1     M         1.354   1.365   1.448   1.614   1.622   1.751   1.469   1.487   1.617
2     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     V        -0.414  -0.427  -0.321  -0.663  -0.702  -0.521  -0.683  -0.695  -0.550
7     S        -0.155  -0.165  -0.223  -0.175  -0.180  -0.270  -0.318  -0.320  -0.408
8     P         0.121  -0.013  -0.175   0.456   0.266  -0.000   0.103  -0.089  -0.336
9     L         1.354   1.365   1.448   1.037   1.050   1.193   1.469   1.487   1.617
10    T        -1.151  -1.215  -1.151  -0.866  -0.934  -0.844  -1.053  -1.104  -0.999
11    K         0.121   0.110  -0.140   0.592   0.567   0.213   0.103   0.084  -0.283
12    I         1.354   1.365   1.448   1.238   1.253   1.387   1.469   1.487   1.617
13    I         1.354   1.365   1.448   1.238   1.253   1.387   1.469   1.487   1.617
14    S        -1.551  -1.568  -1.470  -1.549  -1.552  -1.372  -1.263  -1.267  -1.129
15    L         1.354   1.365   1.448   1.037   1.050   1.193   1.469   1.487   1.617
16    S         1.354   1.365   1.448   1.344   1.359   1.490   1.469   1.487   1.617
17    G        -1.151  -1.215  -1.151  -1.145  -1.256  -1.179  -1.053  -1.104  -0.999
18    F         0.192   0.216   0.323  -0.098  -0.036   0.127  -0.213  -0.174  -0.018
19    L         1.354   1.365   1.448   1.037   1.050   1.193   1.469   1.487   1.617
20    A         1.354   1.365   1.448   1.477   1.472   1.618   1.469   1.487   1.617
21    L        -0.860  -0.850  -0.787  -1.197  -1.149  -1.060  -0.948  -0.934  -0.832
22    G         1.354   1.365   1.448   1.444   1.454   1.587   1.469   1.487   1.617
23    F         1.354   1.365   1.448   1.296   1.339   1.444   1.469   1.487   1.617
24    L         0.722   0.634   0.513   0.485   0.373   0.227   0.733   0.590   0.350
25    L         0.722   0.771   0.536   0.434   0.503   0.151   0.733   0.806   0.391
26    V         0.192   0.210   0.315  -0.141  -0.114   0.060  -0.213  -0.186  -0.034
27    I         0.411   0.458   0.429   0.062   0.149   0.033   0.208   0.286   0.191
28    L         1.354   1.365   1.448   1.037   1.050   1.193   1.469   1.487   1.617
29    S         1.354   1.365   1.448   1.344   1.359   1.490   1.469   1.487   1.617
30    C         1.354   1.365   1.448   1.664   1.671   1.799   1.469   1.487   1.617
31    A         1.354   1.365   1.448   1.477   1.472   1.618   1.469   1.487   1.617
32    L         1.354   1.365   1.448   1.037   1.050   1.193   1.469   1.487   1.617
33    F        -0.460  -0.456  -0.340  -0.514  -0.481  -0.329  -0.738  -0.732  -0.576
34    H        -0.860  -0.855  -0.792  -0.623  -0.613  -0.549  -0.948  -0.943  -0.836
35    N         0.722   0.672   0.518   1.010   0.940   0.695   0.733   0.652   0.358
36    Y         0.245   0.232   0.319   0.372   0.347   0.468  -0.107  -0.141  -0.026
37    Y        -0.446  -0.399  -0.661  -0.068  -0.008  -0.437  -0.423  -0.365  -0.681
38    P         0.722   0.789   0.542   1.012   1.089   0.748   0.733   0.834   0.403
39    L         1.354   1.365   1.448   1.037   1.050   1.193   1.469   1.487   1.617
40    F        -0.860  -0.863  -0.790  -1.199  -1.234  -1.152  -0.948  -0.948  -0.834
41    D        -0.679  -0.663  -0.731  -0.584  -0.580  -0.702  -0.738  -0.706  -0.767
42    I        -0.279  -0.212  -0.260  -0.455  -0.340  -0.387  -0.528  -0.434  -0.471
43    L        -0.679  -0.753  -0.753  -1.061  -1.187  -1.142  -0.738  -0.824  -0.793
44    I        -0.446  -0.577  -0.709  -0.411  -0.592  -0.766  -0.423  -0.587  -0.738
45    F         0.722   0.672   0.518   0.746   0.715   0.478   0.733   0.652   0.358
46    L        -0.446  -0.577  -0.709  -0.658  -0.860  -1.018  -0.423  -0.587  -0.738
47    L         0.722   0.739   0.532   0.425   0.447   0.124   0.733   0.757   0.384
48    A         1.354   1.365   1.448   1.477   1.472   1.618   1.469   1.487   1.617
49    P         1.354   1.365   1.448   1.578   1.585   1.716   1.469   1.487   1.617
50    I        -0.279  -0.271  -0.270  -0.865  -0.848  -0.802  -0.528  -0.511  -0.487
