1     M         1.276   1.296   1.342   1.461   1.490   1.554   1.372   1.400   1.467
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     -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    S         0.156   0.212   0.216  -0.126  -0.020  -0.049  -0.129  -0.031  -0.058
38    T        -0.504  -0.457  -0.471  -0.713  -0.630  -0.678  -0.692  -0.623  -0.627
39    S        -0.554  -0.546  -0.491  -0.636  -0.624  -0.536  -0.738  -0.731  -0.652
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    S        -0.581  -0.587  -0.505  -0.830  -0.850  -0.720  -0.789  -0.786  -0.672
42    V        -1.321  -1.378  -1.347  -0.925  -1.031  -1.036  -1.109  -1.159  -1.089
43    R        -0.972  -0.985  -0.958  -1.043  -1.054  -0.952  -0.971  -0.981  -0.913
44    F        -0.755  -0.806  -0.927  -0.690  -0.794  -0.988  -0.695  -0.757  -0.874
45    A        -0.972  -1.052  -0.971  -1.038  -1.151  -1.028  -0.971  -1.039  -0.923
46    F         1.276   1.296   1.342   1.269   1.301   1.373   1.372   1.400   1.467
47    R        -1.104  -1.041  -0.991  -1.104  -1.016  -0.926  -1.109  -1.039  -0.944
48    R         1.276   1.296   1.342   1.291   1.314   1.393   1.372   1.400   1.467
49    F        -0.406  -0.383  -0.436  -0.296  -0.249  -0.308  -0.558  -0.509  -0.582
50    W         0.074   0.127   0.182  -0.112   0.001   0.054  -0.282  -0.188  -0.123
51    Q        -0.406  -0.333  -0.447  -0.277  -0.168  -0.309  -0.558  -0.454  -0.594
52    S         0.554   0.419   0.316   0.611   0.454   0.319   0.545   0.327   0.124
53    E         0.223   0.149   0.207   0.317   0.186   0.260  -0.006  -0.148  -0.076
54    T        -0.126  -0.282  -0.396  -0.047  -0.284  -0.491  -0.144  -0.359  -0.522
55    G         1.276   1.296   1.342   1.269   1.303   1.373   1.372   1.400   1.467
56    P         0.554   0.528   0.324   0.740   0.710   0.399   0.545   0.502   0.140
57    K         0.554   0.640   0.329   0.658   0.768   0.338   0.545   0.674   0.149
58    T         1.276   1.296   1.342   1.242   1.279   1.347   1.372   1.400   1.467
59    V         1.276   1.296   1.342   1.214   1.242   1.321   1.372   1.400   1.467
60    H         1.276   1.296   1.342   1.492   1.522   1.584   1.372   1.400   1.467
61    F         1.276   1.296   1.342   1.269   1.301   1.373   1.372   1.400   1.467
62    W         1.276   1.296   1.342   1.382   1.408   1.480   1.372   1.400   1.467
63    A         1.276   1.296   1.342   1.052   1.073   1.167   1.372   1.400   1.467
64    P         1.276   1.296   1.342   1.371   1.401   1.470   1.372   1.400   1.467
65    T        -0.406  -0.480  -0.456  -0.528  -0.647  -0.636  -0.558  -0.637  -0.606
66    L        -0.492  -0.425  -0.475  -0.537  -0.422  -0.492  -0.695  -0.615  -0.636
67    K         1.276   1.296   1.342   1.285   1.315   1.388   1.372   1.400   1.467
68    W         1.276   1.296   1.342   1.382   1.408   1.480   1.372   1.400   1.467
69    G        -0.972  -0.988  -0.953  -0.986  -0.992  -0.929  -0.971  -0.973  -0.907
70    L         1.276   1.296   1.342   1.125   1.158   1.236   1.372   1.400   1.467
71    V         1.276   1.296   1.342   1.214   1.242   1.321   1.372   1.400   1.467
72    F        -0.972  -0.926  -0.949  -1.064  -1.029  -1.048  -0.971  -0.929  -0.902
73    A         0.554   0.419   0.316   0.409   0.218   0.071   0.545   0.327   0.124
74    G         1.276   1.296   1.342   1.269   1.303   1.373   1.372   1.400   1.467
75    F        -0.623  -0.560  -0.515  -0.812  -0.694  -0.660  -0.833  -0.743  -0.683
76    S        -0.972  -1.000  -0.951  -0.957  -0.983  -0.919  -0.971  -0.986  -0.902
77    D         1.276   1.296   1.342   1.461   1.496   1.554   1.372   1.400   1.467
78    M        -1.452  -1.456  -1.361  -1.270  -1.253  -1.122  -1.247  -1.237  -1.102
79    K        -0.972  -0.885  -0.965  -1.052  -0.946  -0.997  -0.971  -0.862  -0.917
