1     M         1.270   1.276   1.285   1.647   1.661   1.662   1.325   1.330   1.341
2     G         1.270   1.276   1.285   1.507   1.494   1.524   1.325   1.330   1.341
3     L         1.270   1.276   1.285   1.453   1.456   1.471   1.325   1.330   1.341
4     C         1.270   1.276   1.285   1.750   1.752   1.763   1.325   1.330   1.341
5     G        -0.313  -0.307  -0.370  -0.208  -0.216  -0.337  -0.396  -0.386  -0.479
6     S         1.270   1.276   1.285   1.216   1.172   1.238   1.325   1.330   1.341
7     K         1.270   1.276   1.285   0.811   0.787   0.839   1.325   1.330   1.341
8     T        -0.454  -0.448  -0.425  -0.701  -0.686  -0.648  -0.611  -0.600  -0.563
9     Q        -0.454  -0.448  -0.425  -0.469  -0.456  -0.420  -0.611  -0.600  -0.563
10    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    P         1.270   1.276   1.285   1.577   1.568   1.593   1.325   1.330   1.341
13    S         1.270   1.276   1.285   1.216   1.172   1.238   1.325   1.330   1.341
14    Q        -0.313  -0.358  -0.374  -0.385  -0.503  -0.556  -0.396  -0.463  -0.485
15    T        -1.462  -1.448  -1.424  -1.130  -1.116  -1.071  -1.257  -1.235  -1.198
16    T        -0.313  -0.358  -0.374  -0.150  -0.228  -0.231  -0.396  -0.463  -0.485
17    T        -1.462  -1.448  -1.424  -1.304  -1.304  -1.242  -1.257  -1.235  -1.198
18    V        -1.462  -1.448  -1.424  -1.227  -1.237  -1.166  -1.257  -1.235  -1.198
19    A        -0.313  -0.307  -0.370  -0.517  -0.541  -0.615  -0.396  -0.386  -0.479
20    T        -1.462  -1.448  -1.424  -1.584  -1.616  -1.517  -1.257  -1.235  -1.198
21    K        -0.313  -0.244  -0.351  -0.266  -0.097  -0.381  -0.396  -0.292  -0.451
22    A        -0.313  -0.358  -0.374  -0.517  -0.632  -0.622  -0.396  -0.463  -0.485
23    R        -0.313  -0.358  -0.374  -0.291  -0.332  -0.413  -0.396  -0.463  -0.485
24    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    P         1.270   1.276   1.285   1.607   1.608   1.622   1.325   1.330   1.341
27    I        -0.454  -0.448  -0.425  -0.043  -0.032  -0.001  -0.611  -0.600  -0.563
28    N        -0.454  -0.448  -0.425  -0.218  -0.206  -0.173  -0.611  -0.600  -0.563
29    R         1.270   1.276   1.285   1.375   1.377   1.394   1.325   1.330   1.341
30    D        -0.454  -0.448  -0.425  -0.350  -0.338  -0.303  -0.611  -0.600  -0.563
31    T        -0.454  -0.448  -0.425  -0.401  -0.388  -0.353  -0.611  -0.600  -0.563
32    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    H         1.270   1.276   1.285   1.675   1.675   1.689   1.325   1.330   1.341
41    K        -0.454  -0.448  -0.425  -0.889  -0.873  -0.833  -0.611  -0.600  -0.563
42    E        -1.462  -1.448  -1.424  -1.965  -1.917  -1.891  -1.257  -1.235  -1.198
43    K        -0.313  -0.358  -0.374  -0.644  -0.719  -0.684  -0.396  -0.463  -0.485
44    K        -0.313  -0.307  -0.370  -0.833  -0.871  -0.909  -0.396  -0.386  -0.479
45    D        -0.313  -0.358  -0.374  -0.093  -0.177  -0.230  -0.396  -0.463  -0.485
46    K        -1.462  -1.448  -1.424  -1.512  -1.458  -1.446  -1.257  -1.235  -1.198
47    K        -1.462  -1.448  -1.424  -1.646  -1.590  -1.578  -1.257  -1.235  -1.198
48    K        -0.313  -0.307  -0.370  -0.873  -0.893  -0.956  -0.396  -0.386  -0.479
49    K        -0.313  -0.358  -0.374  -0.766  -0.858  -0.832  -0.396  -0.463  -0.485
50    T        -0.313  -0.307  -0.370  -0.150  -0.156  -0.226  -0.396  -0.386  -0.479
51    Q        -0.454  -0.448  -0.425  -0.444  -0.456  -0.395  -0.611  -0.600  -0.563
52    L        -0.454  -0.448  -0.425  -0.872  -0.888  -0.816  -0.611  -0.600  -0.563
53    K         1.270   1.276   1.285   0.748   0.726   0.778   1.325   1.330   1.341
54    S         1.270   1.276   1.285   1.216   1.172   1.238   1.325   1.330   1.341
