1     M         1.256   1.298   1.390   1.586   1.622   1.742   1.323   1.388   1.529
2     S        -0.973  -1.252  -1.190  -0.679  -1.115  -1.075  -0.851  -1.159  -1.049
3     T        -1.846  -1.866  -1.636  -1.497  -1.513  -1.173  -1.575  -1.536  -1.251
4     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.505  -1.466  -1.222  -1.311  -1.215  -0.883  -1.468  -1.388  -1.081
6     I        -1.807  -1.712  -1.634  -1.616  -1.551  -1.486  -1.516  -1.419  -1.249
7     V         0.404   0.267   0.182   0.260   0.099  -0.013   0.377   0.152  -0.030
8     K        -0.398  -0.373  -0.596  -0.501  -0.465  -0.759  -0.412  -0.406  -0.680
9     A        -0.728  -0.631  -0.656  -0.994  -0.844  -0.729  -0.885  -0.811  -0.762
10    S        -0.728  -0.742  -0.642  -0.933  -0.959  -0.888  -0.885  -0.880  -0.742
11    N         0.404   0.267   0.182   0.733   0.499   0.249   0.377   0.152  -0.030
12    W         1.256   1.298   1.390   1.512   1.561   1.678   1.323   1.388   1.529
13    R         1.256   1.298   1.390   1.173   1.217   1.382   1.323   1.388   1.529
14    L        -0.613  -0.558  -0.605  -0.466  -0.359  -0.378  -0.730  -0.632  -0.693
15    V         1.256   1.298   1.390   0.983   1.053   1.215   1.323   1.388   1.529
16    E         1.256   1.298   1.390   1.404   1.435   1.584   1.323   1.388   1.529
17    V        -0.272  -0.287  -0.559  -0.432  -0.483  -0.885  -0.247  -0.288  -0.630
18    G         1.256   1.298   1.390   1.389   1.434   1.570   1.323   1.388   1.529
19    R         1.256   1.298   1.390   1.173   1.217   1.382   1.323   1.388   1.529
20    V         0.473   0.328   0.214   0.321   0.151   0.017   0.478   0.250   0.027
21    V         0.473   0.390   0.226   0.297   0.202  -0.026   0.478   0.347   0.046
22    L         0.473   0.390   0.226   0.507   0.397   0.093   0.478   0.347   0.046
23    I        -0.767  -0.755  -0.633  -1.058  -1.009  -0.776  -0.971  -0.924  -0.736
24    K        -1.846  -1.807  -1.628  -1.671  -1.536  -1.217  -1.575  -1.500  -1.245
25    K        -1.395  -1.261  -1.198  -1.453  -1.325  -1.124  -1.358  -1.202  -1.058
26    G        -0.728  -0.744  -0.645  -0.752  -0.757  -0.665  -0.885  -0.882  -0.745
27    Q        -0.829  -0.814  -0.660  -0.719  -0.671  -0.435  -1.043  -0.979  -0.765
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    S        -0.717  -0.854  -0.677  -0.537  -0.722  -0.466  -0.841  -1.027  -0.786
32    A        -1.324  -1.425  -1.224  -1.438  -1.492  -1.166  -1.253  -1.346  -1.083
33    G         1.256   1.298   1.390   1.364   1.417   1.549   1.323   1.388   1.529
34    K         0.320   0.277   0.188   0.147   0.103  -0.023   0.250   0.168  -0.019
35    L         1.256   1.298   1.390   1.222   1.289   1.425   1.323   1.388   1.529
36    A         1.256   1.298   1.390   0.942   1.038   1.180   1.323   1.388   1.529
37    A        -1.263  -1.266  -1.174  -1.265  -1.223  -1.191  -1.213  -1.175  -1.033
38    I         0.473   0.638   0.246   0.661   0.870   0.259   0.478   0.706   0.082
39    V         0.473   0.328   0.214   0.256   0.054  -0.155   0.478   0.250   0.027
40    E         0.473   0.374   0.217   0.757   0.609   0.402   0.478   0.323   0.032
41    I         1.256   1.298   1.390   1.378   1.435   1.561   1.323   1.388   1.529
42    I        -0.118  -0.086   0.088  -0.378  -0.443  -0.158  -0.488  -0.463  -0.201
43    D         1.256   1.298   1.390   1.483   1.521   1.652   1.323   1.388   1.529
44    Q        -0.118  -0.086   0.088  -0.021   0.035   0.298  -0.488  -0.463  -0.201
45    K         0.473   0.328   0.214   0.339   0.174   0.035   0.478   0.250   0.027
46    K        -0.272   0.125  -0.514  -0.195   0.283  -0.559  -0.247   0.255  -0.570
47    V         0.088   0.152   0.116  -0.350  -0.245  -0.359  -0.126  -0.040  -0.148
48    L         1.256   1.298   1.390   1.222   1.289   1.425   1.323   1.388   1.529
49    I         0.473   0.390   0.226   0.661   0.538   0.218   0.478   0.347   0.046
50    D         1.256   1.298   1.390   1.483   1.521   1.652   1.323   1.388   1.529
