1     M         1.095   1.104   1.167   1.471   1.476   1.535   1.161   1.177   1.276
2     S         1.095   1.104   1.167   1.162   1.175   1.267   1.161   1.177   1.276
3     D        -0.301  -0.355  -0.739   0.027  -0.039  -0.664  -0.220  -0.293  -0.802
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     V        -0.638  -0.623  -0.771  -0.792  -0.750  -0.914  -0.680  -0.646  -0.848
9     E         0.383   0.317   0.028   0.321   0.260  -0.079   0.425   0.330  -0.154
10    E        -0.818  -0.851  -0.801  -1.043  -1.081  -1.016  -0.956  -0.982  -0.888
11    V        -2.133  -2.071  -2.077  -2.049  -1.962  -1.929  -1.601  -1.559  -1.468
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    V        -2.448  -2.427  -2.103  -2.295  -2.303  -1.862  -1.877  -1.840  -1.486
15    E        -1.896  -1.812  -1.742  -2.172  -2.080  -1.831  -1.601  -1.527  -1.354
16    V        -0.301  -0.439  -0.739  -0.357  -0.512  -0.889  -0.220  -0.399  -0.802
17    Q        -0.126  -0.080  -0.043  -0.376  -0.300  -0.228  -0.361  -0.294  -0.278
18    E         0.326   0.277   0.017   0.242   0.197  -0.118   0.346   0.272  -0.173
19    E        -0.053  -0.013  -0.019  -0.481  -0.409  -0.449  -0.237  -0.181  -0.236
20    T        -1.512  -1.438  -1.344  -1.838  -1.692  -1.555  -1.426  -1.353  -1.190
21    V         0.326   0.250   0.011   0.120   0.029  -0.345   0.346   0.233  -0.184
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    V        -1.115  -1.047  -0.817  -1.758  -1.634  -1.265  -1.286  -1.205  -0.907
26    E        -1.468  -1.354  -1.331  -1.658  -1.510  -1.322  -1.402  -1.293  -1.178
27    Q        -1.385  -1.399  -1.324  -1.038  -1.060  -1.020  -1.325  -1.331  -1.172
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    T        -1.819  -1.800  -1.735  -1.484  -1.473  -1.435  -1.509  -1.479  -1.345
30    A        -1.385  -1.380  -1.331  -1.446  -1.436  -1.397  -1.325  -1.305  -1.177
31    E        -2.643  -2.565  -2.393  -2.327  -2.201  -1.915  -1.877  -1.820  -1.570
32    V        -1.581  -1.494  -1.325  -1.855  -1.729  -1.390  -1.509  -1.408  -1.173
33    T        -0.308  -0.268  -0.096  -0.362  -0.309  -0.060  -0.680  -0.624  -0.372
34    I        -0.818  -0.890  -0.815  -0.901  -1.071  -1.041  -0.956  -1.042  -0.905
35    E         0.383   0.306   0.016   0.249   0.160  -0.314   0.425   0.314  -0.174
36    D         1.095   1.104   1.167   1.220   1.233   1.317   1.161   1.177   1.276
37    A         0.383   0.317   0.028   0.384   0.298  -0.104   0.425   0.330  -0.154
38    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
39    K         1.095   1.104   1.167   1.197   1.210   1.298   1.161   1.177   1.276
40    V        -1.251  -1.389  -1.347  -1.462  -1.645  -1.496  -1.140  -1.288  -1.192
41    V         1.095   1.104   1.167   0.804   0.834   0.956   1.161   1.177   1.276
42    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
43    R        -0.308  -0.282  -0.096  -0.390  -0.371  -0.097  -0.680  -0.650  -0.373
44    T        -1.251  -1.389  -1.347  -0.774  -0.984  -0.990  -1.140  -1.288  -1.192
45    A        -0.308  -0.253  -0.095  -0.649  -0.573  -0.309  -0.680  -0.597  -0.372
46    L         0.383   0.293   0.020   0.248   0.131  -0.333   0.425   0.296  -0.168
47    V        -0.301  -0.460  -0.749  -0.308  -0.476  -0.774  -0.220  -0.427  -0.816
48    H         0.383   0.293   0.020   0.894   0.786   0.350   0.425   0.296  -0.168
49    D         1.095   1.104   1.167   1.220   1.233   1.317   1.161   1.177   1.276
50    G         1.095   1.104   1.167   1.193   1.206   1.294   1.161   1.177   1.276
51    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
52    A         0.383   0.293   0.020   0.338   0.213  -0.257   0.425   0.296  -0.168
53    R         1.095   1.104   1.167   1.273   1.284   1.363   1.161   1.177   1.276
54    G         1.095   1.104   1.167   1.193   1.206   1.294   1.161   1.177   1.276
55    L         0.014  -0.014  -0.040  -0.151  -0.189  -0.207  -0.128  -0.183  -0.273
56    R         1.095   1.104   1.167   1.273   1.284   1.363   1.161   1.177   1.276
57    E         1.095   1.104   1.167   0.880   0.907   1.023   1.161   1.177   1.276