55    T        -0.313  -0.307  -0.370  -0.191  -0.200  -0.275  -0.396  -0.386  -0.479
56    T        -0.313  -0.358  -0.374  -0.191  -0.278  -0.281  -0.396  -0.463  -0.485
57    V        -1.462  -1.448  -1.424  -1.195  -1.144  -1.134  -1.257  -1.235  -1.198
58    P        -0.313  -0.307  -0.370   0.003   0.005  -0.101  -0.396  -0.386  -0.479
59    V        -1.462  -1.448  -1.424  -0.975  -0.894  -0.918  -1.257  -1.235  -1.198
60    V        -0.454  -0.448  -0.425  -0.106  -0.095  -0.063  -0.611  -0.600  -0.563
61    Q        -0.454  -0.448  -0.425  -0.889  -0.873  -0.833  -0.611  -0.600  -0.563
62    R        -0.454  -0.448  -0.425  -0.522  -0.508  -0.472  -0.611  -0.600  -0.563
63    K         1.270   1.276   1.285   0.725   0.731   0.754   1.325   1.330   1.341
64    E        -0.454  -0.448  -0.425  -1.170  -1.152  -1.109  -0.611  -0.600  -0.563
65    G        -0.454  -0.448  -0.425  -0.831  -0.816  -0.776  -0.611  -0.600  -0.563
66    S        -0.454  -0.448  -0.425  -0.452  -0.439  -0.403  -0.611  -0.600  -0.563
67    K        -0.454  -0.448  -0.425  -0.831  -0.816  -0.776  -0.611  -0.600  -0.563
68    L        -0.454  -0.448  -0.425  -0.300  -0.288  -0.254  -0.611  -0.600  -0.563
69    T        -0.454  -0.448  -0.425  -0.350  -0.338  -0.303  -0.611  -0.600  -0.563
70    D        -0.313  -0.307  -0.370  -0.101  -0.031  -0.231  -0.396  -0.386  -0.479
71    T        -0.313  -0.244  -0.351  -0.037   0.069  -0.117  -0.396  -0.292  -0.451
72    S        -1.462  -1.448  -1.424  -1.383  -1.380  -1.319  -1.257  -1.235  -1.198
73    D        -0.454  -0.448  -0.425  -0.218  -0.206  -0.173  -0.611  -0.600  -0.563
74    P        -1.462  -1.448  -1.424  -1.238  -1.178  -1.176  -1.257  -1.235  -1.198
75    S        -0.313  -0.307  -0.370  -0.455  -0.454  -0.560  -0.396  -0.386  -0.479
76    K        -1.462  -1.448  -1.424  -1.512  -1.447  -1.446  -1.257  -1.235  -1.198
77    N        -1.462  -1.448  -1.424  -0.955  -0.924  -0.898  -1.257  -1.235  -1.198
78    K        -0.313  -0.358  -0.374  -0.766  -0.858  -0.832  -0.396  -0.463  -0.485
79    V        -1.462  -1.448  -1.424  -0.935  -0.910  -0.879  -1.257  -1.235  -1.198
80    S         1.270   1.276   1.285   1.216   1.172   1.238   1.325   1.330   1.341
81    P        -0.313  -0.307  -0.370  -0.142  -0.147  -0.276  -0.396  -0.386  -0.479
82    K        -0.313  -0.358  -0.374  -0.747  -0.785  -0.809  -0.396  -0.463  -0.485
83    E         1.270   1.276   1.285   1.198   1.269   1.220   1.325   1.330   1.341
84    A         1.270   1.276   1.285   1.141   1.130   1.164   1.325   1.330   1.341
85    A         1.270   1.276   1.285   1.141   1.130   1.164   1.325   1.330   1.341
86    R         1.270   1.276   1.285   1.382   1.456   1.401   1.325   1.330   1.341
87    L        -0.313  -0.358  -0.374  -0.053  -0.121  -0.142  -0.396  -0.463  -0.485
88    A         1.270   1.276   1.285   1.141   1.130   1.164   1.325   1.330   1.341
89    A         1.270   1.276   1.285   1.141   1.130   1.164   1.325   1.330   1.341
90    E         1.270   1.276   1.285   1.198   1.269   1.220   1.325   1.330   1.341
91    K        -0.313  -0.358  -0.374  -0.700  -0.773  -0.752  -0.396  -0.463  -0.485
92    R         1.270   1.276   1.285   1.382   1.456   1.401   1.325   1.330   1.341
93    F        -1.462  -1.448  -1.424  -0.712  -0.684  -0.659  -1.257  -1.235  -1.198
94    Q        -0.313  -0.358  -0.374  -0.241  -0.334  -0.377  -0.396  -0.463  -0.485
95    E        -1.462  -1.448  -1.424  -1.634  -1.580  -1.566  -1.257  -1.235  -1.198
96    T        -1.462  -1.448  -1.424  -1.429  -1.408  -1.365  -1.257  -1.235  -1.198
97    N        -1.462  -1.448  -1.424  -1.109  -1.062  -1.050  -1.257  -1.235  -1.198
