1     M         1.019   1.021   1.033   1.423   1.423   1.436   1.054   1.055   1.068
2     S         1.019   1.021   1.033   1.158   1.158   1.176   1.054   1.055   1.068
3     A        -0.493  -0.529  -0.554   0.079   0.039   0.006  -0.595  -0.648  -0.682
4     Q        -0.493  -0.529  -0.554  -0.949  -0.971  -0.919  -0.595  -0.648  -0.682
5     D        -0.493  -0.482  -0.544   0.219   0.233   0.131  -0.595  -0.577  -0.666
6     Y         1.019   1.021   1.033   1.028   1.034   1.049   1.054   1.055   1.068
7     Y        -0.493  -0.529  -0.554  -0.146  -0.184  -0.193  -0.595  -0.648  -0.682
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     G         1.019   1.021   1.033   1.162   1.166   1.180   1.054   1.055   1.068
10    N        -0.628  -0.626  -0.589  -0.135  -0.135  -0.090  -0.801  -0.797  -0.736
11    S        -0.628  -0.626  -0.589  -0.364  -0.364  -0.314  -0.801  -0.797  -0.736
12    A        -0.628  -0.626  -0.589  -0.183  -0.183  -0.137  -0.801  -0.797  -0.736
13    S         1.019   1.021   1.033   1.185   1.189   1.203   1.054   1.055   1.068
14    K         1.019   1.021   1.033   1.501   1.506   1.512   1.054   1.055   1.068
15    Q         1.019   1.021   1.033   0.176   0.177   0.215   1.054   1.055   1.068
16    S        -0.628  -0.626  -0.589  -1.078  -1.079  -1.013  -0.801  -0.797  -0.736
17    Y         1.019   1.021   1.033   0.995   0.999   1.017   1.054   1.055   1.068
18    S        -0.493  -0.529  -0.554  -0.211  -0.274  -0.318  -0.595  -0.648  -0.682
19    R        -0.493  -0.529  -0.554   0.226   0.178   0.137  -0.595  -0.648  -0.682
20    P         1.019   1.021   1.033   0.912   0.915   0.935   1.054   1.055   1.068
21    S        -0.493  -0.458  -0.544  -0.046  -0.010  -0.099  -0.595  -0.541  -0.666
22    A        -0.493  -0.529  -0.554  -0.096  -0.152  -0.214  -0.595  -0.648  -0.682
23    P         1.019   1.021   1.033   0.912   0.915   0.935   1.054   1.055   1.068
24    P         1.019   1.021   1.033   0.912   0.915   0.935   1.054   1.055   1.068
25    P         1.019   1.021   1.033   0.912   0.915   0.935   1.054   1.055   1.068
26    G        -1.591  -1.585  -1.538  -0.946  -0.935  -0.884  -1.420  -1.411  -1.337
27    Y        -0.493  -0.458  -0.544  -0.735  -0.654  -0.917  -0.595  -0.541  -0.666
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -0.628  -0.626  -0.589  -0.794  -0.795  -0.735  -0.801  -0.797  -0.736
32    -         1.019   1.021   1.033   0.258   0.259   0.295   1.054   1.055   1.068
33    -        -0.628  -0.626  -0.589  -0.526  -0.526  -0.472  -0.801  -0.797  -0.736
34    E        -1.591  -1.585  -1.538  -1.197  -1.251  -1.130  -1.420  -1.411  -1.337
35    T        -1.591  -1.585  -1.538  -1.301  -1.351  -1.231  -1.420  -1.411  -1.337
36    A        -1.591  -1.585  -1.538  -1.157  -1.165  -1.091  -1.420  -1.411  -1.337
37    S        -0.493  -0.529  -0.554  -0.600  -0.700  -0.824  -0.595  -0.648  -0.682
38    R        -0.493  -0.529  -0.554  -0.301  -0.399  -0.541  -0.595  -0.648  -0.682
39    G        -0.493  -0.529  -0.554  -0.241  -0.300  -0.334  -0.595  -0.648  -0.682
40    Y         1.019   1.021   1.033   1.028   1.034   1.049   1.054   1.055   1.068
41    A        -0.628  -0.626  -0.589  -0.466  -0.467  -0.414  -0.801  -0.797  -0.736
