1     M         1.664   1.677   1.716   1.998   2.018   2.080   1.800   1.816   1.870
2     A        -0.233  -0.194  -0.311  -0.218  -0.153  -0.314  -0.289  -0.234  -0.390
3     N        -0.995  -0.952  -0.984  -0.697  -0.621  -0.691  -0.886  -0.834  -0.849
4     T        -0.529  -0.513  -0.459  -1.157  -1.184  -1.040  -0.687  -0.662  -0.587
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    G        -0.529  -0.513  -0.459  -0.868  -0.906  -0.754  -0.687  -0.662  -0.587
21    C        -0.529  -0.513  -0.459  -0.325  -0.286  -0.217  -0.687  -0.662  -0.587
22    L         0.666   0.731   0.545   0.794   0.882   0.623   0.606   0.710   0.390
23    S        -0.233  -0.274  -0.330  -0.284  -0.341  -0.429  -0.289  -0.342  -0.417
24    P        -0.441  -0.453  -0.423  -0.224  -0.229  -0.175  -0.587  -0.593  -0.544
25    G        -0.995  -0.993  -0.975  -0.941  -0.939  -0.912  -0.886  -0.878  -0.839
26    A        -0.233  -0.194  -0.311   0.032   0.101  -0.077  -0.289  -0.234  -0.390
27    F         1.664   1.677   1.716   1.947   1.966   2.029   1.800   1.816   1.870
28    L        -0.233  -0.293  -0.332  -0.063  -0.148  -0.196  -0.289  -0.368  -0.418
29    S        -0.995  -0.996  -0.979  -1.009  -1.011  -0.966  -0.886  -0.881  -0.844
30    K        -0.233  -0.274  -0.330  -0.686  -0.746  -0.802  -0.289  -0.342  -0.417
31    V        -0.233  -0.129  -0.318  -0.127   0.029  -0.258  -0.289  -0.145  -0.400
32    P        -1.548  -1.539  -1.470  -1.644  -1.660  -1.520  -1.184  -1.168  -1.078
33    E        -0.233  -0.293  -0.332  -0.229  -0.342  -0.456  -0.289  -0.368  -0.418
34    F        -0.995  -0.938  -0.976  -0.762  -0.660  -0.744  -0.886  -0.818  -0.841
35    F         0.666   0.653   0.534   0.951   0.932   0.728   0.606   0.584   0.371
36    Q        -1.103  -1.089  -1.029  -1.191  -1.133  -1.072  -0.998  -0.977  -0.894
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    T        -0.233  -0.293  -0.332  -0.138  -0.229  -0.302  -0.289  -0.368  -0.418
40    A        -0.441  -0.449  -0.411  -0.730  -0.765  -0.738  -0.587  -0.588  -0.529
41    N         0.321   0.307   0.356  -0.038  -0.105  -0.033   0.009  -0.018   0.052
42    E        -0.233  -0.280  -0.341  -0.052  -0.119  -0.234  -0.289  -0.350  -0.430
43    K        -0.233  -0.280  -0.341  -0.716  -0.788  -0.856  -0.289  -0.350  -0.430
44    H        -0.441  -0.446  -0.409  -0.670  -0.668  -0.597  -0.587  -0.587  -0.528
45    I        -1.548  -1.539  -1.470  -1.267  -1.237  -1.147  -1.184  -1.168  -1.078
46    T        -0.441  -0.453  -0.423  -0.574  -0.581  -0.517  -0.587  -0.593  -0.544
47    V         0.321   0.307   0.356   0.168   0.135   0.215   0.009  -0.018   0.052
48    R        -0.995  -0.952  -0.984  -0.790  -0.744  -0.801  -0.886  -0.834  -0.849
49    L        -0.995  -0.948  -0.963  -0.818  -0.739  -0.763  -0.886  -0.829  -0.828
50    T         0.321   0.331   0.358   0.077   0.096   0.119   0.009   0.025   0.054
51    A        -0.995  -0.952  -0.984  -0.657  -0.587  -0.651  -0.886  -0.834  -0.849
52    K         1.664   1.677   1.716   1.197   1.211   1.288   1.800   1.816   1.870
53    R         1.664   1.677   1.716   1.955   1.975   2.038   1.800   1.816   1.870
54    L        -0.233  -0.219  -0.326  -0.082  -0.069  -0.212  -0.289  -0.269  -0.410
55    I        -0.411  -0.464  -0.425  -0.294  -0.395  -0.345  -0.531  -0.598  -0.543
56    E        -1.103  -1.089  -1.029  -1.305  -1.236  -1.185  -0.998  -0.977  -0.894
57    H        -1.103  -1.089  -1.029  -1.011  -1.011  -0.895  -0.998  -0.977  -0.894
58    D        -0.411  -0.464  -0.425  -0.248  -0.331  -0.268  -0.531  -0.598  -0.543
59    P        -0.411  -0.393  -0.400  -0.064  -0.029  -0.044  -0.531  -0.505  -0.509
60    V         0.542   0.490   0.466   0.613   0.532   0.496   0.401   0.310   0.252
61    E         0.394   0.347   0.379   0.532   0.468   0.505   0.142   0.054   0.093
62    G         0.394   0.347   0.379   0.180   0.026   0.044   0.142   0.054   0.093
