1     M         0.592   0.599   0.638   0.932   0.928   0.938   0.607   0.619   0.669
2     S        -2.123  -2.076  -1.918  -2.298  -2.227  -1.916  -2.186  -2.116  -1.819
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    N        -3.572  -3.562  -3.123  -3.017  -3.077  -2.550  -2.921  -2.894  -2.333
15    V        -3.089  -3.076  -2.600  -2.758  -2.793  -2.220  -2.774  -2.743  -2.143
16    V        -1.917  -2.018  -1.924  -1.807  -1.999  -1.958  -1.892  -2.053  -1.826
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    Q        -0.458  -0.468  -0.953   0.105   0.076  -0.694  -0.422  -0.445  -1.160
20    A        -2.123  -2.054  -1.923  -2.358  -2.268  -2.042  -2.186  -2.105  -1.824
21    R        -0.458  -0.313  -0.948  -0.519  -0.364  -1.142  -0.422  -0.245  -1.151
22    D        -2.181  -2.198  -1.926  -1.850  -1.924  -1.623  -2.181  -2.232  -1.828
23    N        -2.610  -2.248  -2.579  -2.496  -2.066  -2.605  -2.297  -1.913  -2.126
24    S        -1.322  -1.264  -0.978  -1.288  -1.222  -0.845  -1.716  -1.650  -1.200
25    Q        -1.322  -1.264  -0.978  -1.175  -1.146  -0.790  -1.716  -1.650  -1.200
26    V         0.592   0.599   0.638   0.518   0.545   0.606   0.607   0.619   0.669
27    F         0.592   0.599   0.638   0.915   0.913   0.925   0.607   0.619   0.669
28    G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
29    V         0.592   0.599   0.638   0.518   0.545   0.606   0.607   0.619   0.669
30    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
31    R        -0.884  -0.754  -0.959  -0.974  -0.825  -1.014  -1.019  -0.844  -1.170
32    I         0.592   0.599   0.638   0.725   0.726   0.772   0.607   0.619   0.669
33    Y        -0.884  -0.663  -0.954  -0.374  -0.125  -0.595  -1.019  -0.713  -1.161
34    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
35    S         0.592   0.599   0.638   0.690   0.705   0.744   0.607   0.619   0.669
36    F         0.592   0.599   0.638   0.915   0.913   0.925   0.607   0.619   0.669
37    N         0.592   0.599   0.638   1.005   1.000   0.997   0.607   0.619   0.669
38    D         0.592   0.599   0.638   0.720   0.731   0.768   0.607   0.619   0.669
39    T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
40    F         0.592   0.599   0.638   0.915   0.913   0.925   0.607   0.619   0.669
41    V         0.592   0.599   0.638   0.518   0.545   0.606   0.607   0.619   0.669
42    H         0.592   0.599   0.638   0.994   0.992   0.988   0.607   0.619   0.669
43    V        -1.182  -1.189  -0.983  -1.291  -1.325  -1.042  -1.484  -1.524  -1.208
44    T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
45    D         0.592   0.599   0.638   0.720   0.731   0.768   0.607   0.619   0.669
46    L         0.592   0.599   0.638   0.749   0.749   0.791   0.607   0.619   0.669
47    S        -1.182  -1.189  -0.983  -1.248  -1.312  -1.082  -1.484  -1.524  -1.208
48    G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
49    K        -2.097  -1.964  -1.917  -2.163  -2.037  -1.814  -2.181  -2.031  -1.819
50    E         0.592   0.599   0.638   0.864   0.854   0.883   0.607   0.619   0.669
51    T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
52    I         0.592   0.599   0.638   0.725   0.726   0.772   0.607   0.619   0.669
53    A        -2.610  -2.784  -2.602  -2.535  -2.715  -2.341  -2.297  -2.458  -2.145
54    R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
55    V         0.592   0.599   0.638   0.518   0.545   0.606   0.607   0.619   0.669
56    T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
57    G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
58    G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
59    M         0.592   0.599   0.638   0.932   0.928   0.938   0.607   0.619   0.669
60    K         0.592   0.599   0.638   0.702   0.720   0.753   0.607   0.619   0.669
61    V         0.592   0.599   0.638   0.518   0.545   0.606   0.607   0.619   0.669
62    K         0.592   0.599   0.638   0.702   0.720   0.753   0.607   0.619   0.669
63    A        -0.884  -0.754  -0.959  -1.222  -1.035  -1.351  -1.019  -0.844  -1.170
64    D         0.592   0.599   0.638   0.720   0.731   0.768   0.607   0.619   0.669
65    R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
66    D         0.592   0.599   0.638   0.720   0.731   0.768   0.607   0.619   0.669
67    E         0.592   0.599   0.638   0.864   0.854   0.883   0.607   0.619   0.669
68    S        -0.380  -0.665  -0.963  -0.019  -0.339  -0.768  -0.322  -0.716  -1.176
69    S        -0.380  -0.665  -0.963  -0.085  -0.449  -1.033  -0.322  -0.716  -1.176
70    P         0.592   0.599   0.638   0.841   0.842   0.865   0.607   0.619   0.669
71    Y         0.592   0.599   0.638   1.044   1.042   1.028   0.607   0.619   0.669
72    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
73    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
74    M         0.592   0.599   0.638   0.932   0.928   0.938   0.607   0.619   0.669
75    L         0.592   0.599   0.638   0.749   0.749   0.791   0.607   0.619   0.669
76    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
77    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
78    Q         0.592   0.599   0.638   0.926   0.929   0.934   0.607   0.619   0.669
79    D         0.592   0.599   0.638   0.720   0.731   0.768   0.607   0.619   0.669
80    V        -1.182  -1.189  -0.983  -1.530  -1.589  -1.344  -1.484  -1.524  -1.208
81    A        -0.380  -0.665  -0.963  -0.562  -0.899  -1.334  -0.322  -0.716  -1.176
