1     M         0.808   0.836   0.883   1.054   1.089   1.134   0.840   0.879   0.943
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S         0.808   0.836   0.883   0.964   1.006   1.059   0.840   0.879   0.943
4     A         0.808   0.836   0.883   0.416   0.466   0.597   0.840   0.879   0.943
5     D         0.808   0.836   0.883   1.049   1.082   1.131   0.840   0.879   0.943
6     H         0.004  -0.183  -0.359   0.497   0.268  -0.050   0.001  -0.278  -0.577
7     S        -1.269  -1.209  -1.153  -1.191  -1.111  -1.141  -1.436  -1.292  -1.191
8     R         0.808   0.836   0.883   0.874   0.911   0.983   0.840   0.879   0.943
9     D         0.808   0.836   0.883   1.049   1.082   1.131   0.840   0.879   0.943
10    P         0.808   0.836   0.883   0.893   0.939   0.999   0.840   0.879   0.943
11    C         0.808   0.836   0.883   1.091   1.129   1.166   0.840   0.879   0.943
12    P         0.808   0.836   0.883   0.893   0.939   0.999   0.840   0.879   0.943
13    I        -0.761  -0.968  -1.149  -0.421  -0.682  -0.891  -0.717  -0.977  -1.187
14    V         0.808   0.836   0.883   0.855   0.914   0.967   0.840   0.879   0.943
15    I         0.808   0.836   0.883   0.865   0.887   0.975   0.840   0.879   0.943
16    L         0.004  -0.183  -0.359   0.244   0.002  -0.325   0.001  -0.278  -0.577
17    N         0.808   0.836   0.883   1.040   1.067   1.123   0.840   0.879   0.943
18    D         0.808   0.836   0.883   1.049   1.082   1.131   0.840   0.879   0.943
19    F         0.808   0.836   0.883   0.908   0.948   1.011   0.840   0.879   0.943
20    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
21    G         0.004  -0.107  -0.359  -0.440  -0.582  -1.008   0.001  -0.163  -0.578
22    A         0.808   0.836   0.883   0.419   0.474   0.599   0.840   0.879   0.943
23    F         0.808   0.836   0.883   0.908   0.948   1.011   0.840   0.879   0.943
24    A        -0.391  -0.370  -0.412  -0.770  -0.718  -0.700  -0.598  -0.576  -0.669
25    M         0.808   0.836   0.883   1.054   1.089   1.134   0.840   0.879   0.943
26    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
27    A        -1.869  -1.927  -1.722  -2.102  -2.118  -1.748  -1.796  -1.785  -1.500
28    I         0.004  -0.183  -0.359   0.172  -0.090  -0.383   0.001  -0.278  -0.577
29    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
30    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
31    V        -2.008  -1.887  -1.726  -1.848  -1.692  -1.549  -1.915  -1.749  -1.503
32    V        -0.603  -0.575  -0.421  -0.771  -0.747  -0.500  -0.957  -0.928  -0.684
33    W         0.808   0.836   0.883   1.082   1.119   1.158   0.840   0.879   0.943
34    H         0.808   0.836   0.883   1.151   1.187   1.216   0.840   0.879   0.943
35    G         0.004  -0.107  -0.359  -0.347  -0.448  -0.717   0.001  -0.163  -0.578
36    I         0.808   0.836   0.883   0.865   0.887   0.975   0.840   0.879   0.943
37    K         0.808   0.836   0.883   1.049   1.085   1.131   0.840   0.879   0.943
38    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
39    F         0.004  -0.107  -0.359   0.247   0.120  -0.253   0.001  -0.163  -0.578
40    R         0.808   0.836   0.883   0.874   0.911   0.983   0.840   0.879   0.943
41    N         0.808   0.836   0.883   1.040   1.067   1.123   0.840   0.879   0.943
