1     M         0.949   0.957   1.003   1.131   1.132   1.197   1.007   1.019   1.082
2     S        -0.476  -0.321  -0.826  -0.446  -0.246  -1.007  -0.445  -0.251  -0.908
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     -        -1.631  -1.631  -1.426  -1.795  -1.841  -1.567  -1.567  -1.562  -1.296
7     K        -1.482  -1.541  -1.407  -1.522  -1.587  -1.365  -1.451  -1.484  -1.277
8     T        -0.794  -0.899  -0.894  -0.565  -0.751  -0.747  -0.892  -1.039  -0.998
9     A         0.949   0.957   1.003   1.010   1.017   1.091   1.007   1.019   1.082
10    Q         0.219   0.165  -0.106   0.444   0.371  -0.128   0.225   0.142  -0.315
11    K        -0.140  -0.227  -0.191  -0.115  -0.264  -0.234  -0.334  -0.492  -0.465
12    R         0.949   0.957   1.003   1.067   1.074   1.141   1.007   1.019   1.082
13    L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
14    L        -0.794  -0.707  -0.869  -0.900  -0.814  -0.930  -0.892  -0.820  -0.966
15    K         0.219   0.097  -0.112   0.391   0.242  -0.080   0.225   0.040  -0.326
16    E         0.949   0.957   1.003   0.874   0.881   0.972   1.007   1.019   1.082
17    L        -0.332  -0.242  -0.175  -0.511  -0.331  -0.278  -0.669  -0.519  -0.436
18    Q        -1.400  -1.509  -1.407  -1.193  -1.378  -1.268  -1.339  -1.450  -1.278
19    Q        -1.130  -1.293  -1.378  -0.771  -1.024  -1.233  -1.004  -1.192  -1.248
20    L         0.219   0.178  -0.104   0.125   0.086  -0.277   0.225   0.162  -0.312
21    I        -1.482  -1.335  -1.383  -1.400  -1.187  -1.262  -1.451  -1.300  -1.256
22    K        -1.945  -2.000  -1.813  -1.796  -1.894  -1.662  -1.674  -1.701  -1.451
23    D        -0.140  -0.227  -0.191  -0.170  -0.320  -0.279  -0.334  -0.492  -0.465
24    S        -0.938  -0.914  -0.879  -1.331  -1.265  -1.155  -1.116  -1.062  -0.978
25    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
26    P        -1.400  -1.490  -1.400  -1.594  -1.725  -1.509  -1.339  -1.435  -1.272
27    G         0.949   0.957   1.003   0.998   1.004   1.080   1.007   1.019   1.082
28    I         0.949   0.957   1.003   0.969   0.991   1.055   1.007   1.019   1.082
29    V        -1.945  -1.934  -1.801  -1.782  -1.792  -1.663  -1.674  -1.656  -1.443
30    A         0.949   0.957   1.003   1.010   1.017   1.091   1.007   1.019   1.082
31    G         0.219   0.196  -0.106   0.346   0.308  -0.177   0.225   0.188  -0.315
32    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
33    K        -1.945  -1.869  -1.777  -1.823  -1.709  -1.600  -1.674  -1.582  -1.422
34    S        -0.794  -0.862  -0.883  -0.875  -0.980  -0.987  -0.892  -0.983  -0.985
35    E        -0.140  -0.067  -0.151  -0.280  -0.174  -0.318  -0.334  -0.220  -0.393
36    N        -0.476  -0.378  -0.819  -0.314  -0.202  -0.846  -0.445  -0.329  -0.899
37    N        -0.332  -0.334  -0.211  -0.459  -0.485  -0.305  -0.669  -0.684  -0.501
38    I        -0.794  -0.722  -0.870  -0.935  -0.854  -0.996  -0.892  -0.836  -0.967
39    F        -0.794  -0.807  -0.876  -0.689  -0.785  -0.881  -0.892  -0.940  -0.976
40    I        -2.743  -2.669  -2.408  -2.331  -2.237  -1.906  -2.009  -1.944  -1.636
41    W         0.949   0.957   1.003   1.195   1.202   1.252   1.007   1.019   1.082
42    D        -0.393  -0.357  -0.211  -0.730  -0.682  -0.426  -0.781  -0.727  -0.502
43    C         0.949   0.957   1.003   1.183   1.190   1.242   1.007   1.019   1.082
44    L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
