1     M         1.259   1.300   1.394   1.590   1.623   1.745   1.325   1.389   1.531
2     S        -0.982  -1.260  -1.199  -0.685  -1.120  -1.081  -0.855  -1.163  -1.052
3     T        -1.861  -1.875  -1.645  -1.510  -1.519  -1.182  -1.581  -1.538  -1.253
4     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.517  -1.474  -1.230  -1.321  -1.219  -0.889  -1.474  -1.390  -1.083
6     I        -1.821  -1.717  -1.643  -1.628  -1.552  -1.494  -1.522  -1.419  -1.252
7     V         0.403   0.266   0.179   0.257   0.097  -0.018   0.376   0.152  -0.033
8     K        -0.403  -0.379  -0.603  -0.509  -0.471  -0.769  -0.415  -0.409  -0.683
9     A        -0.736  -0.638  -0.662  -0.996  -0.846  -0.730  -0.889  -0.814  -0.764
10    S        -0.736  -0.749  -0.649  -0.938  -0.965  -0.894  -0.889  -0.884  -0.744
11    N         0.403   0.266   0.179   0.734   0.500   0.247   0.376   0.152  -0.033
12    W         1.259   1.300   1.394   1.515   1.563   1.680   1.325   1.389   1.531
13    R         1.259   1.300   1.394   1.175   1.218   1.383   1.325   1.389   1.531
14    L        -0.621  -0.564  -0.612  -0.472  -0.363  -0.383  -0.734  -0.635  -0.696
15    V         1.259   1.300   1.394   0.983   1.053   1.217   1.325   1.389   1.531
16    E         1.259   1.300   1.394   1.407   1.436   1.586   1.325   1.389   1.531
17    V        -0.277  -0.292  -0.565  -0.436  -0.488  -0.892  -0.249  -0.292  -0.633
18    G         1.259   1.300   1.394   1.386   1.432   1.568   1.325   1.389   1.531
19    R         1.259   1.300   1.394   1.175   1.218   1.383   1.325   1.389   1.531
20    V         0.473   0.325   0.211   0.318   0.147   0.012   0.477   0.247   0.024
21    V         0.473   0.390   0.223   0.294   0.201  -0.031   0.477   0.347   0.044
22    L         0.473   0.390   0.223   0.505   0.396   0.088   0.477   0.347   0.044
23    I        -0.775  -0.760  -0.638  -1.066  -1.013  -0.781  -0.976  -0.926  -0.737
24    K        -1.861  -1.817  -1.638  -1.683  -1.541  -1.223  -1.581  -1.502  -1.248
25    K        -1.407  -1.268  -1.206  -1.464  -1.329  -1.130  -1.364  -1.204  -1.060
26    G        -0.736  -0.751  -0.651  -0.766  -0.767  -0.677  -0.889  -0.885  -0.748
27    Q        -0.838  -0.820  -0.665  -0.726  -0.675  -0.439  -1.047  -0.981  -0.766
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    S        -0.725  -0.860  -0.684  -0.543  -0.727  -0.471  -0.845  -1.030  -0.789
32    A        -1.335  -1.434  -1.232  -1.444  -1.496  -1.172  -1.258  -1.350  -1.085
33    G         1.259   1.300   1.394   1.360   1.414   1.545   1.325   1.389   1.531
34    K         0.318   0.276   0.185   0.144   0.102  -0.028   0.249   0.168  -0.022
35    L         1.259   1.300   1.394   1.224   1.290   1.426   1.325   1.389   1.531
36    A         1.259   1.300   1.394   0.949   1.042   1.186   1.325   1.389   1.531
37    A        -1.274  -1.273  -1.181  -1.272  -1.226  -1.196  -1.218  -1.177  -1.035
38    I         0.473   0.637   0.243   0.661   0.869   0.255   0.477   0.705   0.080
39    V         0.473   0.325   0.211   0.254   0.051  -0.159   0.477   0.247   0.024
40    E         0.473   0.373   0.214   0.757   0.608   0.398   0.477   0.321   0.029
41    I         1.259   1.300   1.394   1.381   1.436   1.563   1.325   1.389   1.531
42    I        -0.122  -0.089   0.086  -0.383  -0.447  -0.161  -0.491  -0.464  -0.201
43    D         1.259   1.300   1.394   1.486   1.522   1.655   1.325   1.389   1.531
44    Q        -0.122  -0.089   0.086  -0.025   0.033   0.298  -0.491  -0.464  -0.201
45    K         0.473   0.325   0.211   0.336   0.170   0.029   0.477   0.247   0.024
46    K        -0.277   0.126  -0.518  -0.200   0.285  -0.564  -0.249   0.259  -0.571
47    V         0.085   0.150   0.114  -0.353  -0.246  -0.361  -0.128  -0.041  -0.150
48    L         1.259   1.300   1.394   1.224   1.290   1.426   1.325   1.389   1.531
49    I         0.473   0.390   0.223   0.661   0.538   0.214   0.477   0.347   0.044
50    D         1.259   1.300   1.394   1.486   1.522   1.655   1.325   1.389   1.531