63    N         0.394   0.347   0.379   0.538   0.462   0.505   0.142   0.054   0.093
64    L         0.394   0.347   0.379   0.418   0.331   0.384   0.142   0.054   0.093
65    E         1.664   1.677   1.716   1.867   1.897   1.950   1.800   1.816   1.870
66    F        -0.529  -0.513  -0.459  -0.914  -0.859  -0.799  -0.687  -0.662  -0.587
67    D         1.664   1.677   1.716   1.850   1.870   1.934   1.800   1.816   1.870
68    S        -1.103  -1.089  -1.029  -1.101  -1.058  -0.984  -0.998  -0.977  -0.894
69    T         0.542   0.490   0.466   0.675   0.595   0.560   0.401   0.310   0.252
70    N        -1.103  -1.089  -1.029  -1.543  -1.489  -1.421  -0.998  -0.977  -0.894
71    H        -1.103  -1.089  -1.029  -0.745  -0.723  -0.632  -0.998  -0.977  -0.894
72    P         0.542   0.490   0.466   0.606   0.492   0.390   0.401   0.310   0.252
73    D        -1.103  -1.089  -1.029  -0.925  -0.893  -0.810  -0.998  -0.977  -0.894
74    Y        -0.411  -0.464  -0.425  -0.165  -0.258  -0.209  -0.531  -0.598  -0.543
75    D         1.664   1.677   1.716   1.850   1.870   1.934   1.800   1.816   1.870
76    V        -0.411  -0.464  -0.425  -0.398  -0.484  -0.417  -0.531  -0.598  -0.543
77    S         1.664   1.677   1.716   1.569   1.589   1.656   1.800   1.816   1.870
78    K         0.542   0.490   0.466  -0.078  -0.163  -0.212   0.401   0.310   0.252
79    K        -0.411  -0.407  -0.400  -0.447  -0.415  -0.482  -0.531  -0.524  -0.509
80    A        -0.441  -0.439  -0.419  -0.533  -0.534  -0.503  -0.587  -0.577  -0.539
81    S        -1.548  -1.539  -1.470  -1.245  -1.204  -1.127  -1.184  -1.168  -1.078
82    E        -1.548  -1.539  -1.470  -1.680  -1.674  -1.556  -1.184  -1.168  -1.078
83    I        -0.995  -1.040  -0.999  -0.919  -1.011  -0.973  -0.886  -0.927  -0.864
84    S        -1.548  -1.539  -1.470  -1.340  -1.302  -1.220  -1.184  -1.168  -1.078
85    V        -1.548  -1.539  -1.470  -1.376  -1.345  -1.255  -1.184  -1.168  -1.078
86    S        -0.995  -0.989  -0.975  -1.348  -1.316  -1.267  -0.886  -0.874  -0.840
87    S        -0.233  -0.214  -0.322  -0.069  -0.019  -0.224  -0.289  -0.263  -0.405
88    R        -0.995  -0.952  -0.984  -0.843  -0.759  -0.832  -0.886  -0.834  -0.849
89    S        -0.995  -1.040  -0.999  -0.908  -0.942  -0.871  -0.886  -0.927  -0.864
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    D        -0.441  -0.449  -0.411  -0.536  -0.550  -0.500  -0.587  -0.588  -0.529
94    R        -0.233  -0.194  -0.311  -0.574  -0.521  -0.635  -0.289  -0.234  -0.390
95    E        -0.995  -0.996  -0.979  -0.893  -0.873  -0.880  -0.886  -0.881  -0.844
96    Y         1.664   1.677   1.716   1.981   2.003   2.063   1.800   1.816   1.870
97    P         0.666   0.628   0.524   1.003   0.952   0.790   0.606   0.543   0.353
98    L        -0.233  -0.199  -0.311  -0.102  -0.059  -0.215  -0.289  -0.241  -0.390
99    L        -0.233  -0.219  -0.326  -0.121  -0.097  -0.263  -0.289  -0.269  -0.410
100   I         0.321   0.331   0.358   0.334   0.358   0.376   0.009   0.025   0.054
101   R         0.666   0.628   0.524   0.959   0.901   0.717   0.606   0.543   0.353
102   M        -0.441  -0.400  -0.410  -0.320  -0.266  -0.254  -0.587  -0.537  -0.529
103   S        -0.233  -0.213  -0.297  -0.155  -0.123  -0.219  -0.289  -0.261  -0.372
104   Y        -0.441  -0.405  -0.407  -0.097  -0.044  -0.029  -0.587  -0.542  -0.526
105   G        -0.995  -1.040  -0.999  -0.728  -0.793  -0.740  -0.886  -0.927  -0.864
106   S        -0.233  -0.293  -0.332  -0.246  -0.326  -0.381  -0.289  -0.368  -0.418
107   H        -0.995  -0.952  -0.984  -0.650  -0.586  -0.629  -0.886  -0.834  -0.849
108   D        -0.995  -0.938  -0.976  -0.704  -0.606  -0.677  -0.886  -0.818  -0.841
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   K         0.666   0.653   0.534   0.273   0.257   0.119   0.606   0.584   0.371
118   K         0.666   0.628   0.524   0.266   0.214   0.093   0.606   0.543   0.353
119   T         1.664   1.677   1.716   1.754   1.772   1.838   1.800   1.816   1.870