42    S         0.808   0.836   0.883   1.012   1.058   1.099   0.840   0.879   0.943
43    P         0.808   0.836   0.883   0.893   0.939   0.999   0.840   0.879   0.943
44    L        -1.269  -1.272  -1.173  -1.073  -1.048  -0.928  -1.436  -1.396  -1.217
45    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
46    E         0.808   0.836   0.883   1.091   1.123   1.166   0.840   0.879   0.943
47    R         0.004  -0.107  -0.359   0.209   0.077  -0.292   0.001  -0.163  -0.578
48    G        -1.269  -0.960  -1.150  -1.616  -1.019  -1.299  -1.436  -1.022  -1.189
49    S        -2.517  -2.164  -2.146  -2.410  -2.047  -1.874  -2.155  -1.835  -1.668
50    G         0.004  -0.107  -0.359  -0.347  -0.448  -0.717   0.001  -0.163  -0.578
51    A         0.004   0.157  -0.341  -0.252  -0.053  -0.623   0.001   0.206  -0.548
52    M        -2.378  -2.076  -2.129  -2.065  -1.692  -1.742  -2.035  -1.724  -1.655
53    S        -0.761  -0.968  -1.149  -0.403  -0.707  -1.115  -0.717  -0.977  -1.187
54    A         0.808   0.836   0.883   0.419   0.474   0.599   0.840   0.879   0.943
55    I        -0.761  -0.664  -1.127  -0.582  -0.523  -1.255  -0.717  -0.619  -1.160
56    K         0.004  -0.183  -0.359   0.358   0.104  -0.237   0.001  -0.278  -0.577
57    A        -1.778  -1.770  -1.723  -1.878  -1.738  -1.559  -1.676  -1.659  -1.501
58    R         0.808   0.836   0.883   0.874   0.911   0.983   0.840   0.879   0.943
59    A         0.808   0.836   0.883   0.419   0.474   0.599   0.840   0.879   0.943
60    P         0.808   0.836   0.883   0.893   0.939   0.999   0.840   0.879   0.943
61    V         0.004  -0.098  -0.356   0.102  -0.031  -0.569   0.001  -0.150  -0.572
62    L        -0.670  -0.582  -0.427  -0.850  -0.684  -0.466  -1.077  -0.940  -0.694
63    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
64    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
65    N         0.808   0.836   0.883   1.040   1.067   1.123   0.840   0.879   0.943
66    F         0.808   0.836   0.883   0.908   0.948   1.011   0.840   0.879   0.943
67    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
68    V         0.004  -0.183  -0.359   0.189  -0.024  -0.307   0.001  -0.278  -0.577
69    W         0.808   0.836   0.883   1.082   1.119   1.158   0.840   0.879   0.943
70    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
71    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
72    L         0.004  -0.183  -0.359   0.243   0.008  -0.329   0.001  -0.278  -0.577
73    F         0.808   0.836   0.883   0.908   0.948   1.011   0.840   0.879   0.943
74    S         0.808   0.836   0.883   1.012   1.058   1.099   0.840   0.879   0.943
75    T         0.808   0.836   0.883   1.045   1.074   1.127   0.840   0.879   0.943
76    F         0.004  -0.183  -0.359   0.243   0.013  -0.265   0.001  -0.278  -0.577
77    D         0.808   0.836   0.883   1.049   1.082   1.131   0.840   0.879   0.943
78    C         0.808   0.836   0.883   1.091   1.129   1.166   0.840   0.879   0.943
79    A        -1.778  -1.514  -1.702  -2.060  -1.672  -1.864  -1.676  -1.414  -1.483
80    V         0.004  -0.098  -0.356   0.163   0.050  -0.380   0.001  -0.150  -0.572
81    K         0.808   0.836   0.883   1.049   1.085   1.131   0.840   0.879   0.943
