1     M         0.603   0.610   0.644   1.114   1.096   1.050   0.619   0.629   0.675
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     T        -1.302  -1.272  -0.985  -1.280  -1.258  -0.834  -1.680  -1.644  -1.207
7     E        -1.302  -1.239  -0.983  -0.903  -0.842  -0.547  -1.680  -1.588  -1.204
8     L        -0.482  -0.495  -0.948  -0.673  -0.665  -1.162  -0.454  -0.473  -1.149
9     C         0.603   0.610   0.644   1.060   1.063   1.009   0.619   0.629   0.675
10    P         0.603   0.610   0.644   1.060   1.052   1.009   0.619   0.629   0.675
11    V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
12    Y         0.603   0.610   0.644   1.048   1.043   1.000   0.619   0.629   0.675
13    A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
14    P         0.603   0.610   0.644   1.060   1.052   1.009   0.619   0.629   0.675
15    F         0.603   0.610   0.644   0.913   0.917   0.901   0.619   0.629   0.675
16    F         0.603   0.610   0.644   0.913   0.917   0.901   0.619   0.629   0.675
17    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
18    A        -1.990  -1.907  -1.916  -2.298  -2.177  -2.110  -1.987  -1.844  -1.811
19    I        -1.302  -1.262  -0.984  -1.445  -1.388  -0.904  -1.680  -1.627  -1.207
20    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
21    C         0.603   0.610   0.644   1.060   1.063   1.009   0.619   0.629   0.675
22    A        -1.302  -1.295  -0.984  -1.750  -1.694  -1.106  -1.680  -1.681  -1.206
23    S        -0.482  -0.363  -0.942  -0.639  -0.485  -1.164  -0.454  -0.302  -1.140
24    A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
25    I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
26    I        -1.302  -1.159  -0.973  -1.860  -1.604  -1.263  -1.680  -1.457  -1.189
27    F         0.603   0.610   0.644   0.913   0.917   0.901   0.619   0.629   0.675
28    T        -0.482  -0.680  -0.951  -0.047  -0.359  -0.994  -0.454  -0.727  -1.153
29    S        -1.393  -1.299  -0.985  -1.358  -1.223  -0.780  -1.834  -1.688  -1.207
30    L        -1.302  -1.255  -0.984  -1.575  -1.548  -1.156  -1.680  -1.615  -1.206
31    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
32    A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
33    A        -1.393  -1.299  -0.985  -1.912  -1.769  -1.191  -1.834  -1.688  -1.207
34    Y         0.603   0.610   0.644   1.048   1.043   1.000   0.619   0.629   0.675
35    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
36    T         0.603   0.610   0.644   0.956   0.950   0.933   0.619   0.629   0.675
37    A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
38    K         0.603   0.610   0.644   1.150   1.140   1.076   0.619   0.629   0.675
39    S        -0.482  -0.680  -0.951  -0.171  -0.465  -1.074  -0.454  -0.727  -1.153
40    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
41    V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
42    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
43    I        -0.482  -0.524  -0.947  -0.446  -0.504  -1.195  -0.454  -0.512  -1.147
44    C        -1.516  -1.767  -1.917  -0.868  -1.259  -1.742  -1.374  -1.675  -1.812
45    A        -0.482  -0.524  -0.947  -0.700  -0.745  -1.359  -0.454  -0.512  -1.147
46    T        -1.017  -1.139  -0.981  -0.639  -0.867  -0.685  -1.220  -1.424  -1.201
47    C        -2.391  -2.346  -1.937  -2.358  -2.439  -1.857  -2.447  -2.384  -1.834
48    V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
49    L        -0.482  -0.309  -0.943  -0.667  -0.446  -1.137  -0.454  -0.234  -1.141
50    R         0.603   0.610   0.644   1.120   1.111   1.054   0.619   0.629   0.675
51    P         0.603   0.610   0.644   1.060   1.052   1.009   0.619   0.629   0.675
52    D         0.603   0.610   0.644   1.108   1.100   1.045   0.619   0.629   0.675
53    L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
54    L        -1.017  -1.139  -0.981  -1.519  -1.736  -1.386  -1.220  -1.424  -1.201
55    F        -2.391  -2.193  -1.927  -2.732  -2.466  -1.972  -2.447  -2.203  -1.824
56    K         0.603   0.610   0.644   1.150   1.140   1.076   0.619   0.629   0.675
57    N        -0.482  -0.524  -0.947   0.260   0.174  -0.612  -0.454  -0.512  -1.147
58    I        -1.990  -1.911  -1.924  -2.006  -1.937  -1.908  -1.987  -1.935  -1.821
59    V        -0.482  -0.680  -0.951  -0.542  -0.801  -1.223  -0.454  -0.727  -1.153
60    P         0.603   0.610   0.644   1.060   1.052   1.009   0.619   0.629   0.675
61    V        -0.482  -0.524  -0.947  -0.542  -0.583  -1.217  -0.454  -0.512  -1.147
62    I        -1.302  -1.270  -0.985  -1.820  -1.798  -1.279  -1.680  -1.639  -1.207
63    M         0.603   0.610   0.644   1.114   1.096   1.050   0.619   0.629   0.675
64    A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
65    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
66    I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
67    I        -0.482  -0.495  -0.948  -0.472  -0.493  -1.281  -0.454  -0.473  -1.149
68    A        -0.482  -0.567  -0.948  -0.734  -0.847  -1.471  -0.454  -0.571  -1.149
69    I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
70    Y         0.603   0.610   0.644   1.048   1.043   1.000   0.619   0.629   0.675
71    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
72    L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
73    V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
74    V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
75    S         0.603   0.610   0.644   0.833   0.844   0.841   0.619   0.629   0.675
76    V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
77    L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
78    V        -1.393  -1.231  -0.974  -2.035  -1.712  -1.253  -1.834  -1.575  -1.190
79    C        -1.990  -1.518  -1.906  -1.596  -0.999  -1.502  -1.987  -1.419  -1.800
80    Y        -3.201  -3.056  -2.606  -2.959  -2.890  -2.213  -2.907  -2.726  -2.143
81    S        -1.516  -1.767  -1.917  -1.033  -1.386  -1.716  -1.374  -1.675  -1.812
82    L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
83    G        -3.889  -3.637  -3.131  -3.536  -3.130  -2.455  -3.213  -2.960  -2.332
