1     M         0.739   0.768   0.800   0.977   0.996   1.020   0.761   0.802   0.843
2     G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
3     N        -0.949  -0.836  -0.662  -1.013  -0.865  -0.593  -1.340  -1.169  -0.890
4     I        -3.092  -2.755  -2.587  -2.845  -2.489  -2.206  -2.566  -2.218  -1.925
5     F        -1.229  -1.564  -1.503  -0.826  -1.390  -1.408  -1.165  -1.573  -1.451
6     S        -0.275  -0.400  -0.616  -0.185  -0.361  -0.725  -0.289  -0.474  -0.815
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     S        -0.740  -0.490  -0.622  -0.806  -0.443  -0.642  -0.990  -0.609  -0.825
10    M        -1.623  -1.626  -1.502  -1.451  -1.496  -1.366  -1.690  -1.646  -1.451
11    F        -0.275  -0.557  -0.625   0.015  -0.472  -0.724  -0.289  -0.712  -0.830
12    D        -1.743  -1.372  -1.483  -1.902  -1.351  -1.481  -1.865  -1.389  -1.429
13    K        -1.743  -1.736  -1.505  -1.709  -1.679  -1.327  -1.865  -1.782  -1.455
14    L        -0.275  -0.400  -0.616  -0.580  -0.691  -0.973  -0.289  -0.474  -0.815
15    W        -1.229  -1.289  -1.488  -0.817  -0.949  -1.370  -1.165  -1.271  -1.434
16    G        -0.275  -0.557  -0.625  -0.184  -0.566  -0.629  -0.289  -0.712  -0.830
17    S        -3.092  -2.686  -2.581  -3.078  -2.554  -2.346  -2.566  -2.155  -1.921
18    N        -1.229  -1.289  -1.488  -0.907  -1.087  -1.392  -1.165  -1.271  -1.434
19    K         0.739   0.768   0.800   0.734   0.794   0.826   0.761   0.802   0.843
20    E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
21    L        -0.949  -0.655  -0.632  -1.533  -0.919  -0.947  -1.340  -0.868  -0.840
22    R         0.739   0.768   0.800   0.916   0.937   0.971   0.761   0.802   0.843
23    I         0.739   0.768   0.800   0.680   0.740   0.784   0.761   0.802   0.843
24    L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
25    I         0.739   0.768   0.800   0.680   0.740   0.784   0.761   0.802   0.843
26    L        -0.275  -0.400  -0.616  -0.590  -0.699  -0.999  -0.289  -0.474  -0.815
27    G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
28    L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
29    D         0.739   0.768   0.800   0.734   0.786   0.826   0.761   0.802   0.843
30    G        -0.275  -0.557  -0.625  -0.203  -0.605  -0.682  -0.289  -0.712  -0.830
31    A         0.739   0.768   0.800   0.696   0.723   0.797   0.761   0.802   0.843
32    G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
33    K         0.739   0.768   0.800   0.734   0.794   0.826   0.761   0.802   0.843
34    T         0.739   0.768   0.800   0.696   0.735   0.797   0.761   0.802   0.843
35    T         0.739   0.768   0.800   0.696   0.735   0.797   0.761   0.802   0.843
36    I        -0.275  -0.557  -0.625  -0.279  -0.730  -0.931  -0.289  -0.712  -0.830
37    L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
38    Y         0.739   0.768   0.800   0.977   1.002   1.020   0.761   0.802   0.843
39    R         0.739   0.768   0.800   0.916   0.937   0.971   0.761   0.802   0.843
40    L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
41    Q        -0.275  -0.557  -0.625   0.009  -0.402  -0.587  -0.289  -0.712  -0.830
42    I        -1.623  -1.516  -1.496  -1.674  -1.554  -1.557  -1.690  -1.511  -1.444
43    G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
44    E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
45    V         0.739   0.768   0.800   0.734   0.771   0.826   0.761   0.802   0.843
46    V        -0.275  -0.048  -0.598  -0.166   0.105  -0.673  -0.289   0.012  -0.786
47    T        -0.275  -0.400  -0.616  -0.195  -0.376  -0.708  -0.289  -0.474  -0.815
48    T         0.739   0.768   0.800   0.696   0.735   0.797   0.761   0.802   0.843