58    S        -0.818  -0.838  -0.790  -0.941  -0.953  -0.812  -0.956  -0.962  -0.870
59    T        -0.638  -0.558  -0.750  -0.460  -0.355  -0.685  -0.680  -0.572  -0.817
60    K         1.095   1.104   1.167   1.197   1.210   1.298   1.161   1.177   1.276
61    A         1.095   1.104   1.167   0.979   0.987   1.108   1.161   1.177   1.276
62    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
63    T        -1.148  -1.084  -0.840  -1.134  -1.052  -0.724  -1.325  -1.250  -0.933
64    R         0.383   0.537   0.040   0.682   0.851   0.167   0.425   0.627  -0.134
65    G        -0.818  -0.688  -0.780  -0.655  -0.473  -0.568  -0.956  -0.790  -0.861
66    E         0.014  -0.014  -0.040  -0.161  -0.192  -0.217  -0.128  -0.183  -0.273
67    A         0.383   0.393   0.035   0.388   0.395  -0.081   0.425   0.437  -0.142
68    L        -1.385  -1.383  -1.338  -1.092  -1.099  -1.169  -1.325  -1.320  -1.185
69    L         0.383   0.306   0.016   0.336   0.256  -0.069   0.425   0.314  -0.174
70    V        -0.638  -0.558  -0.750  -0.421  -0.302  -0.741  -0.680  -0.572  -0.817
71    V         1.095   1.104   1.167   0.804   0.834   0.956   1.161   1.177   1.276
72    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
73    V        -0.818  -0.829  -0.791  -0.762  -0.751  -0.697  -0.956  -0.952  -0.872
74    S        -1.071  -0.962  -0.803  -1.361  -1.209  -0.957  -1.232  -1.098  -0.888
75    S         1.095   1.104   1.167   1.162   1.175   1.267   1.161   1.177   1.276
76    V        -0.205  -0.229  -0.098  -0.521  -0.542  -0.290  -0.496  -0.553  -0.378
77    T        -0.638  -0.728  -0.793  -0.319  -0.474  -0.710  -0.680  -0.799  -0.873
78    E        -0.638  -0.738  -0.790  -0.709  -0.830  -0.868  -0.680  -0.811  -0.870
79    A        -0.301  -0.182  -0.711  -0.325  -0.171  -0.906  -0.220  -0.075  -0.766
80    N        -1.071  -0.962  -0.803  -1.226  -1.089  -0.830  -1.232  -1.098  -0.888
81    I        -0.308  -0.282  -0.096  -0.150  -0.103   0.143  -0.680  -0.650  -0.373
82    I        -1.819  -1.914  -1.765  -1.629  -1.853  -1.719  -1.509  -1.591  -1.370
83    K         1.095   1.104   1.167   1.197   1.210   1.298   1.161   1.177   1.276
84    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
85    V         1.095   1.104   1.167   0.804   0.834   0.956   1.161   1.177   1.276
86    E        -0.301  -0.369  -0.731  -0.255  -0.322  -0.758  -0.220  -0.311  -0.792
87    G        -0.205  -0.144  -0.053  -0.456  -0.371  -0.226  -0.496  -0.404  -0.296
88    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
89    A        -0.205  -0.144  -0.053  -0.178  -0.089  -0.014  -0.496  -0.404  -0.296
90    N        -1.251  -1.319  -1.329  -0.867  -1.006  -1.071  -1.140  -1.219  -1.175
91    D        -0.279  -0.220  -0.088  -0.671  -0.575  -0.351  -0.629  -0.537  -0.359
92    P         1.095   1.104   1.167   1.443   1.445   1.510   1.161   1.177   1.276
93    E         0.383   0.452   0.040   0.315   0.404  -0.080   0.425   0.517  -0.134
94    N        -1.581  -1.584  -1.361  -1.535  -1.510  -1.183  -1.509  -1.496  -1.206
95    K        -0.952  -0.996  -1.285  -0.550  -0.611  -1.075  -0.772  -0.827  -1.128
96    V        -1.071  -1.040  -0.824  -1.157  -1.091  -0.789  -1.232  -1.195  -0.912
97    P         1.095   1.104   1.167   1.429   1.432   1.498   1.161   1.177   1.276
98    L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
99    I         0.014  -0.071  -0.076   0.136  -0.031  -0.200  -0.128  -0.278  -0.337
100   K         1.095   1.104   1.167   1.197   1.210   1.298   1.161   1.177   1.276
101   V         1.095   1.104   1.167   0.804   0.834   0.956   1.161   1.177   1.276
102   A        -0.937  -0.846  -0.810  -0.999  -0.875  -0.788  -1.048  -0.952  -0.896
103   D         1.095   1.104   1.167   1.220   1.233   1.317   1.161   1.177   1.276
104   A        -0.638  -0.728  -0.793  -0.583  -0.711  -0.765  -0.680  -0.799  -0.873
105   K         1.095   1.104   1.167   1.197   1.210   1.298   1.161   1.177   1.276
106   Q        -1.251  -1.139  -1.297  -1.028  -0.804  -1.220  -1.140  -0.994  -1.142
107   L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