45    I        -0.140  -0.036  -0.142  -0.255  -0.072  -0.320  -0.334  -0.169  -0.378
46    Q        -1.130  -1.012  -1.358  -0.747  -0.599  -1.150  -1.004  -0.873  -1.227
47    G         0.949   0.957   1.003   0.998   1.004   1.080   1.007   1.019   1.082
48    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
49    P        -1.400  -1.454  -1.402  -1.640  -1.730  -1.620  -1.339  -1.402  -1.273
50    D        -0.140  -0.227  -0.191  -0.188  -0.347  -0.309  -0.334  -0.492  -0.465
51    T         0.219   0.196  -0.106   0.475   0.438  -0.072   0.225   0.188  -0.315
52    P         0.219   0.196  -0.106   0.104   0.091  -0.277   0.225   0.188  -0.315
53    Y        -0.140  -0.227  -0.191   0.010  -0.147  -0.127  -0.334  -0.492  -0.465
54    A        -0.140   0.038  -0.116  -0.261  -0.004  -0.231  -0.334  -0.051  -0.332
55    D        -0.794  -0.591  -0.844  -0.718  -0.445  -0.815  -0.892  -0.633  -0.932
56    G         0.949   0.957   1.003   0.998   1.004   1.080   1.007   1.019   1.082
57    V        -0.140  -0.186  -0.183  -0.171  -0.276  -0.348  -0.334  -0.422  -0.450
58    F         0.219   0.165  -0.106   0.504   0.431   0.022   0.225   0.142  -0.315
59    N        -0.332  -0.242  -0.175  -0.710  -0.561  -0.434  -0.669  -0.519  -0.436
60    A         0.949   0.957   1.003   1.010   1.017   1.091   1.007   1.019   1.082
61    K        -2.743  -2.573  -2.402  -2.331  -2.135  -1.931  -2.009  -1.880  -1.633
62    L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
63    E        -1.609  -1.468  -1.400  -1.608  -1.378  -1.310  -1.562  -1.395  -1.270
64    F         0.949   0.957   1.003   1.119   1.127   1.186   1.007   1.019   1.082
65    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
66    K        -1.130  -1.306  -1.389  -0.848  -1.103  -1.269  -1.004  -1.207  -1.260
67    D         0.949   0.957   1.003   0.953   0.967   1.041   1.007   1.019   1.082
68    Y         0.949   0.957   1.003   1.119   1.128   1.186   1.007   1.019   1.082
69    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
70    L         0.219   0.097  -0.112   0.138   0.000  -0.253   0.225   0.040  -0.326
71    S        -1.130  -1.293  -1.378  -0.965  -1.191  -1.286  -1.004  -1.192  -1.248
72    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
73    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
74    K        -0.938  -0.904  -0.880  -0.875  -0.803  -0.772  -1.116  -1.051  -0.979
75    L        -0.140  -0.221  -0.192  -0.351  -0.471  -0.391  -0.334  -0.481  -0.466
76    T        -0.393  -0.341  -0.205  -0.507  -0.432  -0.224  -0.781  -0.696  -0.489
77    F         0.949   0.957   1.003   1.119   1.127   1.186   1.007   1.019   1.082
78    T        -1.945  -1.991  -1.802  -1.773  -1.883  -1.646  -1.674  -1.694  -1.443
79    P        -0.794  -0.925  -0.894  -0.932  -1.096  -0.991  -0.892  -1.060  -0.997
80    S        -1.609  -1.618  -1.420  -1.955  -1.956  -1.637  -1.562  -1.554  -1.290
81    I        -1.400  -1.398  -1.392  -1.368  -1.325  -1.316  -1.339  -1.317  -1.262
82    L        -0.794  -0.893  -0.894  -0.905  -1.035  -0.955  -0.892  -1.034  -0.998
83    H         0.949   0.957   1.003   1.202   1.206   1.259   1.007   1.019   1.082
84    P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
85    N         0.949   0.957   1.003   1.055   1.067   1.130   1.007   1.019   1.082
86    I        -0.140  -0.227  -0.191  -0.154  -0.298  -0.267  -0.334  -0.492  -0.465
87    Y         0.949   0.957   1.003   1.119   1.128   1.186   1.007   1.019   1.082