82    A        -1.313  -1.525  -1.915  -1.216  -1.463  -1.789  -1.135  -1.415  -1.815
83    K        -0.380  -0.485  -0.959  -0.094  -0.225  -1.100  -0.322  -0.467  -1.170
84    C        -0.380  -0.665  -0.963   0.244  -0.162  -0.917  -0.322  -0.716  -1.176
85    K        -0.380  -0.266  -0.949  -0.040   0.081  -0.865  -0.322  -0.187  -1.153
86    E         0.592   0.599   0.638   0.864   0.854   0.883   0.607   0.619   0.669
87    V        -0.380  -0.485  -0.959  -0.223  -0.333  -1.003  -0.322  -0.467  -1.170
88    G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
89    I         0.592   0.599   0.638   0.725   0.726   0.772   0.607   0.619   0.669
90    T        -0.380  -0.665  -0.963  -0.232  -0.550  -0.902  -0.322  -0.716  -1.176
91    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
92    V        -1.322  -1.264  -0.978  -1.498  -1.411  -1.009  -1.716  -1.650  -1.200
93    H         0.592   0.599   0.638   0.994   0.992   0.988   0.607   0.619   0.669
94    V        -1.182  -1.012  -0.970  -1.196  -0.941  -1.004  -1.484  -1.237  -1.188
95    K        -0.380  -0.665  -0.963  -0.094  -0.469  -1.110  -0.322  -0.716  -1.176
96    I        -0.884  -0.792  -0.960  -0.638  -0.542  -0.868  -1.019  -0.901  -1.170
97    R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
98    A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
99    T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
100   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
101   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
102   T        -0.380  -0.485  -0.959  -0.232  -0.346  -0.899  -0.322  -0.467  -1.170
103   R        -3.652  -3.672  -3.126  -3.773  -3.796  -3.082  -2.994  -2.976  -2.335
104   T        -0.380  -0.215  -0.953  -0.273  -0.104  -1.051  -0.322  -0.125  -1.160
105   K         0.592   0.599   0.638   0.702   0.720   0.753   0.607   0.619   0.669
106   T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
107   P         0.592   0.599   0.638   0.841   0.842   0.865   0.607   0.619   0.669
108   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
109   P         0.592   0.599   0.638   0.841   0.842   0.865   0.607   0.619   0.669
110   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
111   G        -2.019  -2.165  -1.928  -2.340  -2.472  -2.004  -2.065  -2.203  -1.830
112   Q         0.592   0.599   0.638   0.926   0.929   0.934   0.607   0.619   0.669
113   A        -1.322  -1.261  -0.982  -1.784  -1.642  -1.226  -1.716  -1.645  -1.206
114   A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
115   L        -0.380  -0.665  -0.963  -0.022  -0.393  -0.973  -0.322  -0.716  -1.176
116   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
117   A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
118   L         0.592   0.599   0.638   0.749   0.749   0.791   0.607   0.619   0.669
119   A         0.592   0.599   0.638   0.211   0.243   0.359   0.607   0.619   0.669
120   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
121   S        -1.182  -1.189  -0.983  -1.366  -1.442  -1.233  -1.484  -1.524  -1.208
122   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
123   L        -1.322  -1.264  -0.978  -1.199  -1.137  -0.773  -1.716  -1.650  -1.200
124   R        -0.380  -0.485  -0.959  -0.443  -0.564  -1.168  -0.322  -0.467  -1.170
125   I         0.592   0.599   0.638   0.725   0.726   0.772   0.607   0.619   0.669
126   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
127   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
128   I         0.592   0.599   0.638   0.725   0.726   0.772   0.607   0.619   0.669
129   E         0.592   0.599   0.638   0.864   0.854   0.883   0.607   0.619   0.669
130   D         0.592   0.599   0.638   0.720   0.731   0.768   0.607   0.619   0.669
131   V         0.592   0.599   0.638   0.518   0.545   0.606   0.607   0.619   0.669
132   T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
133   P         0.592   0.599   0.638   0.841   0.842   0.865   0.607   0.619   0.669
134   V        -1.773  -1.746  -1.916  -1.588  -1.555  -1.890  -1.716  -1.676  -1.817
135   P         0.592   0.599   0.638   0.841   0.842   0.865   0.607   0.619   0.669
136   S        -0.884  -0.754  -0.959  -0.747  -0.574  -1.024  -1.019  -0.844  -1.170
137   D         0.592   0.599   0.638   0.720   0.731   0.768   0.607   0.619   0.669
138   S         0.592   0.599   0.638   0.690   0.705   0.744   0.607   0.619   0.669
139   T         0.592   0.599   0.638   0.476   0.489   0.572   0.607   0.619   0.669
140   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
141   K        -1.182  -0.966  -0.964  -1.499  -1.195  -1.172  -1.484  -1.165  -1.177
142   K         0.592   0.599   0.638   0.702   0.720   0.753   0.607   0.619   0.669
143   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
144   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
145   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
146   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
147   G         0.592   0.599   0.638   0.299   0.320   0.429   0.607   0.619   0.669
148   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
149   R         0.592   0.599   0.638   0.305   0.318   0.434   0.607   0.619   0.669
150   L         0.592   0.599   0.638   0.749   0.749   0.791   0.607   0.619   0.669
* 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/P06367
Output conservation file - output/P06367
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
