1     M         1.071   1.082   1.119   1.261   1.262   1.318   1.152   1.166   1.221
2     S        -0.153  -0.172  -0.474   0.142   0.107  -0.348  -0.164  -0.193  -0.620
3     -        -1.146  -1.125  -1.035  -1.139  -1.110  -1.001  -1.181  -1.151  -1.030
4     -        -0.685  -0.647  -0.583  -0.754  -0.706  -0.591  -0.922  -0.872  -0.773
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    T        -1.416  -1.463  -1.388  -1.351  -1.437  -1.299  -1.278  -1.311  -1.189
11    F         0.444   0.379   0.169   0.499   0.426   0.106   0.443   0.340  -0.037
12    N        -1.018  -0.961  -1.000  -1.036  -0.969  -0.992  -1.075  -1.013  -0.999
13    A         0.135   0.108   0.064   0.064   0.021  -0.040  -0.063  -0.117  -0.232
14    E         0.444   0.500   0.182   0.308   0.383  -0.040   0.443   0.525  -0.013
15    T        -0.730  -0.715  -0.598  -0.968  -0.955  -0.794  -0.974  -0.949  -0.791
16    A         1.071   1.082   1.119   0.998   1.013   1.076   1.152   1.166   1.221
17    D        -0.030   0.008   0.045  -0.431  -0.364  -0.295  -0.367  -0.301  -0.268
18    N         1.071   1.082   1.119   1.131   1.137   1.198   1.152   1.166   1.221
19    L        -0.716  -0.756  -0.956  -0.569  -0.637  -0.947  -0.670  -0.719  -0.944
20    E         0.444   0.379   0.169   0.287   0.209  -0.113   0.443   0.340  -0.037
21    D         0.135   0.115   0.073  -0.008  -0.056  -0.185  -0.063  -0.104  -0.215
22    I         1.071   1.082   1.119   1.131   1.139   1.198   1.152   1.166   1.221
23    E         1.071   1.082   1.119   0.851   0.873   0.941   1.152   1.166   1.221
24    K         0.135   0.115   0.073   0.019  -0.014  -0.065  -0.063  -0.104  -0.215
25    Q         1.071   1.082   1.119   1.222   1.237   1.282   1.152   1.166   1.221
26    F         1.071   1.082   1.119   1.043   1.067   1.117   1.152   1.166   1.221
27    A         1.071   1.082   1.119   0.998   1.013   1.076   1.152   1.166   1.221
28    V         1.071   1.082   1.119   1.167   1.178   1.231   1.152   1.166   1.221
29    V        -0.030   0.048   0.072  -0.283  -0.155  -0.115  -0.367  -0.227  -0.217
30    A         1.071   1.082   1.119   0.998   1.013   1.076   1.152   1.166   1.221
31    V         1.071   1.082   1.119   1.167   1.178   1.231   1.152   1.166   1.221
32    E        -0.948  -0.980  -1.009  -0.960  -0.982  -0.932  -0.974  -1.007  -1.005
33    Q         0.444   0.347   0.165   0.708   0.592   0.329   0.443   0.290  -0.044
34    A        -0.153  -0.270  -0.489  -0.070  -0.228  -0.536  -0.164  -0.326  -0.640
35    E        -0.153  -0.242  -0.482  -0.234  -0.339  -0.684  -0.164  -0.285  -0.631
36    T         0.444   0.379   0.169   0.572   0.488   0.169   0.443   0.340  -0.037
37    Y         1.071   1.082   1.119   1.187   1.197   1.249   1.152   1.166   1.221
38    W         1.071   1.082   1.119   1.288   1.299   1.342   1.152   1.166   1.221
39    K        -1.416  -1.370  -1.372  -1.367  -1.311  -1.271  -1.278  -1.232  -1.176
40    L         0.444   0.422   0.173   0.512   0.482   0.125   0.443   0.407  -0.029
41    L         0.135   0.207   0.110   0.074   0.182   0.016  -0.063   0.058  -0.145
42    T        -0.551  -0.573  -0.558  -0.778  -0.773  -0.692  -0.772  -0.771  -0.739