88    P        -1.065  -1.017  -0.903  -1.379  -1.305  -1.095  -1.227  -1.171  -1.007
89    N        -0.938  -0.962  -0.887  -1.027  -1.053  -0.954  -1.116  -1.115  -0.988
90    G         0.949   0.957   1.003   0.998   1.004   1.080   1.007   1.019   1.082
91    E        -0.938  -0.962  -0.887  -1.016  -1.039  -0.972  -1.116  -1.115  -0.988
92    V         0.949   0.957   1.003   1.055   1.064   1.130   1.007   1.019   1.082
93    C         0.949   0.957   1.003   1.183   1.190   1.242   1.007   1.019   1.082
94    I         0.949   0.957   1.003   0.969   0.991   1.055   1.007   1.019   1.082
95    S         0.949   0.957   1.003   0.853   0.869   0.954   1.007   1.019   1.082
96    I         0.949   0.957   1.003   0.969   0.991   1.055   1.007   1.019   1.082
97    L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
98    H         0.949   0.957   1.003   1.202   1.206   1.259   1.007   1.019   1.082
99    S        -1.147  -1.113  -0.915  -1.509  -1.465  -1.160  -1.339  -1.294  -1.023
100   P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
101   G         0.949   0.957   1.003   0.998   1.004   1.080   1.007   1.019   1.082
102   D        -0.794  -0.728  -0.857  -0.849  -0.737  -0.987  -0.892  -0.792  -0.949
103   D         0.949   0.957   1.003   0.953   0.967   1.041   1.007   1.019   1.082
104   P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
105   N         0.949   0.957   1.003   1.055   1.067   1.130   1.007   1.019   1.082
106   M        -0.794  -0.810  -0.864  -0.528  -0.540  -0.638  -0.892  -0.893  -0.958
107   Y         0.949   0.957   1.003   1.119   1.128   1.186   1.007   1.019   1.082
108   E         0.949   0.957   1.003   0.874   0.881   0.972   1.007   1.019   1.082
109   L        -1.945  -1.888  -1.788  -1.840  -1.746  -1.598  -1.674  -1.611  -1.431
110   A        -1.400  -1.385  -1.382  -1.466  -1.431  -1.498  -1.339  -1.305  -1.252
111   E        -0.938  -0.937  -0.895  -1.149  -1.154  -0.994  -1.116  -1.109  -1.000
112   E         0.949   0.957   1.003   0.874   0.881   0.972   1.007   1.019   1.082
113   R         0.949   0.957   1.003   1.067   1.074   1.141   1.007   1.019   1.082
114   W         0.949   0.957   1.003   1.195   1.202   1.252   1.007   1.019   1.082
115   S         0.949   0.957   1.003   0.853   0.869   0.954   1.007   1.019   1.082
116   P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
117   V        -0.140  -0.221  -0.192  -0.099  -0.251  -0.252  -0.334  -0.481  -0.466
118   Q         0.949   0.957   1.003   1.111   1.127   1.179   1.007   1.019   1.082
119   S         0.949   0.957   1.003   0.853   0.869   0.954   1.007   1.019   1.082
120   V        -0.140  -0.036  -0.142  -0.099   0.060  -0.153  -0.334  -0.169  -0.378
121   E         0.219   0.178  -0.104   0.236   0.177  -0.235   0.225   0.162  -0.312
122   K         0.219   0.196  -0.106   0.394   0.369  -0.062   0.225   0.188  -0.315
123   I         0.949   0.957   1.003   0.969   0.991   1.055   1.007   1.019   1.082
124   L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
125   L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
126   S         0.949   0.957   1.003   0.853   0.869   0.954   1.007   1.019   1.082
127   V         0.949   0.957   1.003   1.055   1.064   1.130   1.007   1.019   1.082
128   M         0.949   0.957   1.003   1.131   1.132   1.197   1.007   1.019   1.082
129   S         0.949   0.957   1.003   0.853   0.869   0.954   1.007   1.019   1.082
130   M         0.219   0.196  -0.106   0.495   0.454  -0.025   0.225   0.188  -0.315
