1     M         0.792   0.828   0.875   0.905   0.948   0.999   0.826   0.872   0.938
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     S         0.046   0.226  -0.384   0.068   0.299  -0.521   0.079   0.308  -0.589
9     D        -1.268  -1.391  -1.229  -1.522  -1.586  -1.327  -1.416  -1.491  -1.258
10    E         0.046  -0.301  -0.413   0.028  -0.401  -0.539   0.079  -0.428  -0.636
11    E         0.046   0.225  -0.383  -0.011   0.205  -0.632   0.079   0.306  -0.587
12    H         0.792   0.828   0.875   0.945   0.968   1.030   0.826   0.872   0.938
13    T        -0.356  -0.340  -0.413  -0.390  -0.372  -0.536  -0.503  -0.490  -0.637
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    F         0.792   0.828   0.875   0.941   0.978   1.027   0.826   0.872   0.938
16    E        -0.356  -0.540  -0.462  -0.563  -0.897  -0.788  -0.503  -0.820  -0.721
17    T        -1.048  -1.326  -1.227  -1.000  -1.394  -1.306  -1.084  -1.405  -1.254
18    A        -1.388  -1.471  -1.237  -1.579  -1.760  -1.392  -1.499  -1.596  -1.268
19    D        -1.706  -1.503  -1.770  -1.744  -1.483  -1.780  -1.583  -1.362  -1.525
20    A         0.792   0.828   0.875   0.682   0.751   0.824   0.826   0.872   0.938
21    G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
22    S        -0.610  -0.280  -0.411  -0.872  -0.327  -0.568  -0.918  -0.397  -0.634
23    S        -0.356  -0.116  -0.404  -0.386  -0.014  -0.527  -0.503  -0.150  -0.621
24    A        -2.009  -1.824  -1.782  -1.993  -1.751  -1.647  -1.915  -1.693  -1.538
25    T         0.792   0.828   0.875   0.766   0.825   0.890   0.826   0.872   0.938
26    Y        -0.798  -0.659  -0.464  -0.790  -0.589  -0.320  -1.250  -1.026  -0.724
27    P         0.792   0.828   0.875   0.945   0.978   1.030   0.826   0.872   0.938
28    M        -0.356  -0.227  -0.427  -0.230  -0.053  -0.425  -0.503  -0.314  -0.660
29    Q         0.792   0.828   0.875   1.049   1.070   1.111   0.826   0.872   0.938
30    C         0.792   0.828   0.875   1.089   1.101   1.142   0.826   0.872   0.938
31    S         0.792   0.828   0.875   0.782   0.856   0.903   0.826   0.872   0.938
32    A         0.792   0.828   0.875   0.682   0.751   0.824   0.826   0.872   0.938
33    L         0.792   0.828   0.875   0.766   0.823   0.890   0.826   0.872   0.938
34    R         0.792   0.828   0.875   0.993   1.015   1.068   0.826   0.872   0.938
35    K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
36    N         0.046  -0.301  -0.413   0.377  -0.125  -0.393   0.079  -0.428  -0.636
37    G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
38    F        -0.752  -0.446  -0.430  -0.819  -0.334  -0.355  -1.167  -0.662  -0.666
39    V         0.792   0.828   0.875   0.732   0.761   0.864   0.826   0.872   0.938
40    V         0.792   0.828   0.875   0.732   0.761   0.864   0.826   0.872   0.938
41    I         0.792   0.828   0.875   0.827   0.866   0.938   0.826   0.872   0.938
42    K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
43    S        -1.388  -1.294  -1.238  -1.459  -1.320  -1.219  -1.499  -1.386  -1.268
44    R         0.792   0.828   0.875   0.993   1.015   1.068   0.826   0.872   0.938
45    P         0.792   0.828   0.875   0.945   0.978   1.030   0.826   0.872   0.938
46    C         0.792   0.828   0.875   1.089   1.101   1.142   0.826   0.872   0.938
