1     M         1.407   1.434   1.540   1.673   1.713   1.878   1.544   1.585   1.758
2     T        -1.420  -1.448  -1.286  -1.342  -1.399  -1.169  -1.263  -1.277  -1.066
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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    C        -1.006  -1.010  -0.890  -0.915  -0.937  -0.828  -1.055  -1.055  -0.883
47    G        -0.164  -0.264  -0.321  -0.075  -0.222  -0.311  -0.261  -0.404  -0.495
48    L        -1.299  -1.326  -1.262  -1.403  -1.452  -1.313  -1.163  -1.178  -1.047
49    V        -0.223  -0.225  -0.305  -0.441  -0.442  -0.578  -0.374  -0.370  -0.479
50    R         0.152   0.195   0.325  -0.305  -0.237  -0.031  -0.261  -0.188   0.001
51    I         0.725   0.721   0.508   0.802   0.792   0.469   0.754   0.748   0.356
52    R         1.407   1.434   1.540   1.357   1.406   1.571   1.544   1.585   1.758
53    L         1.407   1.434   1.540   1.316   1.357   1.532   1.544   1.585   1.758
54    A         1.407   1.434   1.540   1.438   1.477   1.650   1.544   1.585   1.758
55    R         0.725   0.726   0.505   0.738   0.752   0.402   0.754   0.755   0.349
56    F         0.725   0.627   0.503   1.054   0.937   0.768   0.754   0.596   0.345
57    G         1.407   1.434   1.540   1.427   1.477   1.639   1.544   1.585   1.758
58    R         0.725   0.627   0.503   0.726   0.599   0.369   0.754   0.596   0.345
59    K        -0.790  -0.781  -0.815  -1.015  -1.005  -1.062  -0.825  -0.819  -0.807
60    N         0.209   0.251   0.327   0.240   0.304   0.414  -0.148  -0.077   0.006
61    S        -1.299  -1.309  -1.250  -1.059  -1.101  -1.008  -1.163  -1.167  -1.037
62    P         1.407   1.434   1.540   1.369   1.404   1.583   1.544   1.585   1.758
63    V        -0.985  -0.976  -0.868  -1.163  -1.107  -0.964  -1.050  -1.025  -0.862
64    Y         1.407   1.434   1.540   1.596   1.638   1.803   1.544   1.585   1.758
65    N         0.725   0.627   0.503   0.977   0.864   0.698   0.754   0.596   0.345
66    I         1.407   1.434   1.540   1.421   1.452   1.633   1.544   1.585   1.758
67    V         1.407   1.434   1.540   1.233   1.280   1.451   1.544   1.585   1.758
68    V         1.407   1.434   1.540   1.233   1.280   1.451   1.544   1.585   1.758
69    A         0.075   0.145  -0.215   0.289   0.380  -0.094   0.077   0.171  -0.341
70    N        -0.790  -0.758  -0.823  -0.702  -0.660  -0.776  -0.825  -0.785  -0.814
71    S        -0.476  -0.368  -0.353  -0.646  -0.467  -0.490  -0.712  -0.554  -0.542
72    R        -1.299  -1.322  -1.236  -1.160  -1.188  -1.070  -1.163  -1.163  -1.022
73    K        -0.537  -0.540  -0.773  -0.474  -0.476  -0.759  -0.486  -0.483  -0.750
74    A         0.725   0.772   0.500   0.825   0.890   0.484   0.754   0.827   0.340
75    R        -0.537  -0.574  -0.763  -0.419  -0.472  -0.767  -0.486  -0.535  -0.738
76    D        -0.476  -0.483  -0.381  -0.423  -0.444  -0.286  -0.712  -0.723  -0.580
77    A        -1.299  -1.245  -1.241  -1.253  -1.187  -1.198  -1.163  -1.106  -1.029
78    K         0.209   0.219   0.322  -0.227  -0.220  -0.065  -0.148  -0.140  -0.005
79    P         1.407   1.434   1.540   1.369   1.404   1.583   1.544   1.585   1.758
80    I         0.075   0.021  -0.226   0.246   0.171  -0.183   0.077   0.006  -0.358
81    E         1.407   1.434   1.540   1.540   1.590   1.749   1.544   1.585   1.758
82    V         0.725   0.627   0.503   0.637   0.522   0.341   0.754   0.596   0.345
83    L         0.152   0.188   0.321  -0.195  -0.135   0.081  -0.261  -0.200  -0.006