131   L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
132   S        -0.332  -0.242  -0.175  -0.551  -0.388  -0.307  -0.669  -0.519  -0.436
133   E         0.949   0.957   1.003   0.874   0.881   0.972   1.007   1.019   1.082
134   P         0.949   0.957   1.003   0.707   0.734   0.827   1.007   1.019   1.082
135   N         0.949   0.957   1.003   1.055   1.067   1.130   1.007   1.019   1.082
136   I        -1.147  -1.047  -0.905  -1.467  -1.285  -1.099  -1.339  -1.213  -1.010
137   E         0.949   0.957   1.003   0.874   0.881   0.972   1.007   1.019   1.082
138   S         0.949   0.957   1.003   0.853   0.869   0.954   1.007   1.019   1.082
139   G         0.219   0.097  -0.112   0.326   0.145  -0.245   0.225   0.040  -0.326
140   A         0.949   0.957   1.003   1.010   1.017   1.091   1.007   1.019   1.082
141   N         0.949   0.957   1.003   1.055   1.067   1.130   1.007   1.019   1.082
142   I         0.219   0.097  -0.112   0.346   0.197  -0.132   0.225   0.040  -0.326
143   D         0.219   0.097  -0.112   0.304   0.136  -0.217   0.225   0.040  -0.326
144   A         0.949   0.957   1.003   1.010   1.017   1.091   1.007   1.019   1.082
145   C        -0.476  -0.628  -0.841  -0.094  -0.320  -0.733  -0.445  -0.649  -0.928
146   I        -0.332  -0.242  -0.175  -0.493  -0.329  -0.254  -0.669  -0.519  -0.436
147   L        -0.332  -0.353  -0.213  -0.640  -0.655  -0.396  -0.669  -0.719  -0.504
148   W         0.949   0.957   1.003   1.195   1.202   1.252   1.007   1.019   1.082
149   R         0.949   0.957   1.003   1.067   1.074   1.141   1.007   1.019   1.082
150   D        -0.140  -0.227  -0.191  -0.228  -0.400  -0.375  -0.334  -0.492  -0.465
151   N        -0.794  -0.925  -0.894  -0.693  -0.906  -0.891  -0.892  -1.060  -0.997
152   R         0.219   0.178  -0.104   0.451   0.396  -0.019   0.225   0.162  -0.312
153   P        -2.071  -2.003  -1.807  -2.249  -2.185  -1.828  -1.786  -1.713  -1.447
154   E         0.219   0.178  -0.104   0.259   0.205  -0.172   0.225   0.162  -0.312
155   F        -0.393  -0.356  -0.211  -0.433  -0.383  -0.164  -0.781  -0.725  -0.501
156   E        -1.400  -1.398  -1.392  -1.362  -1.345  -1.289  -1.339  -1.317  -1.262
157   R        -0.794  -0.844  -0.871  -0.661  -0.731  -0.816  -0.892  -0.942  -0.969
158   Q        -1.130  -1.306  -1.389  -0.733  -0.990  -1.176  -1.004  -1.207  -1.260
159   V        -0.140  -0.036  -0.142  -0.099   0.060  -0.153  -0.334  -0.169  -0.378
160   K        -0.393  -0.360  -0.212  -0.550  -0.502  -0.269  -0.781  -0.732  -0.504
161   L        -2.280  -2.285  -2.133  -2.163  -2.175  -1.885  -1.786  -1.783  -1.558
162   S        -1.945  -1.953  -1.798  -1.805  -1.836  -1.607  -1.674  -1.661  -1.440
163   I        -1.400  -1.335  -1.376  -1.301  -1.187  -1.332  -1.339  -1.243  -1.246
164   L        -0.938  -0.824  -0.871  -1.094  -0.891  -0.937  -1.116  -0.966  -0.968
165   K        -0.476  -0.534  -0.831  -0.265  -0.351  -0.835  -0.445  -0.532  -0.914
166   S        -0.794  -0.804  -0.874  -0.815  -0.829  -0.901  -0.892  -0.900  -0.973
167   L         0.949   0.957   1.003   0.738   0.762   0.854   1.007   1.019   1.082
168   G         0.949   0.957   1.003   0.998   1.004   1.080   1.007   1.019   1.082
169   F        -0.332  -0.242  -0.175  -0.647  -0.507  -0.377  -0.669  -0.519  -0.436
* 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/Q02159
Output conservation file - output/Q02159
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
