1     M         1.343   1.440   1.499   1.515   1.670   1.760   1.440   1.582   1.683
2     S         1.343   1.440   1.499   1.180   1.340   1.436   1.440   1.582   1.683
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     N        -1.476  -1.308  -1.313  -1.561  -1.326  -1.313  -1.318  -1.124  -1.071
9     T        -1.375  -1.413  -1.310  -1.234  -1.277  -1.127  -1.227  -1.208  -1.069
10    L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
11    F         0.657   0.508   0.448   0.864   0.644   0.494   0.662   0.410   0.275
12    D         0.082   0.173   0.276  -0.268  -0.133   0.042  -0.338  -0.204  -0.053
13    D         0.657   0.508   0.448   0.631   0.435   0.339   0.662   0.410   0.275
14    I        -1.375  -1.291  -1.296  -1.222  -1.091  -1.156  -1.227  -1.094  -1.057
15    F         1.343   1.440   1.499   1.506   1.665   1.752   1.440   1.582   1.683
16    Q        -1.375  -1.070  -1.278  -1.219  -0.845  -1.056  -1.227  -0.927  -1.044
17    V         0.005   0.201  -0.240   0.138   0.396  -0.207  -0.005   0.272  -0.351
18    S        -1.494  -1.391  -1.319  -1.657  -1.425  -1.334  -1.338  -1.187  -1.078
19    E        -0.430  -0.431  -0.373  -0.697  -0.650  -0.566  -0.671  -0.617  -0.544
20    V         0.005  -0.001  -0.277   0.138   0.116  -0.266  -0.005  -0.031  -0.403
21    D         0.657   0.526   0.437   0.604   0.418   0.249   0.662   0.440   0.255
22    P        -1.375  -1.431  -1.313  -1.293  -1.414  -1.258  -1.227  -1.225  -1.073
23    G        -0.864  -1.014  -0.900  -0.740  -0.902  -0.752  -0.894  -1.012  -0.874
24    R         0.320   0.205   0.284   0.322   0.081   0.207   0.106  -0.142  -0.036
25    Y         1.343   1.440   1.499   1.355   1.497   1.605   1.440   1.582   1.683
26    N        -0.295  -0.468  -0.391  -0.277  -0.539  -0.467  -0.449  -0.671  -0.571
27    K        -0.430  -0.271  -0.370  -0.480  -0.266  -0.366  -0.671  -0.467  -0.545
28    V         1.343   1.440   1.499   1.327   1.458   1.578   1.440   1.582   1.683
29    C        -0.430  -0.415  -0.358  -0.568  -0.555  -0.462  -0.671  -0.593  -0.525
30    R         1.343   1.440   1.499   1.406   1.559   1.655   1.440   1.582   1.683
31    I         0.657   0.526   0.437   0.814   0.628   0.426   0.662   0.440   0.255
32    E        -0.430  -0.431  -0.373  -0.555  -0.508  -0.443  -0.671  -0.617  -0.544
33    A        -0.295  -0.262  -0.329  -0.212  -0.107  -0.227  -0.449  -0.370  -0.478
34    A        -1.690  -1.609  -1.617  -1.308  -1.287  -1.234  -1.338  -1.243  -1.177
35    S         1.343   1.440   1.499   1.180   1.340   1.436   1.440   1.582   1.683
36    T        -0.497  -0.486  -0.424  -0.838  -0.847  -0.793  -0.733  -0.689  -0.612
37    T        -1.179  -1.319  -1.305  -1.027  -1.263  -1.290  -1.005  -1.124  -1.064
38    Q        -0.864  -0.816  -0.878  -0.760  -0.666  -0.781  -0.894  -0.794  -0.847
39    D        -1.809  -1.732  -1.643  -1.715  -1.593  -1.447  -1.449  -1.335  -1.198
40    Q        -0.430  -0.299  -0.373  -0.611  -0.423  -0.518  -0.671  -0.498  -0.551
41    C        -0.941  -1.061  -0.918  -0.709  -0.845  -0.666  -1.005  -1.066  -0.892
42    K        -1.179  -1.284  -1.292  -0.907  -1.128  -1.106  -1.005  -1.095  -1.053
43    L        -0.295  -0.262  -0.329  -0.483  -0.405  -0.476  -0.449  -0.370  -0.478
44    T         0.657   0.526   0.437   0.778   0.638   0.487   0.662   0.440   0.255
45    L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
46    D         1.343   1.440   1.499   1.237   1.384   1.492   1.440   1.582   1.683
47    I         0.320   0.295   0.302   0.343   0.274   0.233   0.106   0.029  -0.002
48    N         1.343   1.440   1.499   1.411   1.595   1.659   1.440   1.582   1.683
49    V        -1.060  -0.869  -0.906  -1.275  -1.016  -1.022  -1.116  -0.900  -0.883
50    E         0.005  -0.041  -0.265   0.195   0.138  -0.177  -0.005  -0.086  -0.385
51    L         0.657   0.508   0.448   0.509   0.318   0.247   0.662   0.410   0.275
52    F         0.657   0.508   0.448   0.898   0.707   0.581   0.662   0.410   0.275
53    P         1.343   1.440   1.499   1.542   1.700   1.786   1.440   1.582   1.683
