2
  1   10 natttgcataacaatgn
 11  100 nwnwwgcatnacaawnn
-----------------------------------------------------------------------------
From generations 1-10,  positions 2-16 are fixed. 
Any positions labeled as an 'a', 'c', 'g', or 't'
are fixed during the specified generations. That
means that the whole column remains unchanged. In
a sense, it does not matter which base is specified
as long as it is an 'a', 'c', 'g', or 't'.

From generations 11-100,positions 6-9 (gcat) and 
11-14 (acaa) are fixed. 

From generations 11-100,positions 2, 4, 5, and 14
are constrained to 'w', w='a' or 't'.  Only rows
1 and 4 at those positions are subject to mutation
regardless of the values of rows 2 and 3.

From generations 101 and on, no constraints are
imposed. 

Please see gapwm_documentation for details.

w='a' or 't'            s='c' or 'g'
r='a' or 'g'            y='c' or 't'
k='g' or 't'            m='a' or 'c'

b='c', 'g', or 't'      d='a', 'g', or 't'
h='a', 'c', or 't'      v='a', 'c', or 'g'

n='a', 'c', 'g', or 't'

Example:

                          column
    A | 0  7  0  4  4  0  0 11  0  4 11  0 11 11  4  0  1
r   C | 7  0  2  0  0  0 11  0  0  2  0 11  0  0  0  0  1
o   G | 2  1  2  0  0 10  0  0  0  1  0  0  0  0  0 11  1
w   T | 2  3  7  7  7  1  0  0 11  4  0  0  0  0  7  0  1
      ___________________________________________________
        n  w  n  w  w  g  c  a  t  n  a  c  a  a  w  n  n
        ^        ^     ^
        |        |     |_ whole column fixed
        |        |________mutations are restricted to rows 1 and 4
        |_________________no contraints imposed

For questions: see the source code - mutation.c or send
email to li3@niehs.nih.gov