49    K        -1.229  -1.564  -1.503  -1.041  -1.574  -1.499  -1.165  -1.573  -1.451
50    P         0.739   0.768   0.800   1.048   1.067   1.076   0.761   0.802   0.843
51    T         0.739   0.768   0.800   0.696   0.735   0.797   0.761   0.802   0.843
52    I         0.739   0.768   0.800   0.680   0.740   0.784   0.761   0.802   0.843
53    G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
54    F         0.739   0.768   0.800   0.972   1.001   1.016   0.761   0.802   0.843
55    N         0.739   0.768   0.800   0.870   0.891   0.934   0.761   0.802   0.843
56    V         0.739   0.768   0.800   0.734   0.771   0.826   0.761   0.802   0.843
57    E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
58    T        -0.275  -0.557  -0.625  -0.197  -0.618  -0.732  -0.289  -0.712  -0.830
59    L        -0.275  -0.557  -0.625  -0.580  -0.923  -0.986  -0.289  -0.712  -0.830
60    S        -2.417  -1.873  -2.092  -2.373  -1.648  -1.880  -2.216  -1.622  -1.729
61    Y         0.739   0.768   0.800   0.977   1.002   1.020   0.761   0.802   0.843
62    K         0.739   0.768   0.800   0.734   0.794   0.826   0.761   0.802   0.843
63    N         0.739   0.768   0.800   0.870   0.891   0.934   0.761   0.802   0.843
64    L        -0.275  -0.080  -0.596  -0.590  -0.283  -0.970  -0.289  -0.029  -0.783
65    K        -1.623  -1.626  -1.502  -1.631  -1.620  -1.432  -1.690  -1.646  -1.451
66    L        -0.275  -0.557  -0.625  -0.536  -0.838  -0.866  -0.289  -0.712  -0.830
67    N         0.739   0.768   0.800   0.870   0.891   0.934   0.761   0.802   0.843
68    V        -0.740  -0.490  -0.622  -0.863  -0.488  -0.718  -0.990  -0.609  -0.825
69    W         0.739   0.768   0.800   0.983   1.005   1.024   0.761   0.802   0.843
70    D         0.739   0.768   0.800   0.734   0.786   0.826   0.761   0.802   0.843
71    L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
72    G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
73    G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
74    Q         0.739   0.768   0.800   0.901   0.952   0.959   0.761   0.802   0.843
75    T         0.739   0.768   0.800   0.696   0.735   0.797   0.761   0.802   0.843
76    S         0.739   0.768   0.800   0.718   0.771   0.814   0.761   0.802   0.843
77    I         0.739   0.768   0.800   0.680   0.740   0.784   0.761   0.802   0.843
78    R         0.739   0.768   0.800   0.916   0.937   0.971   0.761   0.802   0.843
79    P         0.739   0.768   0.800   1.048   1.067   1.076   0.761   0.802   0.843
80    Y         0.739   0.768   0.800   0.977   1.002   1.020   0.761   0.802   0.843
81    W         0.739   0.768   0.800   0.983   1.005   1.024   0.761   0.802   0.843
82    R         0.739   0.768   0.800   0.916   0.937   0.971   0.761   0.802   0.843
83    C         0.739   0.768   0.800   1.094   1.103   1.112   0.761   0.802   0.843
84    Y         0.739   0.768   0.800   0.977   1.002   1.020   0.761   0.802   0.843
85    Y         0.739   0.768   0.800   0.977   1.002   1.020   0.761   0.802   0.843
86    A        -0.740  -0.490  -0.622  -0.885  -0.525  -0.726  -0.990  -0.609  -0.825
87    D        -0.740  -0.363  -0.605  -0.714  -0.169  -0.568  -0.990  -0.419  -0.796
88    T         0.739   0.768   0.800   0.696   0.735   0.797   0.761   0.802   0.843
89    A        -0.275  -0.080  -0.596  -0.197   0.024  -0.680  -0.289  -0.029  -0.783
90    A         0.739   0.768   0.800   0.696   0.723   0.797   0.761   0.802   0.843
91    V        -0.275  -0.400  -0.616  -0.166  -0.352  -0.706  -0.289  -0.474  -0.815
92    I         0.739   0.768   0.800   0.680   0.740   0.784   0.761   0.802   0.843
93    F         0.739   0.768   0.800   0.972   1.001   1.016   0.761   0.802   0.843
94    V         0.739   0.768   0.800   0.734   0.771   0.826   0.761   0.802   0.843
