The frequency matrix for muscle gene srf sites...

  7.0  9.0  0.0  0.0 18.0  9.0 15.0  8.0 21.0 14.0  0.0  0.0  7.0
  5.0  2.0 21.0 17.0  0.0  0.0  1.0  0.0  0.0  2.0  0.0  0.0  8.0
  7.0  4.0  0.0  0.0  0.0  0.0  4.0  2.0  0.0  0.0 21.0 21.0  6.0
  2.0  6.0  0.0  4.0  3.0 12.0  1.0 11.0  0.0  5.0  0.0  0.0  0.0

    a    a    C    c    a    t    a    t    A    a    G    G    c



The resulting weight matrix...



  0.35  0.67 -2.48 -2.48  1.58  0.67  1.34  0.52  1.79  1.24 -2.48 -2.48  0.35
 -0.06 -1.02  1.79  1.50 -2.48 -2.48 -1.58 -2.48 -2.48 -1.02 -2.48 -2.48  0.52
  0.35 -0.31 -2.48 -2.48 -2.48 -2.48 -0.31 -1.02 -2.48 -2.48  1.79  1.79  0.16
 -1.02  0.16 -2.48 -0.31 -0.63  1.04 -1.58  0.93 -2.48 -0.06 -2.48 -2.48 -2.48



The frequency matrix was generated by aligning the srf 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.
 
 
> mouse vascular smooth muscle actin
ccataacgagctgagctgcctcctgtttcgggagc
agaacagaggaatgcagtggaagagacccagcctc
>  Gallus gallus cardiac alpha-actin gene, complete cds.   M10607 K02171
TGTGGCGGCGGGACGCGCTGCTCCGCACCTGCCTTAGATG 
GCCGGACAGCCGCGCCGCCTTGCGCCATTCATGGCCGCGC
>  Human cardiac actin gene, 5' flank.   M13483
CCTTGGCTCCATGAATGGCCTCGGCAGTCCTAGCGGGTGC
GAAGGGGACCAAATAAGGCAAGGTGGCAGACCGGGCCCCC
>  Xenopus laevis cardiac actin gene.   X04669
CCCTCACCTACTCCATTAATGGCTTCTTTGCTTTTCAATG
GCCCAGAAGCTACCAAATAAGGGCAGGCTGCCTGCCTTTC
> Bos taurus alpha skeletal actin precursor gene, U02285  1ST and 2ND CArG
CGGGCAGACACTCCATATACGGCCCGGCCCGTGTTACCTG
GGCTCAGGCCAGGCCTCTCCTTCTTTGGTCAGCGCAGGGG
>  M.musculus Actsk-1 gene for a-skeletal actin.   X67686  1ST and 2ND CArG
TACTCTCCATATACGGCCTGGTCCGGTCCTAGCTACCTGG
GCCAGGGCCAGTCCTCTCCTTCTTTGGTCAGTGCAGGAGA
>  Rat skeletal muscle alpha-actin gene, complete cds. 3rd CArG
CCCGGGCGGGACCCAGGCTGAGAAGCAGCCGAAGGGACTCTA
GTGCCCAACACCCAAATATGGCTTGGGAAGGGCAACAACATT
>  Sus scrofa skeletal alpha actin gene,   U16368 3rd CArG
CCCCGGGGCCCAGGCCGCTAAGCCGGGGGAGGGGGCTCCA
GTGCCAACACCCAAATATGGCTCGAGAAGGGGAGCGACAT 
>  Chicken DNA for gizzard type caldesmon, 5'-upstream region.   D17553
GGATTTACTTTCAGAGGCCCTGCTAAGGATAACCAAAAAA
GGGCATGTAGCAAGACAGTTTTGGCAGCTTGCATGAATTT
>  Bovine atrial natriuretic peptide (ANP) gene, SECOND CArG  M13145
GCTGCTCAAGGCAGAGGGGCTGTGACAAGCAGGCTGGACT
GATAACTTTAAAAGGGCATCTTCTGCTGCTtcctcactca 
>  Rat atrial natriuretic factor (ANF) gene, 5' end.  J03267 CArG-1
CAGCTGCCTGTATTGCCTCTCCTCCCGCCCTTATTTGGAG
CCCCTGACAGCTGAGATGCAAGCAGAGGGAGCTGGGTGTG
>  Human atrial natriuretic factor gene,   M54947  CArG-1
GGATCCATTTGTCTCGGGCTGCTGGCTGCCTGCCATTTCC
TCCTCTCCACCCTTATTTGGAGGCCCTGACAGCTGAGCCA
>  Human atrial natriuretic factor gene,   M54947  CArG-2
AGAGAGGGGCTGTGACAAGCCCTGCGGATGATAACTTTAA 
AAGGGCATcttctcacttggcagctttatcacgccaagtg  
>  Murine MLC1A gene for myosin alkali light chain (exon 1)   X12971
TGAGATGTCAGCTGCACCCGGCTGGTGTCTCTTCCTTTTA
TAGTCAGCAGCAGTTGCTGCTGCCCTCCCCAGCCCCTCTG
> Human MLC1emb gene for embryonic myosin alkaline light chain,
GTCAGCTGTACCCTGCTGGCGTTTCTTCCTTTTATAGTCA
GCAGCAGTTGCTCTTGCTTTCACCCAGCCCCTCTGTGGGG 
>  Rabbit gene for muscle creatine kinase, exon 1.   X55146
TCGCGAGTCGGGCACCCAGTCCCCTTCCCTGGGGGCCTCG
GGTGCCTTGTAAGGAGGCAAGGCCCAGGACACCCGAGCTG 
>  Rattus norvegicus muscle creatine kinase (ckm) gene,   M27092
CAGCCACCAGGGGTCTTAGGCTATCCATGTAAGGAGGCAA
GGCCTGGGGACATCCGAGATGCCTGGTTATAATTAACCTG