98    E        -1.462  -1.448  -1.424  -1.512  -1.451  -1.446  -1.257  -1.235  -1.198
99    K        -0.313  -0.358  -0.374  -0.873  -0.978  -0.962  -0.396  -0.463  -0.485
100   Y        -0.313  -0.244  -0.351   0.173   0.273   0.118  -0.396  -0.292  -0.451
101   N        -1.462  -1.448  -1.424  -1.315  -1.338  -1.253  -1.257  -1.235  -1.198
102   K         1.270   1.276   1.285   0.811   0.787   0.839   1.325   1.330   1.341
103   G        -0.313  -0.358  -0.374  -0.175  -0.297  -0.305  -0.396  -0.463  -0.485
104   E         1.270   1.276   1.285   1.198   1.269   1.220   1.325   1.330   1.341
105   L         1.270   1.276   1.285   1.453   1.456   1.471   1.325   1.330   1.341
106   G        -0.313  -0.358  -0.374  -0.175  -0.297  -0.305  -0.396  -0.463  -0.485
107   K        -0.313  -0.358  -0.374  -0.700  -0.773  -0.752  -0.396  -0.463  -0.485
108   K         1.270   1.276   1.285   0.811   0.787   0.839   1.325   1.330   1.341
109   L         1.270   1.276   1.285   1.453   1.456   1.471   1.325   1.330   1.341
110   A        -0.313  -0.307  -0.370  -0.526  -0.494  -0.626  -0.396  -0.386  -0.479
111   Q        -0.313  -0.358  -0.374  -0.021  -0.077  -0.108  -0.396  -0.463  -0.485
112   E         1.270   1.276   1.285   1.198   1.269   1.220   1.325   1.330   1.341
113   R         1.270   1.276   1.285   1.382   1.456   1.401   1.325   1.330   1.341
114   A         1.270   1.276   1.285   1.141   1.130   1.164   1.325   1.330   1.341
115   K         1.270   1.276   1.285   0.811   0.787   0.839   1.325   1.330   1.341
116   S         1.270   1.276   1.285   1.216   1.172   1.238   1.325   1.330   1.341
117   H        -0.313  -0.358  -0.374   0.010  -0.029  -0.113  -0.396  -0.463  -0.485
118   K         1.270   1.276   1.285   0.811   0.787   0.839   1.325   1.330   1.341
119   T        -0.313  -0.307  -0.370  -0.325  -0.349  -0.437  -0.396  -0.386  -0.479
120   R        -1.462  -1.448  -1.424  -1.488  -1.408  -1.423  -1.257  -1.235  -1.198
121   L        -1.462  -1.448  -1.424  -0.975  -0.937  -0.918  -1.257  -1.235  -1.198
122   M         1.270   1.276   1.285   1.647   1.661   1.662   1.325   1.330   1.341
123   E         1.270   1.276   1.285   1.198   1.269   1.220   1.325   1.330   1.341
124   E        -0.313  -0.358  -0.374  -0.224  -0.206  -0.281  -0.396  -0.463  -0.485
125   A         1.270   1.276   1.285   1.141   1.130   1.164   1.325   1.330   1.341
126   E        -0.313  -0.358  -0.374  -0.342  -0.342  -0.424  -0.396  -0.463  -0.485
127   K        -0.313  -0.307  -0.370  -0.607  -0.613  -0.637  -0.396  -0.386  -0.479
128   K        -0.454  -0.448  -0.425  -0.947  -0.931  -0.890  -0.611  -0.600  -0.563
129   H        -0.454  -0.448  -0.425  -0.202  -0.190  -0.157  -0.611  -0.600  -0.563
130   A         1.270   1.276   1.285   1.280   1.283   1.301   1.325   1.330   1.341
131   E         1.270   1.276   1.285   1.109   1.113   1.133   1.325   1.330   1.341
132   R         1.270   1.276   1.285   1.375   1.377   1.394   1.325   1.330   1.341
133   E         1.270   1.276   1.285   1.109   1.113   1.133   1.325   1.330   1.341
134   R         1.270   1.276   1.285   1.375   1.377   1.394   1.325   1.330   1.341
135   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   M        -0.454  -0.448  -0.425  -0.218  -0.206  -0.173  -0.611  -0.600  -0.563
138   I        -0.454  -0.448  -0.425  -0.384  -0.371  -0.336  -0.611  -0.600  -0.563
139   Y        -0.454  -0.448  -0.425   0.080   0.090   0.120  -0.611  -0.600  -0.563
140   D         1.270   1.276   1.285   1.584   1.585   1.600   1.325   1.330   1.341
* 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/P53139
Output conservation file - output/P53139
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