108   G         1.095   1.104   1.167   1.193   1.206   1.294   1.161   1.177   1.276
109   E         1.095   1.104   1.167   0.880   0.907   1.023   1.161   1.177   1.276
110   W         1.095   1.104   1.167   1.471   1.479   1.535   1.161   1.177   1.276
111   A         1.095   1.104   1.167   0.979   0.987   1.108   1.161   1.177   1.276
112   G         1.095   1.104   1.167   1.193   1.206   1.294   1.161   1.177   1.276
113   L         1.095   1.104   1.167   0.890   0.907   1.031   1.161   1.177   1.276
114   G        -0.205  -0.144  -0.053  -0.085  -0.000   0.081  -0.496  -0.404  -0.296
115   K        -1.148  -1.084  -0.840  -1.391  -1.335  -0.958  -1.325  -1.250  -0.933
116   I        -0.205  -0.144  -0.053  -0.471  -0.380  -0.225  -0.496  -0.404  -0.296
117   D         1.095   1.104   1.167   1.220   1.233   1.317   1.161   1.177   1.276
118   R         1.095   1.104   1.167   1.273   1.284   1.363   1.161   1.177   1.276
119   E        -0.308  -0.277  -0.103  -0.633  -0.592  -0.338  -0.680  -0.640  -0.386
120   G         1.095   1.104   1.167   1.193   1.206   1.294   1.161   1.177   1.276
121   N         1.095   1.104   1.167   1.386   1.398   1.461   1.161   1.177   1.276
122   A         1.095   1.104   1.167   0.979   0.987   1.108   1.161   1.177   1.276
123   R         1.095   1.104   1.167   1.273   1.284   1.363   1.161   1.177   1.276
124   K         1.095   1.104   1.167   1.197   1.210   1.298   1.161   1.177   1.276
125   V         1.095   1.104   1.167   0.804   0.834   0.956   1.161   1.177   1.276
126   V         1.095   1.104   1.167   0.804   0.834   0.956   1.161   1.177   1.276
127   G         0.383   0.306   0.016   0.626   0.539   0.134   0.425   0.314  -0.174
128   A        -0.205  -0.229  -0.098  -0.363  -0.410  -0.176  -0.496  -0.553  -0.378
129   S         1.095   1.104   1.167   1.162   1.175   1.267   1.161   1.177   1.276
130   V        -0.205  -0.144  -0.053  -0.252  -0.150  -0.091  -0.496  -0.404  -0.296
131   V         1.095   1.104   1.167   0.804   0.834   0.956   1.161   1.177   1.276
132   V         0.014  -0.014  -0.040  -0.341  -0.385  -0.445  -0.128  -0.183  -0.273
133   V         0.383   0.293   0.020   0.230   0.145  -0.191   0.425   0.296  -0.168
134   K        -0.205  -0.232  -0.098  -0.172  -0.227  -0.040  -0.496  -0.559  -0.378
135   N        -0.638  -0.606  -0.764  -0.263  -0.250  -0.535  -0.680  -0.662  -0.837
136   W         0.014  -0.014  -0.040   0.460   0.407   0.307  -0.128  -0.183  -0.273
137   G         1.095   1.104   1.167   1.193   1.206   1.294   1.161   1.177   1.276
138   A        -0.875  -0.714  -0.797  -1.238  -1.057  -0.991  -1.048  -0.882  -0.883
139   E        -0.638  -0.633  -0.753  -0.482  -0.445  -0.659  -0.680  -0.662  -0.821
140   T        -0.205  -0.144  -0.053  -0.204  -0.118   0.000  -0.496  -0.404  -0.296
141   D        -2.133  -2.254  -2.100  -1.820  -2.093  -2.018  -1.601  -1.702  -1.484
142   E        -0.205  -0.232  -0.098  -0.652  -0.718  -0.494  -0.496  -0.559  -0.378
143   L        -0.205  -0.190  -0.096  -0.322  -0.319  -0.261  -0.496  -0.483  -0.373
144   S        -1.581  -1.493  -1.352  -1.433  -1.343  -1.190  -1.509  -1.419  -1.198
145   M        -1.819  -1.856  -1.746  -1.169  -1.208  -1.105  -1.509  -1.530  -1.354
146   I         0.014   0.098   0.004  -0.151  -0.032  -0.146  -0.128  -0.001  -0.196
147   M         0.383   0.448   0.040   0.336   0.410  -0.039   0.425   0.511  -0.134
148   E        -0.952  -1.153  -1.303  -0.837  -1.085  -1.253  -0.772  -1.004  -1.147
149   H        -0.818  -0.883  -0.814  -0.500  -0.621  -0.517  -0.956  -1.035  -0.903
150   F         0.383   0.293   0.020   0.924   0.813   0.360   0.425   0.296  -0.168
151   S        -0.638  -0.773  -0.795  -0.533  -0.765  -0.821  -0.680  -0.867  -0.880
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   Q        -0.531  -0.789  -0.811  -0.226  -0.649  -0.833  -0.513  -0.860  -0.895
154   Q         0.014  -0.014  -0.040   0.177   0.118  -0.031  -0.128  -0.183  -0.273
* 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/P48589
Output conservation file - output/P48589
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
