1     M         0.943   0.952   0.995   1.347   1.354   1.363   0.971   0.983   1.051
2     A         0.174   0.074  -0.332   0.295   0.189  -0.426   0.248   0.121  -0.501
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     Q         0.174   0.085  -0.337   0.456   0.365  -0.244   0.248   0.135  -0.510
5     R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
6     V         0.943   0.952   0.995   0.880   0.910   0.982   0.971   0.983   1.051
7     T         0.943   0.952   0.995   0.995   1.011   1.075   0.971   0.983   1.051
8     F        -0.502  -0.405  -0.387  -0.209  -0.085  -0.112  -0.716  -0.568  -0.592
9     R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
10    R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
11    R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
12    N        -0.241  -0.332  -0.357   0.056  -0.108  -0.210  -0.314  -0.455  -0.542
13    P        -0.954  -1.122  -1.191  -0.577  -0.851  -1.020  -0.877  -1.077  -1.144
14    Y         0.943   0.952   0.995   1.213   1.221   1.253   0.971   0.983   1.051
15    N         0.943   0.952   0.995   1.171   1.176   1.219   0.971   0.983   1.051
16    T         0.943   0.952   0.995   0.995   1.011   1.075   0.971   0.983   1.051
17    R        -1.633  -1.478  -1.779  -1.748  -1.521  -1.928  -1.359  -1.179  -1.442
18    S         0.943   0.952   0.995   1.102   1.123   1.163   0.971   0.983   1.051
19    N         0.943   0.952   0.995   1.171   1.176   1.219   0.971   0.983   1.051
20    K        -0.241  -0.333  -0.392  -0.709  -0.836  -0.937  -0.314  -0.457  -0.599
21    I        -1.182  -1.301  -1.220  -1.043  -1.263  -1.151  -1.198  -1.331  -1.180
22    K        -0.502  -0.569  -0.411  -1.154  -1.274  -0.969  -0.716  -0.832  -0.631
23    V        -0.649  -0.651  -0.415  -0.865  -0.874  -0.490  -0.957  -0.968  -0.638
24    V        -0.502  -0.572  -0.408  -0.621  -0.750  -0.491  -0.716  -0.837  -0.626
25    K         0.943   0.952   0.995   0.498   0.557   0.670   0.971   0.983   1.051
26    T         0.943   0.952   0.995   0.995   1.011   1.075   0.971   0.983   1.051
27    P         0.943   0.952   0.995   1.160   1.163   1.210   0.971   0.983   1.051
28    G         0.943   0.952   0.995   1.000   1.012   1.080   0.971   0.983   1.051
29    G        -0.241  -0.332  -0.357  -0.083  -0.228  -0.281  -0.314  -0.455  -0.542
30    I        -2.617  -2.507  -2.271  -2.560  -2.297  -2.003  -2.081  -1.954  -1.646
31    L        -0.241  -0.332  -0.357  -0.051  -0.218  -0.286  -0.314  -0.455  -0.542
32    R        -0.502  -0.303  -0.360  -0.886  -0.579  -0.646  -0.716  -0.410  -0.547
33    A        -1.821  -1.852  -1.809  -1.569  -1.612  -1.519  -1.600  -1.626  -1.469
34    Q        -0.649  -0.651  -0.415  -0.725  -0.763  -0.398  -0.957  -0.968  -0.638
35    H         0.943   0.952   0.995   1.316   1.327   1.338   0.971   0.983   1.051
36    V        -0.649  -0.651  -0.415  -0.865  -0.874  -0.490  -0.957  -0.968  -0.638
37    K         0.943   0.952   0.995   0.498   0.557   0.670   0.971   0.983   1.051
38    K         0.943   0.952   0.995   0.498   0.557   0.670   0.971   0.983   1.051
39    L        -0.954  -1.019  -1.198  -0.719  -0.841  -1.223  -0.877  -0.942  -1.154
40    A        -0.502  -0.569  -0.411  -0.617  -0.748  -0.510  -0.716  -0.832  -0.631
41    T        -1.182  -1.097  -1.184  -1.040  -0.890  -1.038  -1.198  -1.043  -1.137
42    R        -0.954  -1.113  -1.198  -1.016  -1.257  -1.312  -0.877  -1.067  -1.153