43    S        -0.948  -1.006  -0.996  -0.953  -1.027  -0.992  -0.974  -1.018  -0.990
44    V        -0.551  -0.570  -0.551  -0.549  -0.562  -0.529  -0.772  -0.777  -0.735
45    P         0.135   0.052   0.056   0.221   0.045  -0.012  -0.063  -0.219  -0.248
46    G         1.071   1.082   1.119   1.226   1.240   1.285   1.152   1.166   1.221
47    S         1.071   1.082   1.119   1.218   1.228   1.278   1.152   1.166   1.221
48    K         0.135   0.052   0.056  -0.118  -0.283  -0.319  -0.063  -0.219  -0.248
49    L         1.071   1.082   1.119   1.055   1.067   1.128   1.152   1.166   1.221
50    R        -0.083  -0.058   0.034  -0.358  -0.328  -0.173  -0.468  -0.428  -0.289
51    L         1.071   1.082   1.119   1.055   1.067   1.128   1.152   1.166   1.221
52    T         1.071   1.082   1.119   1.115   1.129   1.184   1.152   1.166   1.221
53    K         1.071   1.082   1.119   0.952   0.968   1.034   1.152   1.166   1.221
54    F        -1.704  -1.666  -1.651  -1.325  -1.281  -1.276  -1.379  -1.342  -1.274
55    D         1.071   1.082   1.119   1.063   1.071   1.136   1.152   1.166   1.221
56    D         1.071   1.082   1.119   1.063   1.071   1.136   1.152   1.166   1.221
57    E        -0.948  -0.980  -1.009  -1.092  -1.123  -1.105  -0.974  -1.007  -1.005
58    I         1.071   1.082   1.119   1.131   1.139   1.198   1.152   1.166   1.221
59    Y        -0.551  -0.614  -0.563  -0.566  -0.648  -0.553  -0.772  -0.837  -0.749
60    E        -0.716  -0.738  -0.968  -0.764  -0.793  -1.107  -0.670  -0.700  -0.958
61    N        -1.813  -1.729  -1.676  -1.499  -1.374  -1.357  -1.481  -1.406  -1.294
62    F        -0.030   0.048   0.072  -0.260  -0.113  -0.097  -0.367  -0.227  -0.217
63    M        -1.524  -1.473  -1.389  -1.416  -1.364  -1.229  -1.379  -1.322  -1.190
64    E        -1.236  -1.328  -1.357  -1.270  -1.391  -1.416  -1.075  -1.169  -1.161
65    R        -1.416  -1.430  -1.379  -1.238  -1.261  -1.146  -1.278  -1.276  -1.181
66    F         1.071   1.082   1.119   1.043   1.067   1.117   1.152   1.166   1.221
67    P         1.071   1.082   1.119   1.265   1.271   1.321   1.152   1.166   1.221
68    E         1.071   1.082   1.119   0.851   0.873   0.941   1.152   1.166   1.221
69    Y        -0.030  -0.010   0.046  -0.193  -0.155  -0.076  -0.367  -0.335  -0.267
70    K        -0.716  -0.771  -0.964  -0.678  -0.765  -1.052  -0.670  -0.740  -0.953
71    D        -0.153  -0.153  -0.468  -0.038  -0.039  -0.520  -0.164  -0.165  -0.612
72    V        -1.704  -1.645  -1.666  -1.297  -1.218  -1.303  -1.379  -1.323  -1.286
73    E        -0.427  -0.446  -0.532  -0.623  -0.640  -0.766  -0.569  -0.580  -0.702
74    R        -1.813  -1.796  -1.674  -1.705  -1.685  -1.502  -1.481  -1.453  -1.292
75    V        -0.725  -0.691  -0.585  -0.905  -0.850  -0.698  -0.964  -0.916  -0.774
76    K        -1.179  -1.178  -1.041  -1.321  -1.274  -1.068  -1.228  -1.212  -1.038
77    K        -0.600  -0.625  -0.573  -0.782  -0.783  -0.709  -0.832  -0.844  -0.760
78    F        -1.018  -1.092  -1.025  -1.039  -1.121  -1.016  -1.075  -1.130  -1.022
79    T        -1.813  -1.699  -1.668  -1.705  -1.555  -1.503  -1.481  -1.385  -1.288
80    E         1.071   1.082   1.119   0.851   0.873   0.941   1.152   1.166   1.221