95    V         0.739   0.768   0.800   0.734   0.771   0.826   0.761   0.802   0.843
96    D         0.739   0.768   0.800   0.734   0.786   0.826   0.761   0.802   0.843
97    S         0.739   0.768   0.800   0.718   0.771   0.814   0.761   0.802   0.843
98    T         0.739   0.768   0.800   0.696   0.735   0.797   0.761   0.802   0.843
99    D         0.739   0.768   0.800   0.734   0.786   0.826   0.761   0.802   0.843
100   K        -0.275  -0.557  -0.625  -0.116  -0.484  -0.586  -0.289  -0.712  -0.830
101   D        -1.623  -1.675  -1.503  -1.631  -1.736  -1.437  -1.690  -1.720  -1.453
102   R         0.739   0.768   0.800   0.916   0.937   0.971   0.761   0.802   0.843
103   M        -1.743  -1.718  -1.506  -1.830  -1.896  -1.570  -1.865  -1.759  -1.455
104   S        -2.417  -2.183  -2.112  -2.300  -1.962  -1.819  -2.216  -1.930  -1.746
105   T        -1.623  -1.502  -1.493  -1.647  -1.446  -1.408  -1.690  -1.493  -1.441
106   A        -0.275  -0.400  -0.616  -0.133  -0.305  -0.545  -0.289  -0.474  -0.815
107   S        -2.417  -2.416  -2.123  -2.197  -2.272  -1.811  -2.216  -2.133  -1.756
108   K        -1.229  -1.564  -1.503  -1.041  -1.569  -1.499  -1.165  -1.573  -1.451
109   E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
110   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
111   H        -0.275  -0.557  -0.625   0.224  -0.244  -0.454  -0.289  -0.712  -0.830
112   L        -2.907  -2.791  -2.594  -3.034  -2.869  -2.430  -2.391  -2.240  -1.930
113   M         0.739   0.768   0.800   0.977   0.996   1.020   0.761   0.802   0.843
114   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
115   Q        -2.417  -2.416  -2.123  -2.214  -2.249  -1.839  -2.216  -2.133  -1.756
116   E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
117   E        -0.275  -0.400  -0.616  -0.211  -0.386  -0.719  -0.289  -0.474  -0.815
118   E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
119   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
120   Q        -1.229  -1.292  -1.485  -0.945  -1.083  -1.517  -1.165  -1.274  -1.431
121   D        -0.275  -0.400  -0.616  -0.135  -0.299  -0.622  -0.289  -0.474  -0.815
122   A        -0.949  -0.726  -0.651  -1.267  -0.916  -0.778  -1.340  -0.983  -0.872
123   A        -0.275  -0.400  -0.616  -0.195  -0.391  -0.708  -0.289  -0.474  -0.815
124   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
125   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
126   V         0.739   0.768   0.800   0.734   0.771   0.826   0.761   0.802   0.843
127   F         0.739   0.768   0.800   0.972   1.001   1.016   0.761   0.802   0.843
128   A         0.739   0.768   0.800   0.696   0.723   0.797   0.761   0.802   0.843
129   N         0.739   0.768   0.800   0.870   0.891   0.934   0.761   0.802   0.843
130   K         0.739   0.768   0.800   0.734   0.794   0.826   0.761   0.802   0.843
131   Q         0.739   0.768   0.800   0.901   0.952   0.959   0.761   0.802   0.843
132   D         0.739   0.768   0.800   0.734   0.786   0.826   0.761   0.802   0.843
133   Q         0.739   0.768   0.800   0.901   0.952   0.959   0.761   0.802   0.843
134   P        -0.275  -0.400  -0.616   0.147  -0.064  -0.491  -0.289  -0.474  -0.815
135   G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
136   A         0.739   0.768   0.800   0.696   0.723   0.797   0.761   0.802   0.843
137   L        -1.743  -1.718  -1.506  -1.990  -1.832  -1.535  -1.865  -1.759  -1.455
138   S        -1.623  -1.582  -1.496  -1.703  -1.671  -1.522  -1.690  -1.594  -1.443
139   A         0.739   0.768   0.800   0.696   0.723   0.797   0.761   0.802   0.843
140   S        -0.949  -0.655  -0.632  -1.267  -0.791  -0.743  -1.340  -0.868  -0.840
141   E        -0.275  -0.557  -0.625  -0.211  -0.623  -0.735  -0.289  -0.712  -0.830