43    P         0.174   0.311  -0.325   0.543   0.680  -0.229   0.248   0.412  -0.490
44    K        -0.241  -0.332  -0.357  -0.709  -0.834  -0.874  -0.314  -0.455  -0.542
45    C         0.943   0.952   0.995   1.234   1.247   1.270   0.971   0.983   1.051
46    G         0.943   0.952   0.995   1.000   1.012   1.080   0.971   0.983   1.051
47    D         0.174   0.074  -0.332   0.711   0.596  -0.040   0.248   0.121  -0.501
48    C        -0.502  -0.525  -0.410  -0.319  -0.389  -0.307  -0.716  -0.759  -0.630
49    G         0.943   0.952   0.995   1.000   1.012   1.080   0.971   0.983   1.051
50    S        -2.289  -2.087  -1.810  -2.084  -1.878  -1.454  -2.001  -1.806  -1.470
51    A        -1.182  -1.264  -1.217  -1.161  -1.292  -1.286  -1.198  -1.282  -1.177
52    L         0.943   0.952   0.995   1.060   1.057   1.128   0.971   0.983   1.051
53    Q        -1.305  -1.319  -1.232  -1.112  -1.152  -1.091  -1.278  -1.293  -1.192
54    G         0.943   0.952   0.995   1.000   1.012   1.080   0.971   0.983   1.051
55    I        -0.241  -0.257  -0.400  -0.091  -0.138  -0.452  -0.314  -0.342  -0.612
56    S        -1.289  -1.236  -1.213  -1.113  -1.052  -1.014  -1.359  -1.288  -1.172
57    T        -0.502  -0.569  -0.411  -0.575  -0.721  -0.505  -0.716  -0.832  -0.631
58    L         0.943   0.952   0.995   1.060   1.057   1.128   0.971   0.983   1.051
59    R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
60    P         0.943   0.952   0.995   1.160   1.163   1.210   0.971   0.983   1.051
61    R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
62    Q        -0.649  -0.550  -0.405  -0.654  -0.487  -0.326  -0.957  -0.800  -0.620
63    Y        -0.954  -1.122  -1.191  -0.407  -0.648  -0.800  -0.877  -1.077  -1.144
64    A         0.943   0.952   0.995   0.913   0.939   1.009   0.971   0.983   1.051
65    T        -2.085  -2.065  -1.803  -2.027  -2.065  -1.631  -1.840  -1.804  -1.465
66    V        -1.182  -1.212  -1.215  -1.155  -1.235  -1.142  -1.198  -1.251  -1.174
67    S         0.943   0.952   0.995   1.102   1.123   1.163   0.971   0.983   1.051
68    K        -1.305  -1.385  -1.218  -1.658  -1.742  -1.461  -1.278  -1.374  -1.177
69    T        -1.305  -1.443  -1.226  -1.082  -1.308  -0.998  -1.278  -1.444  -1.186
70    H        -1.821  -1.948  -1.793  -1.565  -1.810  -1.659  -1.600  -1.693  -1.456
71    K         0.943   0.952   0.995   0.498   0.557   0.670   0.971   0.983   1.051
72    T         0.174   0.076  -0.326   0.337   0.215  -0.505   0.248   0.123  -0.492
73    V         0.943   0.952   0.995   0.880   0.910   0.982   0.971   0.983   1.051
74    S        -0.502  -0.405  -0.387  -0.449  -0.300  -0.328  -0.716  -0.568  -0.592
75    R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
76    A         0.174   0.194  -0.331   0.295   0.330  -0.424   0.248   0.273  -0.500
77    Y         0.943   0.952   0.995   1.213   1.221   1.253   0.971   0.983   1.051
78    G         0.943   0.952   0.995   1.000   1.012   1.080   0.971   0.983   1.051
79    G         0.943   0.952   0.995   1.000   1.012   1.080   0.971   0.983   1.051
80    S        -0.241  -0.332  -0.357   0.032  -0.100  -0.183  -0.314  -0.455  -0.542
81    R        -1.182  -1.181  -1.213  -1.426  -1.467  -1.484  -1.198  -1.225  -1.172
82    C        -0.502  -0.525  -0.410  -0.277  -0.339  -0.250  -0.716  -0.759  -0.630
83    A         0.174   0.085  -0.337   0.309   0.217  -0.385   0.248   0.135  -0.510
84    N         0.943   0.952   0.995   1.171   1.176   1.219   0.971   0.983   1.051