47    K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
48    I         0.792   0.828   0.875   0.827   0.866   0.938   0.826   0.872   0.938
49    V         0.046   0.066  -0.391   0.124   0.136  -0.480   0.079   0.103  -0.600
50    D         0.792   0.828   0.875   0.606   0.683   0.765   0.826   0.872   0.938
51    M         0.792   0.828   0.875   0.905   0.948   0.999   0.826   0.872   0.938
52    S         0.792   0.828   0.875   0.782   0.856   0.903   0.826   0.872   0.938
53    T         0.792   0.828   0.875   0.766   0.825   0.890   0.826   0.872   0.938
54    S         0.792   0.828   0.875   0.782   0.856   0.903   0.826   0.872   0.938
55    K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
56    T         0.792   0.828   0.875   0.766   0.825   0.890   0.826   0.872   0.938
57    G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
58    K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
59    H         0.792   0.828   0.875   0.945   0.968   1.030   0.826   0.872   0.938
60    G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
61    H         0.792   0.828   0.875   0.945   0.968   1.030   0.826   0.872   0.938
62    A         0.792   0.828   0.875   0.682   0.751   0.824   0.826   0.872   0.938
63    K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
64    V         0.792   0.828   0.875   0.732   0.761   0.864   0.826   0.872   0.938
65    H         0.792   0.828   0.875   0.945   0.968   1.030   0.826   0.872   0.938
66    L        -0.356  -0.340  -0.413  -0.367  -0.343  -0.495  -0.503  -0.490  -0.637
67    V         0.792   0.828   0.875   0.732   0.761   0.864   0.826   0.872   0.938
68    A         0.792   0.828   0.875   0.682   0.751   0.824   0.826   0.872   0.938
69    I        -1.048  -1.033  -1.207  -0.918  -0.913  -1.204  -1.084  -1.058  -1.230
70    D         0.792   0.828   0.875   0.606   0.683   0.765   0.826   0.872   0.938
71    I         0.792   0.828   0.875   0.827   0.866   0.938   0.826   0.872   0.938
72    F         0.792   0.828   0.875   0.941   0.978   1.027   0.826   0.872   0.938
73    T        -0.356  -0.340  -0.413  -0.323  -0.295  -0.420  -0.503  -0.490  -0.637
74    G        -0.356  -0.192  -0.433  -0.404  -0.180  -0.502  -0.503  -0.263  -0.670
75    K        -0.356  -0.340  -0.413  -0.419  -0.402  -0.488  -0.503  -0.490  -0.637
76    K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
77    L        -0.356  -0.340  -0.413  -0.295  -0.267  -0.372  -0.503  -0.490  -0.637
78    E         0.792   0.828   0.875   0.623   0.674   0.778   0.826   0.872   0.938
79    D         0.792   0.828   0.875   0.606   0.683   0.765   0.826   0.872   0.938
80    L        -0.356  -0.340  -0.413  -0.347  -0.318  -0.462  -0.503  -0.490  -0.637
81    S         0.046  -0.301  -0.413   0.203  -0.186  -0.371   0.079  -0.428  -0.636
82    P         0.792   0.828   0.875   0.945   0.978   1.030   0.826   0.872   0.938
83    S         0.792   0.828   0.875   0.782   0.856   0.903   0.826   0.872   0.938
84    T         0.792   0.828   0.875   0.766   0.825   0.890   0.826   0.872   0.938
85    H         0.792   0.828   0.875   0.945   0.968   1.030   0.826   0.872   0.938
86    N         0.792   0.828   0.875   1.001   1.020   1.074   0.826   0.872   0.938
87    M         0.792   0.828   0.875   0.905   0.948   0.999   0.826   0.872   0.938