142   V        -0.275  -0.557  -0.625  -0.166  -0.594  -0.724  -0.289  -0.712  -0.830
143   S         0.739   0.768   0.800   0.718   0.771   0.814   0.761   0.802   0.843
144   K        -1.743  -1.627  -1.499  -1.761  -1.540  -1.389  -1.865  -1.656  -1.447
145   E        -0.949  -0.655  -0.632  -1.290  -0.811  -0.761  -1.340  -0.868  -0.840
146   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
147   N        -2.113  -2.224  -2.115  -1.703  -1.962  -1.802  -1.865  -1.967  -1.749
148   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
149   V        -2.417  -2.248  -2.114  -2.427  -2.262  -1.998  -2.216  -1.997  -1.748
150   E        -1.623  -1.516  -1.496  -1.698  -1.538  -1.502  -1.690  -1.511  -1.444
151   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
152   K        -0.275  -0.557  -0.625  -0.127  -0.504  -0.615  -0.289  -0.712  -0.830
153   D         0.739   0.768   0.800   0.734   0.786   0.826   0.761   0.802   0.843
154   R         0.739   0.768   0.800   0.916   0.937   0.971   0.761   0.802   0.843
155   S        -0.275  -0.557  -0.625  -0.151  -0.543  -0.647  -0.289  -0.712  -0.830
156   W         0.739   0.768   0.800   0.983   1.005   1.024   0.761   0.802   0.843
157   S         0.739   0.768   0.800   0.718   0.771   0.814   0.761   0.802   0.843
158   I         0.739   0.768   0.800   0.680   0.740   0.784   0.761   0.802   0.843
159   V        -0.740  -0.830  -0.662  -0.750  -0.917  -0.621  -0.990  -1.158  -0.890
160   A        -0.275  -0.400  -0.616  -0.141  -0.315  -0.565  -0.289  -0.474  -0.815
161   S        -0.740  -0.830  -0.662  -0.719  -0.845  -0.561  -0.990  -1.158  -0.890
162   S         0.739   0.768   0.800   0.718   0.771   0.814   0.761   0.802   0.843
163   A         0.739   0.768   0.800   0.696   0.723   0.797   0.761   0.802   0.843
164   I        -1.229  -1.564  -1.503  -1.166  -1.728  -1.696  -1.165  -1.573  -1.451
165   K        -0.275  -0.557  -0.625  -0.166  -0.576  -0.724  -0.289  -0.712  -0.830
166   G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
167   E        -0.275  -0.557  -0.625  -0.217  -0.640  -0.753  -0.289  -0.712  -0.830
168   G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
169   I        -0.949  -0.818  -0.661  -1.533  -1.293  -1.036  -1.340  -1.137  -0.889
170   T        -0.275  -0.400  -0.616  -0.197  -0.380  -0.715  -0.289  -0.474  -0.815
171   E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
172   G         0.739   0.768   0.800   0.664   0.705   0.771   0.761   0.802   0.843
173   L        -0.275  -0.557  -0.625  -0.536  -0.840  -0.863  -0.289  -0.712  -0.830
174   D         0.739   0.768   0.800   0.734   0.786   0.826   0.761   0.802   0.843
175   W         0.739   0.768   0.800   0.983   1.005   1.024   0.761   0.802   0.843
176   L         0.739   0.768   0.800   0.312   0.422   0.492   0.761   0.802   0.843
177   I        -2.417  -2.416  -2.123  -2.292  -2.347  -1.880  -2.216  -2.133  -1.756
178   D        -1.229  -1.564  -1.503  -1.011  -1.510  -1.431  -1.165  -1.573  -1.451
179   V        -0.275  -0.557  -0.625  -0.164  -0.595  -0.717  -0.289  -0.712  -0.830
180   I        -0.275  -0.557  -0.625  -0.211  -0.614  -0.735  -0.289  -0.712  -0.830
181   K         0.739   0.768   0.800   0.734   0.794   0.826   0.761   0.802   0.843
182   E        -0.949  -0.695  -0.645  -1.270  -0.852  -0.770  -1.340  -0.932  -0.862
183   E         0.739   0.768   0.800   0.680   0.724   0.784   0.761   0.802   0.843
184   Q        -0.375  -0.622  -0.646  -0.121  -0.532  -0.627  -0.430  -0.815  -0.864
185   L        -0.375  -0.234  -0.631  -0.670  -0.460  -0.874  -0.430  -0.236  -0.840
* 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/P38116
Output conservation file - output/P38116
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
