1     M         1.292   1.334   1.369   1.813   1.867   1.916   1.390   1.446   1.502
2     V        -0.115  -0.059   0.033   0.113   0.203   0.331  -0.470  -0.379  -0.243
3     N        -1.877  -1.712  -1.698  -1.360  -1.083  -1.154  -1.503  -1.315  -1.263
4     E        -1.408  -1.397  -1.294  -1.139  -1.035  -0.892  -1.297  -1.248  -1.107
5     T        -0.074   0.027   0.067   0.242   0.414   0.442  -0.395  -0.226  -0.182
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    G        -1.523  -1.457  -1.303  -1.176  -1.086  -0.871  -1.400  -1.299  -1.116
21    E        -0.115  -0.062   0.033  -0.376  -0.288  -0.128  -0.470  -0.384  -0.243
22    S        -0.819  -0.756  -0.739  -0.344  -0.254  -0.283  -0.935  -0.838  -0.813
23    Q        -0.115  -0.062   0.033  -0.679  -0.594  -0.395  -0.470  -0.384  -0.243
24    K         0.150   0.228   0.098   0.217   0.354  -0.077  -0.005   0.117  -0.127
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    A        -1.976  -1.901  -1.733  -2.217  -2.112  -1.841  -1.586  -1.478  -1.290
27    A        -0.850  -0.792  -0.740  -0.465  -0.359  -0.284  -0.991  -0.896  -0.815
28    K        -0.000   0.075   0.083  -0.934  -0.768  -0.754  -0.263  -0.141  -0.154
29    G         1.292   1.334   1.369   1.860   1.909   1.960   1.390   1.446   1.502
30    T        -1.877  -1.768  -1.726  -1.567  -1.385  -1.436  -1.503  -1.377  -1.285
31    P        -0.762  -0.840  -0.729  -0.438  -0.539  -0.389  -0.883  -0.947  -0.802
32    V         1.292   1.334   1.369   1.725   1.791   1.834   1.390   1.446   1.502
33    S        -0.000   0.075   0.083   0.382   0.501   0.481  -0.263  -0.141  -0.154
34    G         0.377   0.531   0.189   0.831   1.067   0.346   0.357   0.583   0.031
35    K        -0.000   0.119   0.090  -0.934  -0.699  -0.742  -0.263  -0.066  -0.141
36    V        -1.408  -1.397  -1.294  -0.804  -0.763  -0.622  -1.297  -1.248  -1.107
37    W         1.292   1.334   1.369   1.907   1.967   2.004   1.390   1.446   1.502
38    K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
39    A        -1.877  -1.768  -1.726  -1.150  -1.004  -0.993  -1.503  -1.377  -1.285
40    E        -0.000   0.075   0.083  -0.674  -0.506  -0.582  -0.263  -0.141  -0.154
41    K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
42    T        -1.408  -1.362  -1.291  -1.517  -1.631  -1.399  -1.297  -1.222  -1.105
43    P        -0.115  -0.036   0.048   0.090   0.175   0.309  -0.470  -0.338  -0.217
44    L        -0.762  -0.840  -0.729  -0.355  -0.415  -0.252  -0.883  -0.947  -0.802
45    R         0.377   0.176   0.138   0.389   0.104   0.106   0.357   0.030  -0.055
46    A        -0.762  -0.840  -0.729  -0.665  -0.863  -0.685  -0.883  -0.947  -0.802
47    K        -0.470  -0.536  -0.654  -0.869  -0.903  -0.929  -0.470  -0.571  -0.704
48    S        -1.408  -1.397  -1.294  -0.761  -0.735  -0.595  -1.297  -1.248  -1.107
49    R        -0.115  -0.036   0.048  -0.420  -0.247  -0.105  -0.470  -0.338  -0.217
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    V         1.292   1.334   1.369   1.719   1.781   1.829   1.390   1.446   1.502
52    V         1.292   1.334   1.369   1.720   1.786   1.830   1.390   1.446   1.502
53    K        -0.637  -0.787  -0.721  -1.154  -1.272  -1.068  -0.693  -0.879  -0.790
54    N        -0.637  -0.787  -0.721  -0.322  -0.650  -0.664  -0.693  -0.879  -0.790