120   K         1.664   1.677   1.716   1.197   1.211   1.288   1.800   1.816   1.870
121   C        -0.995  -0.952  -0.984  -0.670  -0.621  -0.622  -0.886  -0.834  -0.849
122   S        -0.233  -0.293  -0.332  -0.258  -0.340  -0.397  -0.289  -0.368  -0.418
123   T         1.664   1.677   1.716   1.754   1.772   1.838   1.800   1.816   1.870
124   V        -0.995  -1.004  -0.976  -0.864  -0.879  -0.831  -0.886  -0.890  -0.840
125   V         1.664   1.677   1.716   1.763   1.782   1.847   1.800   1.816   1.870
126   K        -0.995  -0.938  -0.976  -1.005  -0.881  -1.001  -0.886  -0.818  -0.841
127   A        -0.995  -1.001  -0.970  -0.890  -0.899  -0.849  -0.886  -0.887  -0.835
128   S        -0.995  -0.996  -0.979  -1.296  -1.313  -1.286  -0.886  -0.881  -0.844
129   E        -0.441  -0.453  -0.423  -0.405  -0.411  -0.375  -0.587  -0.593  -0.544
130   L         1.664   1.677   1.716   1.736   1.749   1.821   1.800   1.816   1.870
131   D         1.664   1.677   1.716   1.842   1.861   1.926   1.800   1.816   1.870
132   Q        -0.233  -0.293  -0.332  -0.088  -0.204  -0.325  -0.289  -0.368  -0.418
133   F         1.664   1.677   1.716   1.947   1.966   2.029   1.800   1.816   1.870
134   W         1.664   1.677   1.716   2.091   2.113   2.172   1.800   1.816   1.870
135   Q        -0.441  -0.439  -0.419  -0.824  -0.870  -0.821  -0.587  -0.577  -0.539
136   E        -0.233  -0.208  -0.299   0.013   0.058  -0.085  -0.289  -0.254  -0.374
137   Y         1.664   1.677   1.716   1.981   2.003   2.063   1.800   1.816   1.870
138   S        -0.441  -0.449  -0.411  -0.653  -0.642  -0.583  -0.587  -0.588  -0.529
139   S        -0.995  -1.040  -0.999  -0.926  -0.967  -0.892  -0.886  -0.927  -0.864
140   V         1.664   1.677   1.716   1.763   1.782   1.847   1.800   1.816   1.870
141   F        -0.995  -0.989  -0.975  -0.714  -0.695  -0.666  -0.886  -0.874  -0.840
142   K         1.664   1.677   1.716   1.197   1.211   1.288   1.800   1.816   1.870
143   G        -1.548  -1.539  -1.470  -1.358  -1.321  -1.238  -1.184  -1.168  -1.078
144   G         0.666   0.628   0.524   0.874   0.817   0.615   0.606   0.543   0.353
145   M         0.666   0.653   0.534   1.051   1.037   0.852   0.606   0.584   0.371
146   Q        -1.103  -1.089  -1.029  -1.096  -1.099  -0.978  -0.998  -0.977  -0.894
147   N        -0.233  -0.208  -0.299   0.061   0.107  -0.043  -0.289  -0.254  -0.374
148   L         1.664   1.677   1.716   1.736   1.749   1.821   1.800   1.816   1.870
149   I         0.321   0.313   0.361   0.027  -0.014   0.049   0.009  -0.008   0.060
150   K         1.664   1.677   1.716   1.197   1.211   1.288   1.800   1.816   1.870
151   K         1.664   1.677   1.716   1.197   1.211   1.288   1.800   1.816   1.870
152   K         0.321   0.313   0.361  -0.258  -0.261  -0.167   0.009  -0.008   0.060
153   K         1.664   1.677   1.716   1.197   1.211   1.288   1.800   1.816   1.870
154   K         1.664   1.677   1.716   1.197   1.211   1.288   1.800   1.816   1.870
155   K         0.321   0.333   0.367  -0.183  -0.168  -0.085   0.009   0.029   0.072
156   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   K         1.664   1.677   1.716   1.167   1.190   1.258   1.800   1.816   1.870
164   T        -0.411  -0.464  -0.425  -0.451  -0.553  -0.495  -0.531  -0.598  -0.543
165   G         0.542   0.611   0.495   0.769   0.879   0.691   0.401   0.515   0.302
166   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   A         0.394   0.450   0.408  -0.099   0.002  -0.057   0.142   0.240   0.147
172   K         0.666   0.653   0.534   0.210   0.190   0.023   0.606   0.584   0.371
173   K        -0.233  -0.274  -0.330  -0.696  -0.752  -0.816  -0.289  -0.342  -0.417
174   N         0.321   0.313   0.361  -0.038  -0.083  -0.013   0.009  -0.008   0.060
* 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/P38985
Output conservation file - output/P38985
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