88    E        -0.610  -0.655  -0.466  -1.002  -1.126  -0.796  -0.918  -1.020  -0.727
89    V         0.792   0.828   0.875   0.732   0.761   0.864   0.826   0.872   0.938
90    P         0.792   0.828   0.875   0.945   0.978   1.030   0.826   0.872   0.938
91    V        -0.752  -0.666  -0.465  -0.963  -0.835  -0.499  -1.167  -1.038  -0.726
92    V         0.792   0.828   0.875   0.732   0.761   0.864   0.826   0.872   0.938
93    K        -0.674  -0.354  -1.168  -0.568  -0.191  -1.267  -0.586  -0.199  -1.182
94    R         0.792   0.828   0.875   0.993   1.015   1.068   0.826   0.872   0.938
95    N        -2.901  -2.526  -2.576  -2.614  -2.181  -2.116  -2.330  -1.963  -1.827
96    E         0.046  -0.301  -0.413  -0.011  -0.481  -0.688   0.079  -0.428  -0.636
97    Y        -0.752  -0.662  -0.459  -0.727  -0.598  -0.306  -1.167  -1.032  -0.715
98    Q         0.792   0.828   0.875   1.049   1.070   1.111   0.826   0.872   0.938
99    L         0.046  -0.301  -0.413   0.170  -0.252  -0.445   0.079  -0.428  -0.636
100   L        -1.706  -1.930  -1.795  -1.564  -1.906  -1.713  -1.583  -1.784  -1.549
101   D        -1.048  -1.326  -1.227  -1.016  -1.314  -1.120  -1.084  -1.405  -1.254
102   I         0.792   0.828   0.875   0.827   0.866   0.938   0.826   0.872   0.938
103   D         0.792   0.828   0.875   0.606   0.683   0.765   0.826   0.872   0.938
104   D         0.046  -0.301  -0.413  -0.026  -0.474  -0.693   0.079  -0.428  -0.636
105   G         0.046  -0.301  -0.413   0.048  -0.420  -0.647   0.079  -0.428  -0.636
106   F        -0.610  -0.511  -0.454  -0.498  -0.374  -0.315  -0.918  -0.771  -0.706
107   L         0.792   0.828   0.875   0.766   0.823   0.890   0.826   0.872   0.938
108   S        -1.048  -1.326  -1.227  -0.900  -1.289  -1.179  -1.084  -1.405  -1.254
109   L         0.792   0.828   0.875   0.766   0.823   0.890   0.826   0.872   0.938
110   M        -0.674  -0.999  -1.210  -0.294  -0.740  -1.070  -0.586  -1.009  -1.234
111   N        -1.268  -1.282  -1.216  -1.275  -1.280  -1.217  -1.416  -1.348  -1.241
112   M        -2.583  -2.502  -2.233  -2.397  -2.329  -1.932  -2.247  -2.101  -1.722
113   D         0.046  -0.301  -0.413   0.017  -0.377  -0.526   0.079  -0.428  -0.636
114   G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
115   D        -2.009  -1.999  -1.791  -2.216  -2.214  -1.872  -1.915  -1.863  -1.546
116   T         0.046  -0.301  -0.413   0.134  -0.334  -0.581   0.079  -0.428  -0.636
117   K         0.792   0.828   0.875   0.669   0.716   0.815   0.826   0.872   0.938
118   D         0.046  -0.301  -0.413   0.016  -0.378  -0.529   0.079  -0.428  -0.636
119   D         0.792   0.828   0.875   0.606   0.683   0.765   0.826   0.872   0.938
120   V         0.792   0.828   0.875   0.732   0.761   0.864   0.826   0.872   0.938
121   K        -1.372  -1.258  -1.224  -1.413  -1.276  -1.146  -1.583  -1.398  -1.253
122   A        -2.781  -2.490  -2.227  -2.773  -2.313  -1.973  -2.413  -2.068  -1.718
123   P         0.792   0.828   0.875   0.945   0.978   1.030   0.826   0.872   0.938
124   E         0.792   0.828   0.875   0.623   0.674   0.778   0.826   0.872   0.938
125   G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
126   E         0.792   0.828   0.875   0.623   0.674   0.778   0.826   0.872   0.938
127   L         0.046   0.066  -0.391   0.157   0.199  -0.457   0.079   0.103  -0.600
