4.0  0.0 16.0  7.0  0.0  6.0  0.0  0.0  6.0  0.0
  8.0  0.0  2.0 15.0  0.0  0.0 15.0  0.0  0.0 10.0  0.0  0.0
  1.0  7.0 10.0  1.0  0.0  9.0  1.0  0.0 16.0  6.0  0.0 16.0
  0.0  0.0  0.0  0.0  0.0  0.0  0.0 10.0  0.0  0.0 10.0  0.0

    c    a    g    c    A    g    c    t    G    c    t    G


The resulting weight matrix...


  0.68  1.00  0.00 -2.32  1.77  0.68 -2.32  0.49 -2.32 -2.32  0.49 -2.32
  0.85 -2.32 -0.74  1.68 -2.32 -2.32  1.68 -2.32 -2.32  1.14 -2.32 -2.32
 -1.32  0.68  1.14 -1.32 -2.32  1.00 -1.32 -2.32  1.77  0.49 -2.32  1.77
 -2.32 -2.32 -2.32 -2.32 -2.32 -2.32 -2.32  1.14 -2.32 -2.32  1.14 -2.32




The frequency matrix was generated by aligning the myf 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.



> AChR alpha, mouse ebox#1
agctttgaggctgtgggcagctcagctgtcatg
> AChR alpha, mouse ebox#2
cgggcacacaggtgatgtaagacaatagct
> AChR alpha, mouse ebox#3
gtggagtcagctggcttccaagg
> AChR beta, mouse promoter/enhancer, e-box#1 
GGAGGGCGACTGCAGTTGCTCCGGGCGGGACCA
> AChR beta, mouse promoter/enhancer, e-box#2
gtcccccgacaacaggtgcacattcctgggcgc
> AChR beta, mouse promoter/enhancer,e-box#3 
AAGGTTGTTGGAGGAGGCAGCTGGAGCAGGGTTG
> AChR gamma, mouse e-box#1
cccacacccatctgtccttggccat
> AChR gamma, mouse e-box#2
tccttggccatttgctgagtctccta
> AChR gamma, mouse e-box#3
catatcctgggaacagctgacaatgcagt
> AChR gamma, mouse e-box#4
ggtcagacagctggtggggccagctagag
> AChR delta, mouse e-box
ctaaaccaccagcacctgtccccttgcttg
> Actin, alpha cardiac, human e-box
ccccggctgctccaactgaccctgtccatc
> MCK 5' enhancer, mouse, e-box
CCCCCCAACACCTGCTGCCTGAGCCTCACC
> Desmin enhancer, human, e-box
gggttggcagctgttgctgccagggagatgg
> myogenin promoter, mouse, e-box#1
ggaaggggaatcacatgtaatccactggaaac
> myogenin promoter, mouse, e-box#2
taaatggcacccagcagttggtgtgaggggctg
> MLC1/3 3' e-box#1 , rat
TAACTCAAGTCGCAGCAGGTGCAAAAATGGAGC
> MLC1/3 3' e-box#2 , rat
TTTTAAAATCCCCACCAGCTGGCGAAGCAAC
> MLC1/3 3' e-box#3 , rat
GAAGCAACAGGTGCCTAATTCCTCATCTTTTAA
>MLC1A e-box #1 mouse
agagccagctccaccagctgttgcttcagggctc
>MLC1A e-box #2 mouse
agtcagcagcagttgctgctgccctcccc
> TnI slow human e-box???
CTAAAAATACCCGGTAAACAGGTGCAGCCCCTGT 
>aldolase-a e-box
TGGTTGTGAGCACATGTGGTGCTAACTG
>cytochrome oxidase viii-h ebox#1
AGGGCCCAGCTCATCACCTACGTGTTGAGGGGTCAC
>cytochrome oxidase viii-h ebox#2
TCTTGTGACAGGAGACAGCTGCAGTTCTCCGCCCCAA
> Chicken MLC1-f/MLC3-f 5' flank. e-box#1
catccccaggagctgcagatgccagcaata 
> Chicken MLC1-f/MLC3-f 5' flank. e-box#2
tctcacatcctcagctgctgctgctttcccttagaagtgg
> Chicken MLC1-f/MLC3-f 5' flank. e-box#3
atcctgctgcggcagctgcagagcacagggacacatctcc