80    R         1.276   1.296   1.342   1.291   1.314   1.393   1.372   1.400   1.467
81    P         0.554   0.419   0.316   0.729   0.544   0.360   0.545   0.327   0.124
82    V        -0.755  -0.856  -0.913  -0.653  -0.807  -0.912  -0.695  -0.813  -0.859
83    E         0.554   0.603   0.320   0.802   0.868   0.489   0.545   0.618   0.133
84    K        -0.126  -0.190  -0.382   0.064  -0.018  -0.298  -0.144  -0.241  -0.502
85    I        -0.406  -0.335  -0.456  -0.571  -0.459  -0.631  -0.558  -0.456  -0.610
86    S         1.276   1.296   1.342   1.203   1.237   1.310   1.372   1.400   1.467
87    G        -0.126  -0.282  -0.396  -0.006  -0.226  -0.439  -0.144  -0.359  -0.522
88    A        -0.406  -0.480  -0.456  -0.534  -0.625  -0.614  -0.558  -0.637  -0.606
89    Q         1.276   1.296   1.342   1.334   1.360   1.434   1.372   1.400   1.467
90    N        -0.406  -0.463  -0.441  -0.290  -0.342  -0.321  -0.558  -0.612  -0.586
91    L        -0.972  -0.869  -0.965  -1.217  -1.073  -1.171  -0.971  -0.851  -0.917
92    S         0.223   0.274   0.224  -0.082  -0.006  -0.088  -0.006   0.079  -0.043
93    L         1.276   1.296   1.342   1.125   1.158   1.236   1.372   1.400   1.467
94    L        -0.972  -1.052  -0.971  -0.946  -1.018  -0.904  -0.971  -1.039  -0.923
95    S         0.223   0.274   0.224  -0.082  -0.006  -0.088  -0.006   0.079  -0.043
96    T         1.276   1.296   1.342   1.242   1.279   1.347   1.372   1.400   1.467
97    A         0.223   0.274   0.224   0.071   0.162   0.024  -0.006   0.079  -0.043
98    L        -0.972  -0.900  -0.951  -1.220  -1.130  -1.162  -0.971  -0.891  -0.905
99    I         1.276   1.296   1.342   1.280   1.309   1.383   1.372   1.400   1.467
100   W         1.276   1.296   1.342   1.382   1.408   1.480   1.372   1.400   1.467
101   T         1.276   1.296   1.342   1.242   1.279   1.347   1.372   1.400   1.467
102   R         1.276   1.296   1.342   1.291   1.314   1.393   1.372   1.400   1.467
103   W         1.276   1.296   1.342   1.382   1.408   1.480   1.372   1.400   1.467
104   S        -0.623  -0.574  -0.494  -0.775  -0.687  -0.568  -0.833  -0.763  -0.656
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   F         0.074   0.076   0.169  -0.207  -0.221  -0.069  -0.282  -0.286  -0.147
107   V         0.074   0.076   0.169  -0.157  -0.159  -0.007  -0.282  -0.286  -0.147
108   I         0.554   0.419   0.316   0.640   0.454   0.282   0.545   0.327   0.124
109   K        -0.126  -0.211  -0.377   0.053  -0.071  -0.310  -0.144  -0.267  -0.495
110   P         1.276   1.296   1.342   1.371   1.401   1.470   1.372   1.400   1.467
111   R         0.074   0.120   0.180  -0.092  -0.015   0.072  -0.282  -0.202  -0.127
112   N         1.276   1.296   1.342   1.334   1.368   1.434   1.372   1.400   1.467
113   I        -0.492  -0.446  -0.477  -0.321  -0.258  -0.299  -0.695  -0.634  -0.638
114   L         0.554   0.419   0.316   0.494   0.320   0.163   0.545   0.327   0.124
115   L         0.554   0.419   0.316   0.506   0.337   0.189   0.545   0.327   0.124
116   A         1.276   1.296   1.342   1.052   1.073   1.167   1.372   1.400   1.467
117   S        -0.126  -0.282  -0.396  -0.094  -0.320  -0.540  -0.144  -0.359  -0.522
118   V         1.276   1.296   1.342   1.214   1.242   1.321   1.372   1.400   1.467
119   N         1.276   1.296   1.342   1.334   1.368   1.434   1.372   1.400   1.467
120   S         0.223   0.274   0.224   0.128   0.215   0.098  -0.006   0.079  -0.043
121   F         1.276   1.296   1.342   1.269   1.301   1.373   1.372   1.400   1.467
122   L         1.276   1.296   1.342   1.125   1.158   1.236   1.372   1.400   1.467
123   C        -0.755  -0.806  -0.927  -0.572  -0.675  -0.845  -0.695  -0.757  -0.874
124   L        -1.104  -1.043  -0.995  -1.132  -1.044  -0.924  -1.109  -1.041  -0.948