51    G         0.473   0.373   0.214   0.714   0.578   0.328   0.477   0.321   0.029
52    P         1.259   1.300   1.394   1.517   1.566   1.682   1.325   1.389   1.531
53    K        -1.861  -1.792  -1.636  -1.740  -1.574  -1.288  -1.581  -1.487  -1.247
54    A        -0.853  -0.639  -0.657  -0.928  -0.627  -0.695  -1.043  -0.814  -0.759
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    G        -0.552  -0.667  -0.638  -0.422  -0.642  -0.661  -0.612  -0.772  -0.729
60    V        -0.982  -1.049  -1.162  -1.017  -1.123  -1.225  -0.855  -0.937  -1.014
61    P        -0.621  -0.602  -0.606  -0.374  -0.370  -0.463  -0.734  -0.685  -0.689
62    R         1.259   1.300   1.394   1.175   1.218   1.383   1.325   1.389   1.531
63    Q         0.473   0.390   0.223   0.742   0.650   0.376   0.477   0.347   0.044
64    A        -0.775  -0.557  -0.628  -1.338  -1.015  -0.992  -0.976  -0.723  -0.723
65    I        -0.277  -0.507  -0.598  -0.070  -0.456  -0.730  -0.249  -0.557  -0.677
66    N        -1.635  -1.581  -1.621  -1.154  -1.146  -1.308  -1.339  -1.279  -1.233
67    L         0.473   0.373   0.214   0.598   0.499   0.311   0.477   0.321   0.029
68    G        -0.982  -1.084  -1.169  -0.727  -0.939  -1.176  -0.855  -0.979  -1.021
69    Q        -1.861  -1.907  -1.657  -1.695  -1.732  -1.385  -1.581  -1.566  -1.263
70    V        -0.277  -0.247  -0.558  -0.329  -0.284  -0.643  -0.249  -0.223  -0.624
71    V        -0.277  -0.507  -0.598  -0.357  -0.653  -0.760  -0.249  -0.557  -0.677
72    L         1.259   1.300   1.394   1.224   1.290   1.426   1.325   1.389   1.531
73    T         1.259   1.300   1.394   1.397   1.458   1.577   1.325   1.389   1.531
74    P         0.473   0.373   0.214   0.886   0.761   0.537   0.477   0.321   0.029
75    L        -0.775  -0.801  -0.651  -0.784  -0.763  -0.504  -0.976  -0.971  -0.752
76    T        -0.122   0.147   0.155  -0.517  -0.100  -0.065  -0.491  -0.045  -0.076
77    F        -1.499  -1.410  -1.219  -1.440  -1.399  -1.071  -1.460  -1.329  -1.073
78    A        -1.997  -1.751  -1.640  -1.967  -1.595  -1.437  -1.702  -1.445  -1.250
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    L         0.085   0.118   0.111  -0.101  -0.065  -0.158  -0.128  -0.095  -0.155
81    P         0.473   0.325   0.211   0.800   0.574   0.310   0.477   0.247   0.024
82    R         1.259   1.300   1.394   1.175   1.218   1.383   1.325   1.389   1.531
83    G         1.259   1.300   1.394   1.386   1.432   1.568   1.325   1.389   1.531
84    A        -0.277  -0.305  -0.565  -0.336  -0.332  -0.619  -0.249  -0.307  -0.633
85    R         0.085   0.118   0.111  -0.144  -0.128  -0.188  -0.128  -0.095  -0.155
86    T        -0.122  -0.082   0.076  -0.187  -0.148   0.077  -0.491  -0.452  -0.220
87    A        -1.362  -1.213  -1.182  -1.576  -1.302  -1.243  -1.339  -1.153  -1.038
88    T        -0.775  -0.758  -0.640  -0.781  -0.760  -0.622  -0.976  -0.922  -0.739
89    V         0.473   0.325   0.211   0.318   0.147   0.012   0.477   0.247   0.024
90    S        -1.861  -1.700  -1.635  -1.821  -1.740  -1.523  -1.581  -1.410  -1.246
91    K         0.473   0.325   0.211   0.271   0.076  -0.144   0.477   0.247   0.024
92    K         0.473   0.390   0.223   0.271   0.174  -0.122   0.477   0.347   0.044
93    W         0.473   0.325   0.211   0.798   0.569   0.304   0.477   0.247   0.024
94    A        -0.621  -0.763  -0.657  -0.908  -1.098  -0.902  -0.734  -0.926  -0.759
95    A         1.259   1.300   1.394   0.949   1.042   1.186   1.325   1.389   1.531
96    A        -0.277  -0.521  -0.596  -0.370  -0.651  -0.731  -0.249  -0.576  -0.675
97    G        -1.362  -1.251  -1.196  -1.057  -0.919  -0.791  -1.339  -1.203  -1.053
98    V        -0.621  -0.717  -0.643  -0.896  -1.049  -0.914  -0.734  -0.847  -0.740
99    C        -1.861  -1.640  -1.621  -1.269  -1.021  -0.963  -1.581  -1.368  -1.236
100   E        -1.861  -1.830  -1.643  -1.792  -1.845  -1.523  -1.581  -1.514  -1.252
101   K        -0.277  -0.254  -0.564  -0.318  -0.293  -0.650  -0.249  -0.248  -0.631