55    K        -0.470  -0.602  -0.664  -0.937  -1.088  -1.046  -0.470  -0.648  -0.718
56    K         0.377   0.176   0.138  -0.140  -0.371  -0.377   0.357   0.030  -0.055
57    L        -0.470  -0.602  -0.664  -0.448  -0.749  -1.034  -0.470  -0.648  -0.718
58    T        -0.470  -0.368  -0.643   0.199   0.333  -0.091  -0.470  -0.326  -0.689
59    S        -0.470  -0.594  -0.665   0.190   0.014  -0.095  -0.470  -0.639  -0.718
60    W        -0.470  -0.602  -0.664   0.339   0.141   0.044  -0.470  -0.648  -0.718
61    E         0.377   0.447   0.185   0.157   0.282  -0.289   0.357   0.460   0.024
62    L        -1.231  -1.284  -1.279  -1.023  -1.290  -1.179  -1.090  -1.132  -1.092
63    K        -0.115  -0.036   0.048  -1.096  -0.878  -0.709  -0.470  -0.338  -0.217
64    K        -0.762  -0.840  -0.729  -1.561  -1.511  -1.289  -0.883  -0.947  -0.802
65    Q        -0.470  -0.602  -0.664  -0.088  -0.389  -0.527  -0.470  -0.648  -0.718
66    K         0.377   0.176   0.138  -0.140  -0.371  -0.377   0.357   0.030  -0.055
67    R        -0.000  -0.036   0.036  -0.674  -0.875  -0.765  -0.263  -0.337  -0.237
68    L         0.377   0.176   0.138   0.610   0.246   0.128   0.357   0.030  -0.055
69    E         0.377   0.176   0.138   0.157  -0.257  -0.413   0.357   0.030  -0.055
70    D        -1.408  -1.405  -1.277  -1.277  -1.279  -1.082  -1.297  -1.255  -1.092
71    K        -1.231  -1.220  -1.243  -1.073  -1.014  -1.277  -1.090  -1.071  -1.057
72    Q         0.377   0.176   0.138   0.774   0.399   0.272   0.357   0.030  -0.055
73    F        -0.762  -0.815  -0.712  -0.092  -0.164  -0.033  -0.883  -0.913  -0.781
74    K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
75    E        -0.470  -0.368  -0.643  -0.436  -0.289  -0.631  -0.470  -0.326  -0.689
76    R         0.377   0.466   0.177   0.157   0.281  -0.309   0.357   0.488   0.011
77    L        -0.470  -0.588  -0.672  -0.206  -0.463  -0.596  -0.470  -0.631  -0.727
78    K        -0.470  -0.352  -0.614  -1.078  -0.874  -1.235  -0.470  -0.305  -0.652
79    A        -0.762  -0.719  -0.710  -0.794  -0.810  -0.733  -0.883  -0.824  -0.779
80    L         1.292   1.334   1.369   1.554   1.625   1.675   1.390   1.446   1.502
81    K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
82    D        -1.231  -1.273  -1.256  -0.894  -1.100  -1.091  -1.090  -1.121  -1.070
83    E         1.292   1.334   1.369   1.204   1.275   1.348   1.390   1.446   1.502
84    K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
85    E        -0.470  -0.287  -0.621  -0.725  -0.421  -1.082  -0.470  -0.221  -0.661
86    E        -1.231  -1.104  -1.235  -1.126  -0.949  -1.056  -1.090  -0.924  -1.049
87    A        -1.231  -1.227  -1.252  -0.917  -0.932  -0.979  -1.090  -1.077  -1.066
88    R        -0.000  -0.014   0.041  -0.934  -0.957  -0.812  -0.263  -0.297  -0.229
89    Q        -1.877  -1.768  -1.726  -1.381  -1.267  -1.239  -1.503  -1.377  -1.285
90    A        -0.115  -0.054   0.036  -0.047   0.033   0.181  -0.470  -0.369  -0.238
91    K        -1.877  -1.768  -1.726  -1.923  -1.628  -1.640  -1.503  -1.377  -1.285
92    I         0.377   0.176   0.138   1.003   0.662   0.555   0.357   0.030  -0.055
93    T        -1.877  -1.695  -1.692  -1.615  -1.418  -1.310  -1.503  -1.300  -1.258
94    M        -1.408  -1.362  -1.291  -1.280  -1.411  -1.196  -1.297  -1.222  -1.105
95    L        -0.470  -0.536  -0.654  -0.022  -0.115  -0.252  -0.470  -0.571  -0.704