51    P         1.354   1.365   1.448   1.578   1.585   1.716   1.469   1.487   1.617
52    N         1.354   1.365   1.448   1.583   1.596   1.721   1.469   1.487   1.617
53    T        -1.551  -1.507  -1.443  -1.745  -1.696  -1.566  -1.263  -1.223  -1.110
54    I         0.245   0.253   0.330  -0.324  -0.319  -0.227  -0.107  -0.101  -0.004
55    F        -0.860  -0.895  -0.795  -0.911  -0.917  -0.769  -0.948  -0.975  -0.838
56    N        -1.551  -1.581  -1.456  -1.396  -1.427  -1.271  -1.263  -1.276  -1.120
57    A        -1.551  -1.507  -1.446  -1.208  -1.137  -1.043  -1.263  -1.223  -1.112
58    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    Y        -1.151  -1.138  -1.133  -0.988  -0.928  -0.942  -1.053  -1.034  -0.983
62    H        -1.260  -1.194  -1.158  -1.120  -1.065  -0.951  -1.158  -1.100  -1.007
63    T        -0.751  -0.776  -0.753  -0.774  -0.791  -0.745  -0.843  -0.859  -0.796
64    -        -1.649  -1.619  -1.482  -1.260  -1.225  -1.030  -1.334  -1.302  -1.138
65    S        -1.260  -1.247  -1.166  -1.040  -0.992  -0.891  -1.158  -1.139  -1.013
66    D         0.722   0.782   0.534   1.048   1.119   0.783   0.733   0.823   0.388
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    F         1.354   1.365   1.448   1.296   1.339   1.444   1.469   1.487   1.617
70    M        -0.279  -0.293  -0.270  -0.597  -0.621  -0.533  -0.528  -0.532  -0.487
71    S        -1.151  -1.180  -1.132  -0.994  -1.010  -0.905  -1.053  -1.074  -0.982
72    D        -0.860  -0.837  -0.765  -0.836  -0.772  -0.700  -0.948  -0.910  -0.804
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    S        -0.679  -0.697  -0.725  -0.632  -0.639  -0.659  -0.738  -0.747  -0.762
84    S        -1.551  -1.526  -1.442  -1.351  -1.313  -1.162  -1.263  -1.238  -1.109
85    N        -1.260  -1.254  -1.155  -1.081  -1.064  -0.929  -1.158  -1.143  -1.004
86    T        -0.751  -0.735  -0.736  -0.602  -0.587  -0.566  -0.843  -0.823  -0.780
87    G        -0.860  -0.808  -0.782  -1.240  -1.182  -1.076  -0.948  -0.892  -0.826
88    Q        -1.260  -1.219  -1.150  -1.170  -1.198  -0.997  -1.158  -1.114  -1.000
89    D         0.411   0.458   0.429   0.605   0.674   0.607   0.208   0.286   0.191
90    L        -0.155  -0.135  -0.226  -0.405  -0.344  -0.547  -0.318  -0.291  -0.420
91    A         0.121   0.206  -0.117   0.340   0.445   0.007   0.103   0.219  -0.250
92    H        -0.460  -0.417  -0.323  -0.229  -0.161  -0.030  -0.738  -0.680  -0.553
93    F         0.722   0.789   0.542   0.746   0.858   0.516   0.733   0.834   0.403
94    L        -1.441  -1.462  -1.438  -1.628  -1.630  -1.550  -1.158  -1.176  -1.104
95    T         0.722   0.634   0.513   0.930   0.802   0.580   0.733   0.590   0.350
96    G         0.722   0.771   0.536   0.853   0.914   0.558   0.733   0.806   0.391
97    M        -1.151  -1.132  -1.120  -1.233  -1.183  -1.222  -1.053  -1.026  -0.970
98    L        -0.155  -0.215  -0.244  -0.443  -0.518  -0.513  -0.318  -0.392  -0.446
99    V        -0.155  -0.162  -0.250  -0.248  -0.292  -0.528  -0.318  -0.336  -0.456
100   T        -1.151  -1.169  -1.140  -0.955  -0.968  -0.923  -1.053  -1.061  -0.989
101   S         0.121  -0.013  -0.175   0.242   0.063  -0.169   0.103  -0.089  -0.336
102   G         1.354   1.365   1.448   1.444   1.454   1.587   1.469   1.487   1.617
103   I        -0.155  -0.256  -0.271  -0.532  -0.718  -0.816  -0.318  -0.458  -0.481
104   A        -0.679  -0.609  -0.702  -0.748  -0.655  -0.841  -0.738  -0.661  -0.736
105   L         0.722   0.715   0.525   0.425   0.414   0.111   0.733   0.720   0.371
106   P         1.354   1.365   1.448   1.578   1.585   1.716   1.469   1.487   1.617
107   V        -0.860  -0.821  -0.773  -1.283  -1.215  -1.158  -0.948  -0.906  -0.815
108   V        -0.155  -0.129  -0.219  -0.033  -0.003  -0.120  -0.318  -0.274  -0.403
109   F         0.245   0.241   0.322  -0.268  -0.271  -0.204  -0.107  -0.125  -0.021