54    V        -0.610  -0.648  -0.830  -0.464  -0.595  -0.815  -0.560  -0.602  -0.793
55    A        -1.809  -1.635  -1.626  -1.624  -1.419  -1.382  -1.449  -1.261  -1.186
56    A        -1.809  -1.504  -1.620  -1.721  -1.317  -1.453  -1.449  -1.163  -1.182
57    Q        -1.494  -1.380  -1.313  -1.353  -1.235  -1.085  -1.338  -1.184  -1.074
58    D        -0.295  -0.453  -0.375  -0.412  -0.651  -0.528  -0.449  -0.647  -0.551
59    S        -1.375  -1.448  -1.318  -1.410  -1.491  -1.296  -1.227  -1.237  -1.077
60    L         0.005  -0.106  -0.285  -0.085  -0.232  -0.470  -0.005  -0.165  -0.415
61    T        -0.610  -0.824  -0.866  -0.446  -0.798  -0.883  -0.560  -0.812  -0.833
62    V        -0.430  -0.495  -0.384  -0.582  -0.705  -0.529  -0.671  -0.713  -0.565
63    T        -1.060  -1.057  -0.925  -1.020  -0.980  -0.791  -1.116  -1.062  -0.901
64    I        -0.430  -0.283  -0.370  -0.721  -0.523  -0.589  -0.671  -0.488  -0.547
65    A         0.320   0.301   0.311   0.302   0.249   0.229   0.106   0.041   0.017
66    S         0.320   0.312   0.300   0.087   0.074   0.026   0.106   0.060  -0.005
67    S         0.005  -0.106  -0.285   0.007  -0.119  -0.372  -0.005  -0.165  -0.415
68    L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
69    N        -1.809  -1.697  -1.637  -1.735  -1.563  -1.501  -1.449  -1.301  -1.193
70    L        -1.375  -1.281  -1.282  -1.624  -1.524  -1.510  -1.227  -1.087  -1.044
71    E        -0.941  -0.931  -0.881  -1.020  -0.968  -0.874  -1.005  -0.940  -0.855
72    D        -1.060  -0.927  -0.904  -1.340  -1.110  -1.069  -1.116  -0.940  -0.879
73    -         0.432   0.563   0.391   0.215   0.445   0.110   0.302   0.502   0.170
74    -        -1.081  -1.036  -0.946  -1.082  -1.051  -0.943  -1.120  -1.042  -0.920
75    -        -1.585  -1.427  -1.343  -1.764  -1.555  -1.407  -1.405  -1.212  -1.097
76    T        -0.235  -0.175  -0.371  -0.151  -0.059  -0.354  -0.338  -0.247  -0.536
77    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    A        -1.476  -1.452  -1.338  -1.574  -1.558  -1.350  -1.318  -1.239  -1.093
85    T        -1.837  -1.732  -1.663  -1.791  -1.622  -1.576  -1.463  -1.327  -1.211
86    R        -0.980  -0.843  -0.895  -1.038  -0.794  -0.939  -1.028  -0.825  -0.866
87    S         0.254   0.198   0.279  -0.020  -0.133  -0.006  -0.011  -0.157  -0.047
88    W         1.343   1.440   1.499   1.635   1.788   1.876   1.440   1.582   1.683
89    R         1.343   1.440   1.499   1.407   1.563   1.656   1.440   1.582   1.683
90    P        -0.756  -0.888  -0.906  -0.496  -0.786  -0.830  -0.737  -0.884  -0.878
91    P         0.597   0.393   0.389   0.854   0.550   0.514   0.569   0.208   0.166
92    Q        -0.980  -0.979  -0.922  -0.841  -0.868  -0.739  -1.028  -0.986  -0.896
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    A        -1.116  -1.010  -0.922  -1.225  -1.098  -0.950  -1.173  -1.014  -0.897
97    G        -0.756  -0.716  -0.880  -0.669  -0.670  -0.919  -0.737  -0.704  -0.849
98    D        -0.484  -0.340  -0.380  -0.736  -0.484  -0.540  -0.737  -0.522  -0.556
99    R        -0.106  -0.310  -0.366   0.091  -0.204  -0.302  -0.157  -0.451  -0.530
100   S         0.597   0.393   0.389   0.499   0.221   0.184   0.569   0.208   0.166
101   L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
102   A         0.657   0.508   0.448   0.802   0.602   0.506   0.662   0.410   0.275
103   D         0.657   0.508   0.448   0.631   0.435   0.339   0.662   0.410   0.275
104   D         0.005  -0.310  -0.321   0.008  -0.468  -0.512  -0.005  -0.437  -0.465
105   Y         0.657   0.508   0.448   0.754   0.554   0.459   0.662   0.410   0.275
106   D         0.657   0.526   0.437   0.631   0.462   0.321   0.662   0.440   0.255
107   Y         1.343   1.440   1.499   1.355   1.497   1.605   1.440   1.582   1.683
108   V         0.657   0.508   0.448   0.734   0.535   0.454   0.662   0.410   0.275
109   M         0.657   0.526   0.437   0.945   0.806   0.667   0.662   0.440   0.255
110   Y         0.320   0.324   0.304   0.344   0.345   0.328   0.106   0.082   0.003
111   G         1.343   1.440   1.499   1.374   1.526   1.623   1.440   1.582   1.683