51    G         0.473   0.374   0.217   0.720   0.583   0.336   0.478   0.323   0.032
52    P         1.256   1.298   1.390   1.514   1.564   1.679   1.323   1.388   1.529
53    K        -1.846  -1.781  -1.626  -1.728  -1.568  -1.280  -1.575  -1.483  -1.245
54    A        -0.844  -0.637  -0.652  -0.922  -0.628  -0.692  -1.039  -0.815  -0.757
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    G        -0.545  -0.661  -0.631  -0.411  -0.635  -0.651  -0.609  -0.769  -0.726
60    V        -0.973  -1.042  -1.153  -1.009  -1.119  -1.218  -0.851  -0.934  -1.010
61    P        -0.613  -0.596  -0.600  -0.370  -0.365  -0.459  -0.730  -0.681  -0.686
62    R         1.256   1.298   1.390   1.173   1.217   1.382   1.323   1.388   1.529
63    Q         0.473   0.390   0.226   0.743   0.650   0.381   0.478   0.347   0.046
64    A        -0.767  -0.552  -0.623  -1.333  -1.013  -0.989  -0.971  -0.721  -0.722
65    I        -0.272  -0.502  -0.592  -0.067  -0.453  -0.724  -0.247  -0.555  -0.674
66    N        -1.622  -1.572  -1.610  -1.146  -1.141  -1.301  -1.334  -1.276  -1.230
67    L         0.473   0.374   0.217   0.599   0.500   0.315   0.478   0.323   0.032
68    G        -0.973  -1.076  -1.160  -0.716  -0.930  -1.164  -0.851  -0.976  -1.018
69    Q        -1.846  -1.897  -1.647  -1.683  -1.725  -1.376  -1.575  -1.563  -1.260
70    V        -0.272  -0.243  -0.551  -0.324  -0.281  -0.636  -0.247  -0.222  -0.620
71    V        -0.272  -0.502  -0.592  -0.352  -0.649  -0.753  -0.247  -0.555  -0.674
72    L         1.256   1.298   1.390   1.222   1.289   1.425   1.323   1.388   1.529
73    T         1.256   1.298   1.390   1.394   1.457   1.574   1.323   1.388   1.529
74    P         0.473   0.374   0.217   0.886   0.762   0.540   0.478   0.323   0.032
75    L        -0.767  -0.795  -0.645  -0.776  -0.758  -0.499  -0.971  -0.968  -0.749
76    T        -0.118   0.147   0.155  -0.511  -0.100  -0.064  -0.488  -0.047  -0.078
77    F        -1.486  -1.402  -1.211  -1.429  -1.393  -1.064  -1.455  -1.326  -1.071
78    A        -1.982  -1.742  -1.631  -1.958  -1.592  -1.432  -1.696  -1.443  -1.247
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    L         0.088   0.121   0.114  -0.096  -0.062  -0.153  -0.126  -0.093  -0.153
81    P         0.473   0.328   0.214   0.800   0.577   0.315   0.478   0.250   0.027
82    R         1.256   1.298   1.390   1.173   1.217   1.382   1.323   1.388   1.529
83    G         1.256   1.298   1.390   1.389   1.434   1.570   1.323   1.388   1.529
84    A        -0.272  -0.300  -0.559  -0.336  -0.331  -0.616  -0.247  -0.303  -0.630
85    R         0.088   0.121   0.114  -0.140  -0.124  -0.183  -0.126  -0.093  -0.153
86    T        -0.118  -0.079   0.078  -0.182  -0.145   0.079  -0.488  -0.450  -0.219
87    A        -1.351  -1.205  -1.174  -1.565  -1.295  -1.236  -1.334  -1.150  -1.036
88    T        -0.767  -0.753  -0.634  -0.775  -0.757  -0.618  -0.971  -0.920  -0.737
89    V         0.473   0.328   0.214   0.321   0.151   0.017   0.478   0.250   0.027
90    S        -1.846  -1.690  -1.625  -1.810  -1.734  -1.516  -1.575  -1.407  -1.243
91    K         0.473   0.328   0.214   0.273   0.079  -0.140   0.478   0.250   0.027
92    K         0.473   0.390   0.226   0.273   0.174  -0.118   0.478   0.347   0.046
93    W         0.473   0.328   0.214   0.798   0.572   0.309   0.478   0.250   0.027
94    A        -0.613  -0.757  -0.652  -0.906  -1.096  -0.900  -0.730  -0.923  -0.757
95    A         1.256   1.298   1.390   0.942   1.038   1.180   1.323   1.388   1.529
96    A        -0.272  -0.515  -0.590  -0.370  -0.649  -0.729  -0.247  -0.572  -0.672
97    A        -1.846  -1.620  -1.615  -1.488  -1.189  -1.210  -1.575  -1.357  -1.236
98    V        -0.613  -0.711  -0.636  -0.889  -1.044  -0.909  -0.730  -0.844  -0.738
99    C        -1.846  -1.630  -1.612  -1.259  -1.016  -0.957  -1.575  -1.365  -1.234
100   E        -1.846  -1.819  -1.633  -1.782  -1.840  -1.517  -1.575  -1.511  -1.250
101   K        -0.272  -0.248  -0.557  -0.313  -0.287  -0.643  -0.247  -0.243  -0.628