128   G         0.046  -0.301  -0.413   0.057  -0.401  -0.614   0.079  -0.428  -0.636
129   D        -1.048  -1.326  -1.227  -1.081  -1.462  -1.306  -1.084  -1.405  -1.254
130   S        -3.099  -2.783  -2.586  -2.877  -2.503  -2.106  -2.496  -2.173  -1.834
131   L        -1.388  -0.902  -1.195  -1.360  -0.674  -1.136  -1.499  -0.864  -1.217
132   Q        -0.610  -0.655  -0.466  -0.588  -0.806  -0.537  -0.918  -1.020  -0.727
133   T        -2.781  -2.625  -2.234  -2.991  -2.756  -2.176  -2.413  -2.174  -1.723
134   A        -2.144  -2.149  -1.800  -2.455  -2.411  -1.886  -2.081  -1.984  -1.554
135   F         0.046  -0.301  -0.413   0.310  -0.182  -0.458   0.079  -0.428  -0.636
136   D        -0.356  -0.542  -0.461  -0.576  -0.895  -0.787  -0.503  -0.822  -0.719
137   E         0.792   0.828   0.875   0.623   0.674   0.778   0.826   0.872   0.938
138   G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
139   K         0.046   0.047  -0.382   0.080   0.090  -0.443   0.079   0.078  -0.585
140   D         0.792   0.828   0.875   0.606   0.683   0.765   0.826   0.872   0.938
141   L         0.046  -0.301  -0.413   0.170  -0.252  -0.445   0.079  -0.428  -0.636
142   M        -1.946  -1.869  -1.785  -1.837  -1.694  -1.559  -1.915  -1.757  -1.540
143   V        -0.356  -0.340  -0.413  -0.399  -0.404  -0.518  -0.503  -0.490  -0.637
144   T         0.046  -0.301  -0.413   0.141  -0.317  -0.556   0.079  -0.428  -0.636
145   I        -0.752  -0.649  -0.454  -1.037  -0.922  -0.587  -1.167  -1.009  -0.707
146   I        -1.268  -1.434  -1.232  -1.275  -1.467  -1.160  -1.416  -1.549  -1.262
147   S        -1.268  -1.254  -1.213  -1.384  -1.248  -1.280  -1.416  -1.313  -1.238
148   A         0.792   0.828   0.875   0.682   0.751   0.824   0.826   0.872   0.938
149   M         0.792   0.828   0.875   0.905   0.948   0.999   0.826   0.872   0.938
150   G         0.792   0.828   0.875   0.682   0.735   0.824   0.826   0.872   0.938
151   E         0.792   0.828   0.875   0.623   0.674   0.778   0.826   0.872   0.938
152   E         0.792   0.828   0.875   0.623   0.674   0.778   0.826   0.872   0.938
153   A        -0.674  -0.687  -1.192  -0.539  -0.524  -1.248  -0.586  -0.593  -1.212
154   A         0.046   0.066  -0.391   0.062   0.113  -0.554   0.079   0.103  -0.600
155   I        -0.356  -0.340  -0.413  -0.321  -0.314  -0.479  -0.503  -0.490  -0.637
156   S        -1.048  -1.326  -1.227  -1.008  -1.421  -1.371  -1.084  -1.405  -1.254
157   F        -2.009  -2.096  -1.799  -1.625  -1.801  -1.391  -1.915  -1.934  -1.553
158   K        -0.356  -0.340  -0.413  -0.419  -0.402  -0.488  -0.503  -0.490  -0.637
159   E        -0.356  -0.340  -0.413  -0.563  -0.544  -0.690  -0.503  -0.490  -0.637
160   A         0.792   0.828   0.875   0.682   0.751   0.824   0.826   0.872   0.938
161   A        -0.674  -0.858  -1.202  -0.291  -0.582  -1.150  -0.586  -0.859  -1.225
162   R        -1.443  -1.532  -1.244  -1.459  -1.568  -1.139  -1.640  -1.667  -1.275
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   T        -1.509  -1.635  -1.779  -1.267  -1.513  -1.767  -1.327  -1.477  -1.534
165   D        -2.482  -2.206  -2.217  -2.531  -2.118  -2.108  -2.147  -1.835  -1.711
* 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/P23301
Output conservation file - output/P23301
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