110   Y        -0.155  -0.256  -0.271   0.048  -0.122  -0.176  -0.318  -0.458  -0.481
111   H         0.411   0.339   0.357   0.657   0.528   0.512   0.208   0.066   0.050
112   C        -1.151  -1.195  -1.135  -0.919  -1.004  -0.924  -1.053  -1.089  -0.987
113   Q        -1.551  -1.534  -1.452  -1.232  -1.236  -1.111  -1.263  -1.242  -1.116
114   L         0.411   0.380   0.378  -0.074  -0.139  -0.174   0.208   0.143   0.092
115   I         1.354   1.365   1.448   1.238   1.253   1.387   1.469   1.487   1.617
116   G        -1.151  -1.128  -1.127  -0.903  -0.877  -0.830  -1.053  -1.027  -0.979
117   H        -1.551  -1.506  -1.450  -1.484  -1.400  -1.408  -1.263  -1.220  -1.115
118   L        -1.551  -1.486  -1.454  -1.485  -1.385  -1.349  -1.263  -1.207  -1.117
119   S         0.192   0.215   0.320  -0.074  -0.037   0.139  -0.213  -0.176  -0.023
120   C        -0.860  -0.796  -0.771  -0.680  -0.609  -0.557  -0.948  -0.880  -0.814
121   I        -0.446  -0.490  -0.676  -0.477  -0.529  -0.840  -0.423  -0.483  -0.698
122   M         1.354   1.365   1.448   1.614   1.622   1.751   1.469   1.487   1.617
123   C         0.121   0.246  -0.121   0.250   0.408  -0.071   0.103   0.276  -0.256
124   M        -1.260  -1.274  -1.159  -1.338  -1.354  -1.192  -1.158  -1.158  -1.007
125   I        -0.389  -0.388  -0.327  -0.720  -0.720  -0.627  -0.633  -0.634  -0.556
126   G         1.354   1.365   1.448   1.444   1.454   1.587   1.469   1.487   1.617
127   G         1.354   1.365   1.448   1.444   1.454   1.587   1.469   1.487   1.617
128   L         0.722   0.634   0.513   0.442   0.318   0.128   0.733   0.590   0.350
129   I         0.411   0.380   0.378   0.062  -0.012  -0.093   0.208   0.143   0.092
130   I         0.411   0.458   0.429   0.214   0.283   0.230   0.208   0.286   0.191
131   Y         0.722   0.634   0.513   1.026   0.907   0.670   0.733   0.590   0.350
132   S        -1.151  -1.145  -1.125  -1.515  -1.506  -1.416  -1.053  -1.035  -0.977
133   S        -1.260  -1.247  -1.166  -1.134  -1.113  -0.970  -1.158  -1.139  -1.013
134   I         1.354   1.365   1.448   1.238   1.253   1.387   1.469   1.487   1.617
135   V        -0.155  -0.165  -0.228  -0.302  -0.301  -0.394  -0.318  -0.314  -0.418
136   I        -0.970  -1.045  -1.117  -1.152  -1.302  -1.491  -0.843  -0.925  -0.966
137   F         0.722   0.634   0.513   0.746   0.665   0.472   0.733   0.590   0.350
138   K        -1.551  -1.509  -1.455  -1.580  -1.536  -1.379  -1.263  -1.225  -1.118
139   W        -0.446  -0.577  -0.709   0.069  -0.118  -0.338  -0.423  -0.587  -0.738
140   F         0.722   0.634   0.513   0.724   0.632   0.422   0.733   0.590   0.350
141   F         1.354   1.365   1.448   1.296   1.339   1.444   1.469   1.487   1.617
142   K        -1.551  -1.558  -1.446  -1.235  -1.244  -1.057  -1.263  -1.261  -1.112
143   K        -1.151  -1.095  -1.115  -0.802  -0.719  -0.739  -1.053  -0.994  -0.968
144   D        -1.151  -1.137  -1.130  -0.890  -0.850  -0.839  -1.053  -1.033  -0.981
145   F        -0.679  -0.623  -0.719  -0.362  -0.266  -0.433  -0.738  -0.666  -0.754
146   N        -0.279  -0.207  -0.265  -0.123  -0.033  -0.087  -0.528  -0.445  -0.483
147   -        -0.879  -0.826  -0.781  -0.779  -0.693  -0.656  -0.952  -0.888  -0.821
148   E         0.226   0.238   0.326   0.303   0.314   0.443  -0.145  -0.131  -0.012
149   D         0.515   0.501   0.400   0.749   0.723   0.539   0.393   0.363   0.135
150   D         1.354   1.365   1.448   1.585   1.596   1.723   1.469   1.487   1.617
151   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   F         1.354   1.365   1.448   1.265   1.293   1.414   1.469   1.487   1.617
154   G         0.226   0.238   0.326   0.099   0.112   0.248  -0.145  -0.131  -0.012
155   -         0.599   0.593   0.482   0.615   0.609   0.452   0.535   0.522   0.291
* 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/P47111
Output conservation file - output/P47111
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