82    A        -0.391  -0.481  -0.421  -1.012  -1.226  -1.128  -0.598  -0.763  -0.683
83    V        -0.761  -1.032  -1.151  -0.507  -0.865  -1.088  -0.717  -1.061  -1.189
84    R         0.808   0.836   0.883   0.874   0.911   0.983   0.840   0.879   0.943
85    K        -1.112  -1.266  -1.178  -0.824  -1.104  -0.982  -1.197  -1.389  -1.223
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    R        -0.603  -0.575  -0.421  -0.656  -0.593  -0.367  -0.957  -0.928  -0.684
88    E         0.808   0.836   0.883   1.091   1.123   1.166   0.840   0.879   0.943
89    D         0.808   0.836   0.883   1.049   1.082   1.131   0.840   0.879   0.943
90    P        -0.391  -0.198  -0.376  -0.499  -0.167  -0.590  -0.598  -0.301  -0.607
91    W         0.004  -0.183  -0.359   0.395   0.145  -0.199   0.001  -0.278  -0.577
92    N         0.808   0.836   0.883   1.040   1.067   1.123   0.840   0.879   0.943
93    A        -0.391  -0.511  -0.422  -0.770  -0.912  -0.700  -0.598  -0.815  -0.685
94    I        -0.391  -0.198  -0.376  -0.391  -0.112  -0.415  -0.598  -0.301  -0.607
95    I         0.004  -0.098  -0.356   0.183   0.044  -0.342   0.001  -0.150  -0.572
96    A         0.808   0.836   0.883   0.419   0.474   0.599   0.840   0.879   0.943
97    G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
98    F         0.808   0.836   0.883   0.908   0.948   1.011   0.840   0.879   0.943
99    F         0.004  -0.183  -0.359   0.243   0.013  -0.265   0.001  -0.278  -0.577
100   T         0.808   0.836   0.883   1.045   1.074   1.127   0.840   0.879   0.943
101   G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
102   G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
103   A         0.808   0.836   0.883   0.419   0.474   0.599   0.840   0.879   0.943
104   L         0.808   0.836   0.883   0.936   0.987   1.035   0.840   0.879   0.943
105   A         0.808   0.836   0.883   0.419   0.474   0.599   0.840   0.879   0.943
106   V        -1.269  -1.256  -1.163  -1.324  -1.240  -1.123  -1.436  -1.357  -1.205
107   R         0.808   0.836   0.883   0.874   0.911   0.983   0.840   0.879   0.943
108   G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
109   G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
110   W         0.004  -0.098  -0.356   0.432   0.314  -0.083   0.001  -0.150  -0.572
111   R        -0.670  -0.568  -0.423  -0.754  -0.604  -0.387  -1.077  -0.915  -0.687
112   H        -1.112  -1.303  -1.180  -0.861  -1.255  -1.104  -1.197  -1.424  -1.225
113   T        -0.391  -0.511  -0.422  -0.349  -0.676  -0.618  -0.598  -0.815  -0.685
114   R         0.808   0.836   0.883   0.874   0.911   0.983   0.840   0.879   0.943
115   N         0.808   0.836   0.883   1.040   1.067   1.123   0.840   0.879   0.943
116   S        -0.603  -0.575  -0.421  -0.906  -1.033  -0.763  -0.957  -0.928  -0.684
117   S         0.004   0.242  -0.338  -0.252   0.035  -0.619   0.001   0.315  -0.543
118   I         0.808   0.836   0.883   0.865   0.887   0.975   0.840   0.879   0.943
119   T        -1.112  -1.303  -1.180  -1.026  -1.446  -1.288  -1.197  -1.424  -1.225
120   C         0.808   0.836   0.883   1.091   1.129   1.166   0.840   0.879   0.943
121   A         0.004  -0.183  -0.359  -0.357  -0.637  -0.975   0.001  -0.278  -0.577
122   C        -0.761  -1.032  -1.151  -0.276  -0.652  -0.939  -0.717  -1.061  -1.189