81    E        -1.018  -1.027  -1.007  -1.255  -1.238  -1.188  -1.075  -1.072  -1.005
82    E        -0.427  -0.420  -0.543  -0.639  -0.643  -0.769  -0.569  -0.575  -0.721
83    L        -0.030   0.048   0.072  -0.071   0.070   0.075  -0.367  -0.227  -0.217
84    K         1.071   1.082   1.119   0.952   0.968   1.034   1.152   1.166   1.221
85    T        -0.427  -0.294  -0.517  -0.281  -0.079  -0.437  -0.569  -0.375  -0.681
86    K        -0.948  -0.993  -1.013  -0.965  -1.029  -1.030  -0.974  -1.024  -1.010
87    E        -1.524  -1.495  -1.392  -1.589  -1.523  -1.379  -1.379  -1.339  -1.193
88    A        -0.551  -0.573  -0.558  -0.587  -0.575  -0.570  -0.772  -0.771  -0.739
89    K         1.071   1.082   1.119   0.952   0.968   1.034   1.152   1.166   1.221
90    E        -0.551  -0.609  -0.566  -0.872  -0.921  -0.800  -0.772  -0.829  -0.753
91    R        -0.427  -0.507  -0.546  -0.422  -0.557  -0.673  -0.569  -0.675  -0.724
92    W         1.071   1.082   1.119   1.288   1.299   1.342   1.152   1.166   1.221
93    R         1.071   1.082   1.119   1.159   1.174   1.224   1.152   1.166   1.221
94    K        -1.813  -1.836  -1.686  -1.837  -1.865  -1.609  -1.481  -1.482  -1.301
95    F         1.071   1.082   1.119   1.043   1.067   1.117   1.152   1.166   1.221
96    F        -1.813  -1.729  -1.676  -1.469  -1.359  -1.344  -1.481  -1.406  -1.294
97    T        -1.813  -1.699  -1.668  -1.621  -1.466  -1.450  -1.481  -1.385  -1.288
98    I        -2.101  -2.071  -1.931  -1.995  -1.951  -1.728  -1.582  -1.549  -1.375
99    F        -0.030  -0.057   0.032  -0.193  -0.234  -0.093  -0.367  -0.426  -0.294
100   E         0.321   0.304   0.133   0.135   0.118  -0.147   0.252   0.220  -0.103
101   K         0.135   0.097   0.063  -0.025  -0.091  -0.148  -0.063  -0.137  -0.233
102   K        -0.716  -0.738  -0.968  -0.716  -0.747  -1.132  -0.670  -0.700  -0.958
103   I         0.135   0.127   0.067   0.159   0.137   0.017  -0.063  -0.083  -0.227
104   E        -0.551  -0.612  -0.558  -0.890  -0.962  -0.853  -0.772  -0.834  -0.743
105   D         1.071   1.082   1.119   1.063   1.071   1.136   1.152   1.166   1.221
106   Y         0.135   0.207   0.110   0.173   0.289   0.088  -0.063   0.058  -0.145
107   N         1.071   1.082   1.119   1.131   1.137   1.198   1.152   1.166   1.221
108   F         1.071   1.082   1.119   1.043   1.067   1.117   1.152   1.166   1.221
109   G         1.071   1.082   1.119   1.226   1.240   1.285   1.152   1.166   1.221
110   T         1.071   1.082   1.119   1.115   1.129   1.184   1.152   1.166   1.221
111   L         0.444   0.347   0.165   0.512   0.384   0.111   0.443   0.290  -0.044
112   L         1.071   1.082   1.119   1.055   1.067   1.128   1.152   1.166   1.221
113   R         1.071   1.082   1.119   1.159   1.174   1.224   1.152   1.166   1.221
114   T        -1.704  -1.761  -1.682  -1.463  -1.561  -1.462  -1.379  -1.421  -1.298
115   D        -0.551  -0.560  -0.563  -0.732  -0.746  -0.700  -0.772  -0.776  -0.749
116   A        -0.716  -0.746  -0.957  -0.525  -0.573  -0.810  -0.670  -0.708  -0.945
117   S        -1.127  -1.118  -1.028  -1.120  -1.107  -0.984  -1.177  -1.155  -1.026
118   A        -1.813  -1.801  -1.680  -1.873  -1.862  -1.680  -1.481  -1.457  -1.297