42    P        -0.628  -0.626  -0.589  -1.322  -1.324  -1.252  -0.801  -0.797  -0.736
43    S        -1.591  -1.585  -1.538  -0.820  -0.808  -0.760  -1.420  -1.411  -1.337
44    Q        -0.493  -0.482  -0.544  -0.858  -0.835  -1.033  -0.595  -0.577  -0.666
45    S        -1.591  -1.585  -1.538  -1.871  -1.912  -1.790  -1.420  -1.411  -1.337
46    Q        -0.493  -0.529  -0.554  -1.082  -1.118  -1.083  -0.595  -0.648  -0.682
47    Q        -0.493  -0.458  -0.544  -1.005  -0.973  -0.988  -0.595  -0.541  -0.666
48    N        -0.493  -0.482  -0.544  -0.263  -0.254  -0.295  -0.595  -0.577  -0.666
49    Y        -1.591  -1.585  -1.538  -1.544  -1.487  -1.470  -1.420  -1.411  -1.337
50    Y         1.019   1.021   1.033   1.028   1.034   1.049   1.054   1.055   1.068
51    P        -1.591  -1.585  -1.538  -1.871  -1.824  -1.790  -1.420  -1.411  -1.337
52    P        -0.493  -0.482  -0.544  -1.231  -1.218  -1.263  -0.595  -0.577  -0.666
53    Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
54    Q        -1.591  -1.585  -1.538  -1.627  -1.585  -1.551  -1.420  -1.411  -1.337
55    Q        -0.493  -0.458  -0.544  -1.231  -1.186  -1.263  -0.595  -0.541  -0.666
56    Q        -0.493  -0.529  -0.554  -0.949  -0.971  -0.919  -0.595  -0.648  -0.682
57    Q        -1.591  -1.585  -1.538  -1.498  -1.467  -1.424  -1.420  -1.411  -1.337
58    Q        -0.493  -0.529  -0.554  -1.121  -1.160  -1.132  -0.595  -0.648  -0.682
59    Y        -0.493  -0.529  -0.554  -0.175  -0.216  -0.229  -0.595  -0.648  -0.682
60    Q        -1.591  -1.585  -1.538  -1.521  -1.484  -1.447  -1.420  -1.411  -1.337
61    Q        -0.493  -0.529  -0.554  -1.082  -1.118  -1.083  -0.595  -0.648  -0.682
62    -         1.019   1.021   1.033   0.863   0.866   0.888   1.054   1.055   1.068
63    -         1.019   1.021   1.033   0.863   0.866   0.888   1.054   1.055   1.068
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -         1.019   1.021   1.033   0.908   0.911   0.932   1.054   1.055   1.068
83    -         1.019   1.021   1.033   0.908   0.911   0.932   1.054   1.055   1.068
84    -         1.019   1.021   1.033   0.908   0.911   0.932   1.054   1.055   1.068
85    Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
86    P        -1.591  -1.585  -1.538  -1.926  -1.882  -1.844  -1.420  -1.411  -1.337
87    Q        -0.493  -0.529  -0.554  -1.121  -1.160  -1.132  -0.595  -0.648  -0.682
88    Y         1.019   1.021   1.033   1.028   1.034   1.049   1.054   1.055   1.068
89    Y         1.019   1.021   1.033   1.028   1.034   1.049   1.054   1.055   1.068
90    Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
91    Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
92    Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    Q        -0.493  -0.482  -0.544  -0.667  -0.648  -0.851  -0.595  -0.577  -0.666
98    P        -1.591  -1.585  -1.538  -1.365  -1.358  -1.294  -1.420  -1.411  -1.337
99    Q        -1.591  -1.585  -1.538  -1.983  -1.959  -1.899  -1.420  -1.411  -1.337
100   Y        -0.493  -0.458  -0.544  -0.735  -0.654  -0.917  -0.595  -0.541  -0.666
101   Y        -0.493  -0.482  -0.544  -1.160  -1.148  -1.176  -0.595  -0.577  -0.666
102   Q        -0.493  -0.458  -0.544  -1.121  -1.086  -1.128  -0.595  -0.541  -0.666
103   Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