102   W         1.256   1.298   1.390   1.514   1.564   1.679   1.323   1.388   1.529
103   A        -0.613  -0.692  -0.634  -1.005  -1.078  -1.000  -0.730  -0.817  -0.735
104   A        -1.263  -1.205  -1.193  -1.385  -1.275  -1.133  -1.213  -1.168  -1.055
105   S         0.473   0.638   0.246   0.676   0.879   0.361   0.478   0.706   0.082
106   S        -0.973  -1.042  -1.153  -0.650  -0.782  -0.955  -0.851  -0.934  -1.010
107   W         1.256   1.298   1.390   1.514   1.564   1.679   1.323   1.388   1.529
108   A         1.256   1.298   1.390   0.942   1.038   1.180   1.323   1.388   1.529
109   K         1.256   1.298   1.390   1.000   1.077   1.230   1.323   1.388   1.529
110   K         1.256   1.298   1.390   1.000   1.077   1.230   1.323   1.388   1.529
111   I        -0.767  -0.758  -0.647  -0.791  -0.757  -0.578  -0.971  -0.928  -0.752
112   A        -0.272  -0.462  -0.582  -0.391  -0.616  -0.765  -0.247  -0.501  -0.660
113   Q        -0.973  -0.846  -1.136  -0.593  -0.467  -0.899  -0.851  -0.712  -0.993
114   R        -0.613  -0.672  -0.631  -0.761  -0.869  -0.800  -0.730  -0.798  -0.731
115   E         0.473   0.374   0.217   0.690   0.519   0.230   0.478   0.323   0.032
116   R        -0.272  -0.245  -0.553  -0.267  -0.272  -0.787  -0.247  -0.227  -0.623
117   R         1.256   1.298   1.390   1.173   1.217   1.382   1.323   1.388   1.529
118   A        -1.263  -1.243  -1.174  -1.367  -1.309  -1.314  -1.213  -1.150  -1.033
119   A        -0.767  -0.795  -0.645  -0.983  -0.913  -0.649  -0.971  -0.968  -0.749
120   L         1.256   1.298   1.390   1.222   1.289   1.425   1.323   1.388   1.529
121   T        -0.767  -0.769  -0.636  -0.693  -0.650  -0.435  -0.971  -0.941  -0.738
122   D         1.256   1.298   1.390   1.483   1.521   1.652   1.323   1.388   1.529
123   F         1.256   1.298   1.390   1.530   1.574   1.693   1.323   1.388   1.529
124   E         0.088   0.012   0.096   0.240   0.069   0.204  -0.126  -0.284  -0.186
125   R         1.256   1.298   1.390   1.173   1.217   1.382   1.323   1.388   1.529
126   F         1.256   1.298   1.390   1.530   1.574   1.693   1.323   1.388   1.529
127   Q        -0.272  -0.462  -0.582  -0.037  -0.339  -0.672  -0.247  -0.501  -0.660
128   V         1.256   1.298   1.390   0.983   1.053   1.215   1.323   1.388   1.529
129   M         0.088   0.330   0.159   0.332   0.681   0.341  -0.126   0.253  -0.071
130   V         0.088   0.012   0.096  -0.271  -0.427  -0.271  -0.126  -0.284  -0.186
131   L         0.473   0.328   0.214   0.598   0.436   0.307   0.478   0.250   0.027
132   R         0.088   0.126   0.113  -0.255  -0.200  -0.229  -0.126  -0.083  -0.155
133   K         0.473   0.328   0.214   0.307   0.121  -0.050   0.478   0.250   0.027
134   Q         0.473   0.328   0.214   0.746   0.566   0.368   0.478   0.250   0.027
135   K        -0.118   0.147   0.155  -0.557  -0.075  -0.092  -0.488  -0.047  -0.078
136   R         0.473   0.328   0.214   0.457   0.230   0.029   0.478   0.250   0.027
137   Y        -1.351  -1.379  -1.195  -0.968  -1.081  -0.838  -1.334  -1.303  -1.056
138   T        -1.263  -1.226  -1.167  -1.371  -1.265  -1.121  -1.213  -1.130  -1.025
139   V        -0.973  -1.076  -1.160  -0.976  -1.137  -1.162  -0.851  -0.976  -1.018
140   K        -0.973  -1.252  -1.190  -1.031  -1.455  -1.334  -0.851  -1.159  -1.049
141   K         0.473   0.374   0.217   0.279   0.153  -0.119   0.478   0.323   0.032
142   A         1.256   1.298   1.390   0.942   1.038   1.180   1.323   1.388   1.529
143   L        -0.183  -0.080   0.083  -0.704  -0.543  -0.259  -0.609  -0.451  -0.210
144   A         0.473   0.623   0.242   0.221   0.451  -0.121   0.478   0.686   0.075
145   K         1.256   1.298   1.390   1.000   1.077   1.230   1.323   1.388   1.529
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   A         1.256   1.298   1.390   0.942   1.038   1.180   1.323   1.388   1.529
* 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/P36105
Output conservation file - output/P36105
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