119   E         0.444   0.347   0.165   0.322   0.211  -0.029   0.443   0.290  -0.044
120   Y         1.071   1.082   1.119   1.187   1.197   1.249   1.152   1.166   1.221
121   G        -0.948  -1.035  -1.015  -0.773  -0.908  -0.941  -0.974  -1.055  -1.010
122   Q         0.135   0.072   0.063   0.149   0.018  -0.079  -0.063  -0.183  -0.234
123   F        -1.416  -1.463  -1.388  -1.571  -1.647  -1.547  -1.278  -1.311  -1.189
124   T        -1.127  -1.125  -1.030  -1.141  -1.144  -1.026  -1.177  -1.163  -1.027
125   T         1.071   1.082   1.119   1.115   1.129   1.184   1.152   1.166   1.221
126   C        -0.730  -0.719  -0.599  -0.627  -0.632  -0.456  -0.974  -0.954  -0.792
127   F         1.071   1.082   1.119   1.043   1.067   1.117   1.152   1.166   1.221
128   V        -0.030   0.020   0.049  -0.183  -0.088  -0.083  -0.367  -0.279  -0.262
129   V        -0.030  -0.057   0.032  -0.044  -0.099   0.041  -0.367  -0.426  -0.294
130   R         1.071   1.082   1.119   1.159   1.174   1.224   1.152   1.166   1.221
131   L        -0.551  -0.479  -0.553  -0.520  -0.442  -0.513  -0.772  -0.706  -0.738
132   Q         1.071   1.082   1.119   1.222   1.237   1.282   1.152   1.166   1.221
133   F         1.071   1.082   1.119   1.043   1.067   1.117   1.152   1.166   1.221
134   Y         0.135   0.052   0.056   0.177   0.016  -0.020  -0.063  -0.219  -0.248
135   A         1.071   1.082   1.119   0.998   1.013   1.076   1.152   1.166   1.221
136   F        -1.127  -1.159  -1.041  -1.143  -1.170  -0.981  -1.177  -1.197  -1.038
137   E         1.071   1.082   1.119   0.851   0.873   0.941   1.152   1.166   1.221
138   I         1.071   1.082   1.119   1.131   1.139   1.198   1.152   1.166   1.221
139   A         1.071   1.082   1.119   0.998   1.013   1.076   1.152   1.166   1.221
140   R         1.071   1.082   1.119   1.159   1.174   1.224   1.152   1.166   1.221
141   N         1.071   1.082   1.119   1.131   1.137   1.198   1.152   1.166   1.221
142   K        -0.030  -0.007   0.044  -0.214  -0.171  -0.126  -0.367  -0.329  -0.270
143   H        -0.948  -0.856  -0.990  -0.720  -0.598  -0.813  -0.974  -0.853  -0.983
144   G         1.071   1.082   1.119   1.226   1.240   1.285   1.152   1.166   1.221
145   L         1.071   1.082   1.119   1.055   1.067   1.128   1.152   1.166   1.221
146   N         1.071   1.082   1.119   1.131   1.137   1.198   1.152   1.166   1.221
147   D         1.071   1.082   1.119   1.063   1.071   1.136   1.152   1.166   1.221
148   W         1.071   1.082   1.119   1.288   1.299   1.342   1.152   1.166   1.221
149   I        -0.427  -0.454  -0.523  -0.399  -0.418  -0.556  -0.569  -0.587  -0.690
150   V        -0.612  -0.658  -0.587  -0.576  -0.645  -0.528  -0.828  -0.884  -0.777
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   G        -1.127  -1.112  -1.042  -1.113  -1.109  -1.025  -1.177  -1.161  -1.039
172   Q        -1.838  -1.798  -1.678  -1.640  -1.600  -1.389  -1.493  -1.450  -1.295
173   K        -1.813  -1.757  -1.670  -1.909  -1.818  -1.681  -1.481  -1.423  -1.290
* 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/Q08971
Output conservation file - output/Q08971
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