104   H        -0.493  -0.529  -0.554  -0.226  -0.324  -0.471  -0.595  -0.648  -0.682
105   P        -1.591  -1.585  -1.538  -1.926  -1.974  -1.844  -1.420  -1.411  -1.337
106   Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
107   Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
108   P         1.019   1.021   1.033   0.912   0.915   0.935   1.054   1.055   1.068
109   I        -0.493  -0.529  -0.554   0.252   0.200   0.151  -0.595  -0.648  -0.682
110   Y         1.019   1.021   1.033   1.028   1.034   1.049   1.054   1.055   1.068
111   V         1.019   1.021   1.033   1.483   1.485   1.495   1.054   1.055   1.068
112   Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
113   Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
114   Q         1.019   1.021   1.033   0.202   0.205   0.240   1.054   1.055   1.068
115   P         1.019   1.021   1.033   0.912   0.915   0.935   1.054   1.055   1.068
116   A        -1.591  -1.585  -1.538  -0.974  -0.948  -0.911  -1.420  -1.411  -1.337
117   S        -0.493  -0.458  -0.544  -0.600  -0.525  -0.788  -0.595  -0.541  -0.666
118   S        -1.591  -1.585  -1.538  -0.946  -0.960  -0.884  -1.420  -1.411  -1.337
119   G         1.019   1.021   1.033   1.093   1.094   1.113   1.054   1.055   1.068
120   N         1.019   1.021   1.033   1.453   1.455   1.466   1.054   1.055   1.068
121   E        -0.493  -0.482  -0.544   0.166   0.178   0.099  -0.595  -0.577  -0.666
122   D        -0.493  -0.529  -0.554   0.017  -0.044  -0.102  -0.595  -0.648  -0.682
123   C         1.019   1.021   1.033   1.331   1.334   1.346   1.054   1.055   1.068
124   L        -0.493  -0.458  -0.544   0.079   0.119   0.009  -0.595  -0.541  -0.666
125   A        -1.591  -1.585  -1.538  -0.690  -0.686  -0.633  -1.420  -1.411  -1.337
126   G        -0.493  -0.458  -0.544  -0.182  -0.139  -0.247  -0.595  -0.541  -0.666
127   C         1.019   1.021   1.033   1.331   1.334   1.346   1.054   1.055   1.068
128   L         1.019   1.021   1.033   1.315   1.319   1.331   1.054   1.055   1.068
129   A         1.019   1.021   1.033   1.284   1.294   1.300   1.054   1.055   1.068
130   G        -0.493  -0.482  -0.544  -0.096  -0.076  -0.195  -0.595  -0.577  -0.666
131   L         1.019   1.021   1.033   1.315   1.319   1.331   1.054   1.055   1.068
132   C         1.019   1.021   1.033   1.331   1.334   1.346   1.054   1.055   1.068
133   L        -1.591  -1.585  -1.538  -0.606  -0.604  -0.551  -1.420  -1.411  -1.337
134   C         1.019   1.021   1.033   1.331   1.334   1.346   1.054   1.055   1.068
135   C         1.019   1.021   1.033   1.331   1.334   1.346   1.054   1.055   1.068
136   T         1.019   1.021   1.033   1.453   1.458   1.466   1.054   1.055   1.068
137   L         1.019   1.021   1.033   1.315   1.319   1.331   1.054   1.055   1.068
138   D         1.019   1.021   1.033   1.377   1.381   1.391   1.054   1.055   1.068
139   M        -0.493  -0.458  -0.544   0.126   0.170   0.037  -0.595  -0.541  -0.666
140   L         1.019   1.021   1.033   1.315   1.319   1.331   1.054   1.055   1.068
141   F         1.019   1.021   1.033   1.483   1.485   1.495   1.054   1.055   1.068
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/Q12489
Output conservation file - output/Q12489
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