96    K         0.377   0.176   0.138  -0.263  -0.590  -0.652   0.357   0.030  -0.055
97    E        -1.408  -1.374  -1.291  -1.654  -1.520  -1.358  -1.297  -1.231  -1.105
98    R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
99    R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
100   E        -0.470  -0.588  -0.672  -0.466  -0.625  -0.718  -0.470  -0.631  -0.727
101   K        -0.762  -0.840  -0.729  -1.174  -1.203  -0.968  -0.883  -0.947  -0.802
102   K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
103   E        -0.115  -0.036   0.048  -0.420  -0.238  -0.105  -0.470  -0.338  -0.217
104   E         0.377   0.176   0.138   0.378   0.113   0.083   0.357   0.030  -0.055
105   N        -1.231  -1.208  -1.255  -1.738  -1.785  -1.588  -1.090  -1.059  -1.069
106   E         1.292   1.334   1.369   1.204   1.275   1.348   1.390   1.446   1.502
107   R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
108   Y         0.377   0.176   0.138   1.074   0.769   0.678   0.357   0.030  -0.055
109   E         0.377   0.466   0.177   0.378   0.507   0.137   0.357   0.488   0.011
110   R        -0.470  -0.594  -0.665  -0.725  -0.944  -1.183  -0.470  -0.639  -0.718
111   L        -0.000   0.075   0.083   0.181   0.300   0.303  -0.263  -0.141  -0.154
112   A         0.377   0.176   0.138   0.711   0.412   0.347   0.357   0.030  -0.055
113   A        -0.470  -0.368  -0.643  -0.098   0.043  -0.361  -0.470  -0.326  -0.689
114   K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
115   M         0.377   0.176   0.138   0.933   0.603   0.495   0.357   0.030  -0.055
116   H         1.292   1.334   1.369   1.923   1.974   2.018   1.390   1.446   1.502
117   A         0.377   0.176   0.138   0.711   0.412   0.347   0.357   0.030  -0.055
118   K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
119   K         0.377   0.176   0.138  -0.138  -0.362  -0.373   0.357   0.030  -0.055
120   V         0.377   0.176   0.138   0.911   0.633   0.560   0.357   0.030  -0.055
121   E        -0.115  -0.040   0.045  -0.245  -0.059   0.067  -0.470  -0.344  -0.221
122   R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
123   M        -0.762  -0.822  -0.710  -0.543  -0.718  -0.553  -0.883  -0.923  -0.778
124   R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
125   R        -0.000   0.075   0.083  -0.674  -0.539  -0.582  -0.263  -0.141  -0.154
126   R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
127   E         1.292   1.334   1.369   1.204   1.275   1.348   1.390   1.446   1.502
128   K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
129   R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
130   N         1.292   1.334   1.369   1.829   1.887   1.931   1.390   1.446   1.502
131   K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
132   A        -0.762  -0.725  -0.712  -0.523  -0.454  -0.427  -0.883  -0.830  -0.782
133   L         1.292   1.334   1.369   1.554   1.625   1.675   1.390   1.446   1.502
134   K         1.292   1.334   1.369   0.703   0.803   0.881   1.390   1.446   1.502
135   E         1.292   1.334   1.369   1.204   1.275   1.348   1.390   1.446   1.502
136   R         1.292   1.334   1.369   1.204   1.244   1.348   1.390   1.446   1.502
* 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/P53188
Output conservation file - output/P53188
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