84    Q         0.603   0.610   0.644   1.030   1.031   0.987   0.619   0.629   0.675
85    K        -2.489  -2.705  -2.604  -1.554  -1.931  -1.940  -2.140  -2.356  -2.141
86    Q        -2.489  -2.705  -2.604  -1.721  -2.103  -2.094  -2.140  -2.356  -2.141
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    A        -1.017  -1.108  -0.981  -1.371  -1.512  -1.199  -1.220  -1.375  -1.202
89    L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
90    Y         0.603   0.610   0.644   1.048   1.043   1.000   0.619   0.629   0.675
91    T        -1.516  -1.704  -1.915  -0.971  -1.271  -1.795  -1.374  -1.602  -1.810
92    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
93    F         0.603   0.610   0.644   0.913   0.917   0.901   0.619   0.629   0.675
94    I        -0.482  -0.524  -0.947  -0.446  -0.504  -1.195  -0.454  -0.512  -1.147
95    Q         0.603   0.610   0.644   1.030   1.031   0.987   0.619   0.629   0.675
96    L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
97    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
98    A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
99    G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
100   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
101   S        -0.482  -0.567  -0.948  -0.171  -0.297  -1.067  -0.454  -0.571  -1.149
102   V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
103   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
104   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
105   S        -1.017  -1.139  -0.981  -1.016  -1.308  -1.165  -1.220  -1.424  -1.201
106   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
107   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
108   A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
109   A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
110   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
111   F         0.603   0.610   0.644   0.913   0.917   0.901   0.619   0.629   0.675
112   A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
113   I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
114   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
115   I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
116   V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
117   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
118   D         0.603   0.610   0.644   1.108   1.100   1.045   0.619   0.629   0.675
119   A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
120   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
121   V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
122   R         0.603   0.610   0.644   1.120   1.111   1.054   0.619   0.629   0.675
123   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
124   S        -0.482  -0.363  -0.942   0.027   0.149  -0.748  -0.454  -0.302  -1.140
125   S        -0.482  -0.363  -0.942  -0.639  -0.485  -1.164  -0.454  -0.302  -1.140
126   Q         0.603   0.610   0.644   1.030   1.031   0.987   0.619   0.629   0.675
127   Q         0.603   0.610   0.644   1.030   1.031   0.987   0.619   0.629   0.675
128   P         0.603   0.610   0.644   1.060   1.052   1.009   0.619   0.629   0.675
129   R         0.603   0.610   0.644   1.120   1.111   1.054   0.619   0.629   0.675
130   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
131   F         0.603   0.610   0.644   0.913   0.917   0.901   0.619   0.629   0.675
132   V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
133   G        -0.482  -0.680  -0.951  -0.816  -1.086  -1.495  -0.454  -0.727  -1.153
134   M         0.603   0.610   0.644   1.114   1.096   1.050   0.619   0.629   0.675
135   I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
136   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
137   I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
138   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
139   I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
140   F         0.603   0.610   0.644   0.913   0.917   0.901   0.619   0.629   0.675
141   A        -0.482  -0.524  -0.947  -0.639  -0.677  -1.170  -0.454  -0.512  -1.147
142   E         0.603   0.610   0.644   1.234   1.216   1.138   0.619   0.629   0.675
143   V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
144   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
145   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
146   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
147   Y         0.603   0.610   0.644   1.048   1.043   1.000   0.619   0.629   0.675
148   G         0.603   0.610   0.644   0.195   0.231   0.370   0.619   0.629   0.675
149   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
150   I         0.603   0.610   0.644   0.540   0.554   0.625   0.619   0.629   0.675
151   V         0.603   0.610   0.644   0.429   0.460   0.543   0.619   0.629   0.675
152   A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
153   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
154   L         0.603   0.610   0.644   0.243   0.280   0.405   0.619   0.629   0.675
155   L        -1.017  -1.065  -0.980  -1.317  -1.367  -1.074  -1.220  -1.305  -1.199
156   N         0.603   0.610   0.644   1.192   1.172   1.107   0.619   0.629   0.675
157   S        -0.482  -0.680  -0.951  -0.078  -0.333  -0.786  -0.454  -0.727  -1.153
158   R        -1.017  -1.051  -0.979  -0.473  -0.564  -0.575  -1.220  -1.283  -1.198
159   A         0.603   0.610   0.644   0.290   0.316   0.440   0.619   0.629   0.675
160   T        -1.516  -1.369  -1.907  -0.985  -0.838  -1.811  -1.374  -1.204  -1.801
161   Q        -2.489  -2.705  -2.604  -1.857  -2.234  -2.366  -2.140  -2.356  -2.141
162   D        -1.017  -1.139  -0.981  -0.471  -0.701  -0.565  -1.220  -1.424  -1.201
163   V        -0.482  -0.567  -0.948  -0.480  -0.567  -1.027  -0.454  -0.571  -1.149
164   V        -3.700  -3.599  -3.131  -3.361  -3.194  -2.604  -3.060  -2.908  -2.332
165   C         0.603   0.610   0.644   1.060   1.063   1.009   0.619   0.629   0.675
* 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/P25515
Output conservation file - output/P25515
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