112   T         0.320   0.205   0.284   0.282   0.055   0.175   0.106  -0.142  -0.036
113   A         0.139   0.339   0.342  -0.076   0.241   0.246  -0.227   0.111   0.077
114   Y         1.343   1.440   1.499   1.355   1.497   1.605   1.440   1.582   1.683
115   K         0.657   0.508   0.448   0.814   0.603   0.516   0.662   0.410   0.275
116   F         0.657   0.508   0.448   0.894   0.697   0.571   0.662   0.410   0.275
117   E         1.343   1.440   1.499   1.369   1.517   1.619   1.440   1.582   1.683
118   E         0.657   0.526   0.437   0.744   0.562   0.393   0.662   0.440   0.255
119   V        -1.060  -1.047  -0.923  -1.140  -1.101  -0.918  -1.116  -1.052  -0.898
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   S        -1.060  -1.060  -0.920  -1.322  -1.290  -1.082  -1.116  -1.065  -0.896
123   K        -1.060  -1.047  -0.923  -1.114  -1.119  -0.934  -1.116  -1.052  -0.898
124   D        -0.295  -0.462  -0.392  -0.392  -0.633  -0.510  -0.449  -0.665  -0.572
125   L        -0.864  -0.773  -0.871  -0.915  -0.762  -0.952  -0.894  -0.753  -0.840
126   I        -1.060  -0.908  -0.905  -1.085  -0.888  -0.902  -1.116  -0.927  -0.880
127   A        -0.295  -0.439  -0.370  -0.324  -0.579  -0.501  -0.449  -0.629  -0.544
128   V         0.657   0.526   0.437   0.726   0.543   0.415   0.662   0.440   0.255
129   Y         1.343   1.440   1.499   1.355   1.497   1.605   1.440   1.582   1.683
130   Y        -1.060  -1.041  -0.925  -1.089  -1.053  -0.866  -1.116  -1.046  -0.900
131   S         1.343   1.440   1.499   1.180   1.340   1.436   1.440   1.582   1.683
132   F         0.657   0.526   0.437   0.898   0.734   0.562   0.662   0.440   0.255
133   G         1.343   1.440   1.499   1.374   1.526   1.623   1.440   1.582   1.683
134   G         1.343   1.440   1.499   1.374   1.526   1.623   1.440   1.582   1.683
135   L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
136   L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
137   M         0.657   0.771   0.470   0.873   1.048   0.546   0.662   0.830   0.315
138   R        -0.549  -0.499  -0.433  -0.531  -0.492  -0.366  -0.783  -0.717  -0.623
139   L         0.657   0.508   0.448   0.509   0.318   0.247   0.662   0.410   0.275
140   E         0.657   0.526   0.437   0.744   0.562   0.393   0.662   0.440   0.255
141   G         1.343   1.440   1.499   1.374   1.526   1.623   1.440   1.582   1.683
142   N        -0.941  -1.061  -0.918  -0.948  -1.079  -0.898  -1.005  -1.066  -0.892
143   Y         0.657   0.508   0.448   0.787   0.615   0.543   0.662   0.410   0.275
144   R         0.657   0.526   0.437   0.806   0.642   0.492   0.662   0.440   0.255
145   N        -1.494  -1.268  -1.305  -1.555  -1.148  -1.239  -1.338  -1.068  -1.065
146   L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
147   N        -0.941  -1.061  -0.918  -1.089  -1.205  -1.027  -1.005  -1.066  -0.892
148   N        -0.610  -0.854  -0.881  -0.372  -0.689  -0.814  -0.560  -0.841  -0.850
149   L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
150   K         0.005  -0.310  -0.321   0.187  -0.314  -0.356  -0.005  -0.437  -0.465
151   Q         0.005  -0.310  -0.321   0.249  -0.276  -0.343  -0.005  -0.437  -0.465
152   E         0.320   0.205   0.284   0.230  -0.047   0.067   0.106  -0.142  -0.036
153   N        -0.610  -0.802  -0.854  -0.329  -0.571  -0.682  -0.560  -0.790  -0.819
154   A         0.139   0.176   0.278  -0.050  -0.056   0.127  -0.227  -0.199  -0.048
155   Y         1.343   1.440   1.499   1.355   1.497   1.605   1.440   1.582   1.683
156   L         0.320   0.567   0.410   0.042   0.402   0.187   0.106   0.509   0.205
157   L         1.343   1.440   1.499   1.102   1.237   1.361   1.440   1.582   1.683
158   I        -1.179  -1.319  -1.305  -0.854  -1.152  -1.075  -1.005  -1.124  -1.064
159   R         0.657   0.526   0.437   0.806   0.654   0.491   0.662   0.440   0.255
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   R        -1.060  -0.906  -0.906  -1.063  -0.837  -0.827  -1.116  -0.924  -0.882
* 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/P20436
Output conservation file - output/P20436
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