84    G         1.407   1.434   1.540   1.427   1.477   1.639   1.544   1.585   1.758
85    T         1.407   1.434   1.540   1.478   1.527   1.689   1.544   1.585   1.758
86    Y         0.725   0.627   0.503   1.020   0.902   0.726   0.754   0.596   0.345
87    V        -0.223  -0.206  -0.297  -0.123  -0.126  -0.289  -0.374  -0.378  -0.468
88    P         1.407   1.434   1.540   1.369   1.404   1.583   1.544   1.585   1.758
89    V         0.209   0.263   0.344  -0.101  -0.007   0.088  -0.148  -0.054   0.039
90    P         0.725   0.726   0.505   0.782   0.784   0.493   0.754   0.755   0.349
91    S        -0.790  -0.725  -0.827  -1.009  -0.942  -1.046  -0.825  -0.756  -0.818
92    P         0.389   0.331   0.376   0.215   0.088   0.119   0.190   0.075   0.103
93    V        -1.104  -1.118  -1.195  -1.074  -1.101  -1.257  -0.938  -0.949  -0.980
94    T        -0.790  -0.822  -0.824  -0.693  -0.738  -0.768  -0.825  -0.857  -0.815
95    K        -1.613  -1.696  -1.592  -1.471  -1.576  -1.372  -1.276  -1.335  -1.174
96    R        -2.359  -2.315  -2.128  -2.001  -1.900  -1.683  -1.614  -1.568  -1.342
97    E        -0.223  -0.298  -0.318  -0.084  -0.212  -0.250  -0.374  -0.490  -0.499
98    L        -1.001  -1.046  -0.883  -1.388  -1.449  -1.202  -1.063  -1.092  -0.877
99    K        -0.164  -0.299  -0.321  -0.358  -0.579  -0.662  -0.261  -0.454  -0.495
100   R        -0.583  -0.557  -0.398  -0.847  -0.812  -0.563  -0.862  -0.824  -0.604
101   G         0.324   0.251   0.340   0.257   0.126   0.253   0.071  -0.078   0.032
102   V        -0.035  -0.196  -0.271  -0.126  -0.360  -0.490  -0.077  -0.307  -0.424
103   V        -1.400  -1.398  -1.270  -1.727  -1.718  -1.530  -1.255  -1.238  -1.053
104   P        -0.537  -0.680  -0.788  -0.488  -0.721  -0.958  -0.486  -0.658  -0.768
105   I        -1.299  -1.252  -1.231  -1.166  -1.085  -1.047  -1.163  -1.093  -1.018
106   K         1.407   1.434   1.540   1.233   1.277   1.451   1.544   1.585   1.758
107   D         0.075   0.131  -0.211   0.367   0.437  -0.008   0.077   0.158  -0.335
108   V         0.209   0.195   0.323  -0.169  -0.203   0.010  -0.148  -0.187  -0.002
109   K        -1.299  -1.330  -1.243  -1.176  -1.201  -1.086  -1.163  -1.177  -1.030
110   L         1.407   1.434   1.540   1.316   1.357   1.532   1.544   1.585   1.758
111   D         0.725   0.627   0.503   0.920   0.794   0.618   0.754   0.596   0.345
112   F        -0.223  -0.310  -0.314  -0.134  -0.313  -0.374  -0.374  -0.500  -0.492
113   D        -1.104  -1.150  -1.211  -0.745  -0.811  -0.904  -0.938  -0.984  -0.996
114   R         1.407   1.434   1.540   1.357   1.406   1.571   1.544   1.585   1.758
115   T        -0.790  -0.863  -0.828  -0.662  -0.752  -0.687  -0.825  -0.893  -0.820
116   K         1.407   1.434   1.540   1.233   1.277   1.451   1.544   1.585   1.758
117   Y         1.407   1.434   1.540   1.596   1.638   1.803   1.544   1.585   1.758
118   W         1.407   1.434   1.540   1.657   1.697   1.862   1.544   1.585   1.758
119   I         0.725   0.695   0.498   0.802   0.756   0.450   0.754   0.706   0.337
120   G         0.725   0.627   0.503   0.840   0.727   0.543   0.754   0.596   0.345
121   V         0.075   0.068  -0.237   0.087   0.093  -0.301   0.077   0.070  -0.373
122   G         1.407   1.434   1.540   1.427   1.477   1.639   1.544   1.585   1.758
123   A         1.407   1.434   1.540   1.438   1.477   1.650   1.544   1.585   1.758
124   Q         0.075   0.026  -0.237   0.401   0.326  -0.119   0.077   0.012  -0.373
125   P         0.725   0.726   0.505   0.750   0.750   0.413   0.754   0.755   0.349