123   L         0.004  -0.107  -0.359   0.244   0.110  -0.325   0.001  -0.163  -0.578
124   L         0.808   0.836   0.883   0.936   0.987   1.035   0.840   0.879   0.943
125   G        -0.603  -0.575  -0.421  -1.513  -1.463  -1.129  -0.957  -0.928  -0.684
126   V         0.808   0.836   0.883   0.855   0.914   0.967   0.840   0.879   0.943
127   I        -0.603  -0.520  -0.423  -0.739  -0.624  -0.474  -0.957  -0.830  -0.688
128   E         0.808   0.836   0.883   1.091   1.123   1.166   0.840   0.879   0.943
129   G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
130   V         0.004  -0.107  -0.359   0.174   0.059  -0.355   0.001  -0.163  -0.578
131   G         0.808   0.836   0.883   0.324   0.389   0.519   0.840   0.879   0.943
132   L        -1.499  -1.220  -1.168  -1.511  -1.107  -1.025  -1.676  -1.306  -1.209
133   M        -1.112  -1.266  -1.178  -1.111  -1.567  -1.542  -1.197  -1.389  -1.223
134   F        -1.778  -1.849  -1.721  -1.507  -1.595  -1.445  -1.676  -1.700  -1.498
135   Q        -0.391  -0.514  -0.423  -0.276  -0.622  -0.604  -0.598  -0.820  -0.687
136   R         0.004  -0.098  -0.356   0.209   0.088  -0.286   0.001  -0.150  -0.572
137   Y        -1.778  -1.601  -1.717  -1.277  -1.100  -1.296  -1.676  -1.509  -1.496
138   A        -2.747  -2.724  -2.504  -2.569  -2.445  -2.005  -2.155  -2.091  -1.786
139   A         0.808   0.836   0.883   0.419   0.474   0.599   0.840   0.879   0.943
140   W        -2.378  -2.435  -2.158  -2.055  -2.310  -1.961  -2.035  -2.016  -1.676
141   Q        -2.008  -1.914  -1.728  -1.904  -1.889  -1.548  -1.915  -1.770  -1.505
142   A        -1.869  -1.907  -1.718  -1.882  -1.745  -1.471  -1.796  -1.763  -1.496
143   K        -0.259  -0.369  -0.404  -0.017  -0.210  -0.334  -0.387  -0.575  -0.654
144   P        -0.259  -0.368  -0.402  -0.169  -0.338  -0.437  -0.387  -0.573  -0.651
145   M        -1.230  -1.351  -1.182  -0.999  -1.181  -0.978  -1.351  -1.477  -1.227
146   A         0.808   0.836   0.883   0.424   0.480   0.604   0.840   0.879   0.943
147   P         0.808   0.836   0.883   0.885   0.927   0.992   0.840   0.879   0.943
148   P        -1.493  -1.408  -1.186  -1.846  -1.769  -1.417  -1.664  -1.542  -1.232
149   L        -2.378  -2.435  -2.158  -2.075  -2.271  -1.885  -2.035  -2.016  -1.676
150   P         0.808   0.836   0.883   0.893   0.939   0.999   0.840   0.879   0.943
151   E        -1.409  -1.386  -1.194  -1.201  -1.221  -0.964  -1.556  -1.517  -1.241
152   A        -2.496  -2.360  -2.148  -2.579  -2.315  -2.091  -2.133  -1.968  -1.669
153   P        -1.915  -1.891  -1.713  -1.936  -1.775  -1.566  -1.820  -1.744  -1.492
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   Q        -1.869  -1.690  -1.700  -1.818  -1.662  -1.525  -1.796  -1.563  -1.479
162   P        -0.761  -0.725  -1.128  -0.520  -0.456  -1.152  -0.717  -0.683  -1.161
163   L        -1.778  -1.887  -1.723  -1.591  -1.782  -1.621  -1.676  -1.747  -1.501
164   Q        -1.269  -1.145  -1.148  -1.488  -1.325  -1.237  -1.436  -1.216  -1.185
165   A         0.004  -0.107  -0.359  -0.277  -0.396  -0.721   0.001  -0.163  -0.578
* 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/P39515
Output conservation file - output/P39515
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
