Thanks
Sebastian
Look for the pattern list:
<patterns id="patterns" from="1" every="1" >
<alignment idref="alignment"/>
</patterns>
and replace it with this:
<mergePatterns id="patterns">
<patterns from="1" every="1">
<alignment idref="alignment"/>
</patterns>
<constantPatterns>
<alignment idref="alignment">
<counts>
<parameter value="555 434 543 432"/>
</counts>
</constantPatterns>
</mergePatterns>
Where the numbers in value="..." are the counts of constant sites of A, C, G & T