102   W         1.259   1.300   1.394   1.517   1.566   1.682   1.325   1.389   1.531
103   A        -0.621  -0.699  -0.640  -1.008  -1.081  -1.003  -0.734  -0.820  -0.737
104   A        -1.274  -1.212  -1.200  -1.390  -1.277  -1.137  -1.218  -1.170  -1.057
105   S         0.473   0.637   0.243   0.675   0.878   0.357   0.477   0.705   0.080
106   S        -0.982  -1.049  -1.162  -0.657  -0.786  -0.963  -0.855  -0.937  -1.014
107   W         1.259   1.300   1.394   1.517   1.566   1.682   1.325   1.389   1.531
108   A         1.259   1.300   1.394   0.949   1.042   1.186   1.325   1.389   1.531
109   K         1.259   1.300   1.394   1.000   1.078   1.231   1.325   1.389   1.531
110   K         1.259   1.300   1.394   1.000   1.078   1.231   1.325   1.389   1.531
111   I        -0.775  -0.763  -0.653  -0.799  -0.760  -0.584  -0.976  -0.930  -0.754
112   A        -0.277  -0.467  -0.588  -0.390  -0.616  -0.767  -0.249  -0.503  -0.664
113   Q        -0.982  -0.854  -1.145  -0.599  -0.471  -0.905  -0.855  -0.716  -0.996
114   R        -0.621  -0.677  -0.638  -0.769  -0.874  -0.807  -0.734  -0.800  -0.734
115   E         0.473   0.373   0.214   0.689   0.517   0.225   0.477   0.321   0.029
116   R        -0.277  -0.249  -0.560  -0.272  -0.276  -0.796  -0.249  -0.230  -0.626
117   R         1.259   1.300   1.394   1.175   1.218   1.383   1.325   1.389   1.531
118   A        -1.274  -1.249  -1.182  -1.375  -1.309  -1.318  -1.218  -1.150  -1.035
119   A        -0.775  -0.801  -0.651  -0.987  -0.914  -0.650  -0.976  -0.971  -0.752
120   L         1.259   1.300   1.394   1.224   1.290   1.426   1.325   1.389   1.531
121   T        -0.775  -0.775  -0.642  -0.700  -0.654  -0.441  -0.976  -0.943  -0.740
122   D         1.259   1.300   1.394   1.486   1.522   1.655   1.325   1.389   1.531
123   F         1.259   1.300   1.394   1.533   1.576   1.696   1.325   1.389   1.531
124   E         0.085   0.010   0.093   0.237   0.067   0.201  -0.128  -0.285  -0.188
125   R         1.259   1.300   1.394   1.175   1.218   1.383   1.325   1.389   1.531
126   F         1.259   1.300   1.394   1.533   1.576   1.696   1.325   1.389   1.531
127   Q        -0.277  -0.467  -0.588  -0.041  -0.341  -0.678  -0.249  -0.503  -0.664
128   V         1.259   1.300   1.394   0.983   1.053   1.217   1.325   1.389   1.531
129   M         0.085   0.328   0.156   0.330   0.681   0.337  -0.128   0.252  -0.073
130   V         0.085   0.010   0.093  -0.277  -0.430  -0.275  -0.128  -0.285  -0.188
131   L         0.473   0.325   0.211   0.597   0.433   0.303   0.477   0.247   0.024
132   R         0.085   0.125   0.111  -0.260  -0.201  -0.233  -0.128  -0.082  -0.156
133   K         0.473   0.325   0.211   0.304   0.118  -0.056   0.477   0.247   0.024
134   Q         0.473   0.325   0.211   0.745   0.563   0.365   0.477   0.247   0.024
135   K        -0.122   0.147   0.155  -0.564  -0.074  -0.092  -0.491  -0.045  -0.076
136   R         0.473   0.325   0.211   0.455   0.226   0.024   0.477   0.247   0.024
137   Y        -1.362  -1.387  -1.203  -0.975  -1.085  -0.842  -1.339  -1.306  -1.058
138   T        -1.274  -1.232  -1.174  -1.376  -1.265  -1.124  -1.218  -1.131  -1.027
139   V        -0.982  -1.084  -1.169  -0.984  -1.144  -1.171  -0.855  -0.979  -1.021
140   K        -0.982  -1.260  -1.199  -1.039  -1.461  -1.340  -0.855  -1.163  -1.052
141   K         0.473   0.373   0.214   0.276   0.151  -0.125   0.477   0.321   0.029
142   A         1.259   1.300   1.394   0.949   1.042   1.186   1.325   1.389   1.531
143   L        -0.188  -0.082   0.081  -0.711  -0.546  -0.262  -0.612  -0.452  -0.210
144   A         0.473   0.622   0.239   0.224   0.454  -0.122   0.477   0.686   0.073
145   K         1.259   1.300   1.394   1.000   1.078   1.231   1.325   1.389   1.531
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   A         1.259   1.300   1.394   0.949   1.042   1.186   1.325   1.389   1.531
* 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/P38754
Output conservation file - output/P38754
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