125   T         0.074   0.117   0.172  -0.181  -0.104  -0.027  -0.282  -0.208  -0.142
126   A         0.223   0.149   0.207  -0.055  -0.186  -0.081  -0.006  -0.148  -0.076
127   G        -0.755  -0.839  -0.936  -0.657  -0.813  -1.009  -0.695  -0.795  -0.885
128   Y         0.074   0.076   0.169  -0.015  -0.038   0.110  -0.282  -0.286  -0.147
129   Q         1.276   1.296   1.342   1.334   1.360   1.434   1.372   1.400   1.467
130   L        -0.406  -0.425  -0.451  -0.571  -0.623  -0.622  -0.558  -0.602  -0.602
131   G        -1.321  -1.195  -1.340  -1.250  -1.051  -1.311  -1.109  -0.971  -1.083
132   R         1.276   1.296   1.342   1.291   1.314   1.393   1.372   1.400   1.467
133   I         0.554   0.611   0.328   0.625   0.703   0.272   0.545   0.631   0.147
134   A        -1.104  -1.043  -0.989  -1.393  -1.311  -1.196  -1.109  -1.041  -0.943
135   N        -0.972  -1.015  -0.965  -0.736  -0.804  -0.718  -0.971  -1.007  -0.919
136   Y         0.554   0.528   0.324   0.820   0.789   0.495   0.545   0.502   0.140
137   R         0.074   0.076   0.169  -0.061  -0.069   0.084  -0.282  -0.286  -0.147
138   I        -1.801  -1.733  -1.664  -1.625  -1.519  -1.447  -1.384  -1.316  -1.208
139   R        -1.452  -1.443  -1.369  -1.271  -1.262  -1.119  -1.247  -1.228  -1.108
140   N        -1.104  -1.051  -0.991  -1.096  -1.002  -0.915  -1.109  -1.046  -0.945
141   G         0.223   0.149   0.207   0.159   0.029   0.107  -0.006  -0.148  -0.076
142   D        -0.755  -0.839  -0.936  -0.405  -0.530  -0.745  -0.695  -0.795  -0.885
143   S        -0.972  -1.046  -0.963  -0.994  -1.081  -0.963  -0.971  -1.032  -0.917
144   I        -0.623  -0.560  -0.502  -0.709  -0.607  -0.527  -0.833  -0.742  -0.667
145   S        -1.065  -0.974  -0.966  -1.170  -1.086  -0.990  -1.067  -0.968  -0.920
146   Q         1.276   1.296   1.342   1.334   1.359   1.434   1.372   1.400   1.467
147   L        -1.471  -1.470  -1.378  -1.591  -1.599  -1.494  -1.254  -1.245  -1.115
148   C        -0.911  -0.976  -0.962  -0.699  -0.788  -0.757  -0.879  -0.956  -0.913
149   S        -1.065  -0.965  -0.983  -1.037  -0.881  -0.896  -1.067  -0.957  -0.936
150   Y         0.395   0.320   0.243   0.569   0.447   0.279   0.291   0.159  -0.007
151   I        -0.251  -0.329  -0.442  -0.187  -0.320  -0.535  -0.316  -0.427  -0.585
152   L        -0.504  -0.563  -0.483  -0.705  -0.773  -0.638  -0.692  -0.752  -0.645
153   S        -1.065  -1.087  -0.979  -1.148  -1.200  -1.033  -1.067  -1.077  -0.932
154   G         0.483   0.366   0.284   0.501   0.325   0.153   0.434   0.238   0.067
155   A        -0.251  -0.160  -0.413  -0.318  -0.195  -0.532  -0.316  -0.188  -0.546
156   D        -1.878  -1.845  -1.694  -1.713  -1.629  -1.457  -1.442  -1.402  -1.229
157   E        -0.911  -0.819  -0.925  -0.728  -0.580  -0.803  -0.879  -0.764  -0.873
158   S        -1.878  -1.845  -1.694  -1.883  -1.828  -1.618  -1.442  -1.402  -1.229
159   K        -1.065  -1.021  -0.976  -1.021  -0.964  -0.859  -1.067  -1.011  -0.929
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -         0.286   0.256   0.224   0.361   0.312   0.215   0.106   0.047  -0.043
166   K        -1.878  -1.846  -1.694  -1.824  -1.786  -1.562  -1.442  -1.403  -1.229
167   E        -1.471  -1.473  -1.377  -1.223  -1.274  -1.122  -1.254  -1.246  -1.115
168   I        -0.972  -0.999  -0.950  -0.834  -0.873  -0.802  -0.971  -0.985  -0.902
169   T        -1.801  -1.800  -1.687  -1.628  -1.645  -1.517  -1.384  -1.372  -1.224
170   T        -1.801  -1.800  -1.687  -1.812  -1.837  -1.614  -1.384  -1.372  -1.224
171   G        -1.321  -1.331  -1.334  -1.169  -1.224  -1.234  -1.109  -1.115  -1.077
172   R        -0.972  -0.885  -0.965  -1.030  -0.924  -0.965  -0.971  -0.862  -0.917
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P38857
Output conservation file - output/P38857
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