126   S         0.389   0.367   0.358   0.460   0.413   0.356   0.190   0.143   0.068
127   E         0.075   0.117  -0.215   0.317   0.362  -0.119   0.077   0.135  -0.341
128   T         0.389   0.370   0.360   0.361   0.329   0.244   0.190   0.147   0.072
129   V         0.725   0.772   0.500   0.631   0.703   0.321   0.754   0.827   0.340
130   T        -1.104  -1.161  -1.208  -0.846  -0.927  -1.037  -0.938  -0.993  -0.994
131   K        -1.104  -1.168  -1.214  -0.898  -0.969  -1.038  -0.938  -1.001  -0.999
132   L         0.725   0.772   0.500   0.712   0.776   0.393   0.754   0.827   0.340
133   L        -0.223  -0.285  -0.298  -0.256  -0.338  -0.343  -0.374  -0.442  -0.470
134   R        -1.731  -1.718  -1.593  -1.599  -1.578  -1.336  -1.389  -1.359  -1.176
135   K         0.389   0.409   0.366   0.108   0.139   0.022   0.190   0.220   0.083
136   A         0.209   0.190   0.322  -0.085  -0.157   0.040  -0.148  -0.196  -0.005
137   G         0.725   0.627   0.503   0.868   0.767   0.612   0.754   0.596   0.345
138   I        -0.324  -0.342  -0.344  -0.476  -0.541  -0.587  -0.519  -0.552  -0.535
139   L         1.407   1.434   1.540   1.298   1.330   1.514   1.544   1.585   1.758
140   N        -0.906  -0.796  -0.846  -0.917  -0.778  -0.813  -0.961  -0.835  -0.839
141   D        -0.906  -0.901  -0.851  -0.808  -0.806  -0.714  -0.961  -0.951  -0.844
142   A        -2.117  -2.072  -1.892  -1.754  -1.709  -1.444  -1.550  -1.501  -1.279
143   W         0.665   0.593   0.478   1.004   0.912   0.731   0.660   0.540   0.298
144   A        -1.041  -0.971  -0.882  -1.330  -1.249  -1.082  -1.108  -1.029  -0.877
145   T        -0.906  -0.826  -0.842  -1.047  -0.940  -0.926  -0.961  -0.863  -0.835
146   S        -1.299  -1.171  -1.232  -1.350  -1.162  -1.274  -1.163  -1.027  -1.020
147   K        -1.731  -1.665  -1.590  -1.515  -1.404  -1.259  -1.389  -1.318  -1.173
148   N        -1.400  -1.310  -1.263  -1.392  -1.279  -1.169  -1.255  -1.167  -1.047
149   S        -0.906  -0.777  -0.835  -1.010  -0.819  -0.913  -0.961  -0.791  -0.826
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   N        -1.006  -0.962  -0.873  -0.817  -0.745  -0.657  -1.055  -1.001  -0.865
153   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   N        -1.006  -0.971  -0.875  -0.898  -0.856  -0.715  -1.055  -1.012  -0.867
155   R         0.188   0.179   0.318  -0.203  -0.251  -0.040  -0.189  -0.219  -0.013
156   K        -1.006  -0.920  -0.862  -1.268  -1.104  -1.077  -1.055  -0.949  -0.853
157   V         0.501   0.567   0.431   0.303   0.409   0.193   0.389   0.497   0.210
158   V         0.188   0.259   0.345  -0.214  -0.097   0.037  -0.189  -0.063   0.042
159   F        -1.006  -0.950  -0.873  -0.840  -0.766  -0.642  -1.055  -0.982  -0.865
160   E         0.188   0.259   0.345  -0.010   0.124   0.229  -0.189  -0.063   0.042
161   R        -0.314  -0.413  -0.357  -0.455  -0.627  -0.598  -0.477  -0.621  -0.547
162   M        -0.314  -0.336  -0.332  -0.486  -0.543  -0.495  -0.477  -0.515  -0.512
163   E         0.501   0.483   0.420   0.587   0.566   0.430   0.389   0.353   0.188
164   T        -0.503  -0.457  -0.367  -0.857  -0.765  -0.649  -0.766  -0.702  -0.566
165   L        -1.006  -1.010  -0.890  -0.941  -0.946  -0.727  -1.055  -1.055  -0.883
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   E        -1.299  -1.353  -1.259  -1.092  -1.196  -1.048  -1.163  -1.200  -1.044
* 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/Q02608
Output conservation file - output/Q02608
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