85    C        -0.502  -0.525  -0.410  -0.350  -0.421  -0.349  -0.716  -0.759  -0.630
86    V         0.943   0.952   0.995   0.880   0.910   0.982   0.971   0.983   1.051
87    K         0.174   0.085  -0.337  -0.147  -0.216  -0.837   0.248   0.135  -0.510
88    E        -0.649  -0.651  -0.415  -0.513  -0.520  -0.201  -0.957  -0.968  -0.638
89    R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
90    I        -0.241  -0.350  -0.396  -0.091  -0.286  -0.442  -0.314  -0.482  -0.605
91    I         0.174   0.308  -0.325   0.283   0.437  -0.363   0.248   0.410  -0.490
92    R         0.943   0.952   0.995   0.684   0.693   0.822   0.971   0.983   1.051
93    A         0.943   0.952   0.995   0.913   0.939   1.009   0.971   0.983   1.051
94    F         0.943   0.952   0.995   1.327   1.334   1.346   0.971   0.983   1.051
95    L         0.943   0.952   0.995   1.060   1.057   1.128   0.971   0.983   1.051
96    I         0.943   0.952   0.995   1.065   1.067   1.132   0.971   0.983   1.051
97    E         0.943   0.952   0.995   1.139   1.159   1.193   0.971   0.983   1.051
98    E         0.943   0.952   0.995   1.139   1.159   1.193   0.971   0.983   1.051
99    Q         0.943   0.952   0.995   1.049   1.071   1.119   0.971   0.983   1.051
100   K         0.943   0.952   0.995   0.498   0.557   0.670   0.971   0.983   1.051
101   I         0.943   0.952   0.995   1.065   1.067   1.132   0.971   0.983   1.051
102   V         0.943   0.952   0.995   0.880   0.910   0.982   0.971   0.983   1.051
103   K         0.943   0.952   0.995   0.498   0.557   0.670   0.971   0.983   1.051
104   K        -2.085  -2.131  -1.809  -2.520  -2.558  -2.004  -1.840  -1.851  -1.469
105   V        -0.241  -0.332  -0.357  -0.367  -0.520  -0.666  -0.314  -0.455  -0.542
106   V        -0.954  -0.810  -1.181  -0.676  -0.509  -1.058  -0.877  -0.699  -1.133
107   K         0.943   0.952   0.995   0.498   0.557   0.670   0.971   0.983   1.051
108   E        -0.954  -0.927  -1.182  -0.520  -0.545  -0.849  -0.877  -0.882  -1.133
109   Q        -1.282  -1.512  -1.779  -0.694  -0.976  -1.355  -0.957  -1.193  -1.441
110   T        -1.656  -1.493  -1.227  -1.668  -1.415  -1.069  -1.707  -1.507  -1.186
111   E        -1.318  -1.415  -1.222  -0.980  -1.149  -0.908  -1.324  -1.414  -1.181
112   A        -0.673  -0.505  -0.395  -1.297  -0.879  -0.794  -0.996  -0.726  -0.605
113   A        -0.673  -0.609  -0.413  -0.799  -0.688  -0.431  -0.996  -0.898  -0.634
114   K        -0.473  -0.244  -0.374  -1.038  -0.681  -0.784  -0.668  -0.322  -0.570
115   K         0.943   0.952   0.995   0.385   0.420   0.578   0.971   0.983   1.051
116   S        -1.450  -1.265  -1.228  -1.491  -1.240  -1.169  -1.483  -1.249  -1.188
117   E        -1.450  -1.269  -1.235  -1.381  -1.099  -1.106  -1.483  -1.254  -1.196
118   K         0.943   0.952   0.995   0.385   0.420   0.578   0.971   0.983   1.051
119   K         0.943   0.952   0.995   0.385   0.420   0.578   0.971   0.983   1.051
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   A        -1.932  -1.686  -1.791  -1.794  -1.425  -1.720  -1.707  -1.436  -1.452
128   K        -1.065  -1.157  -1.200  -1.428  -1.550  -1.573  -1.012  -1.150  -1.154
129   K         0.174   0.194  -0.331  -0.103  -0.036  -0.661   0.248   0.273  -0.500
* 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/P87262
Output conservation file - output/P87262
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
