1     M         1.028   1.043   1.108   1.376   1.363   1.445   1.054   1.079   1.176
2     A        -1.166  -1.306  -1.192  -1.241  -1.482  -1.305  -1.140  -1.315  -1.136
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
5     F        -0.263  -0.288  -0.296  -0.114  -0.163  -0.232  -0.374  -0.424  -0.478
6     L        -0.263  -0.154  -0.292  -0.109   0.014  -0.221  -0.374  -0.223  -0.472
7     K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
8     A        -2.167  -2.153  -1.796  -2.009  -1.958  -1.522  -1.903  -1.848  -1.429
9     G         0.178  -0.037  -0.264   0.451   0.176  -0.180   0.238  -0.054  -0.425
10    K         0.178  -0.037  -0.264  -0.252  -0.472  -0.743   0.238  -0.054  -0.425
11    V         1.028   1.043   1.108   0.799   0.841   0.964   1.054   1.079   1.176
12    A         0.178  -0.037  -0.264   0.328   0.113  -0.176   0.238  -0.054  -0.425
13    V        -1.558  -1.295  -1.168  -1.680  -1.233  -1.126  -1.598  -1.274  -1.108
14    V         0.178   0.130  -0.245   0.134   0.102  -0.378   0.238   0.173  -0.395
15    V        -0.524  -0.561  -0.351  -0.850  -0.913  -0.578  -0.782  -0.864  -0.567
16    R         1.028   1.043   1.108   1.084   1.076   1.201   1.054   1.079   1.176
17    G         1.028   1.043   1.108   1.121   1.126   1.232   1.054   1.079   1.176
18    R         1.028   1.043   1.108   1.084   1.076   1.201   1.054   1.079   1.176
19    Y        -0.524  -0.483  -0.346  -0.391  -0.366  -0.250  -0.782  -0.735  -0.560
20    A         1.028   1.043   1.108   0.959   0.999   1.098   1.054   1.079   1.176
21    G         1.028   1.043   1.108   1.121   1.126   1.232   1.054   1.079   1.176
22    K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
23    K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
24    V         1.028   1.043   1.108   0.799   0.841   0.964   1.054   1.079   1.176
25    V         1.028   1.043   1.108   0.799   0.841   0.964   1.054   1.079   1.176
26    I         1.028   1.043   1.108   1.221   1.219   1.316   1.054   1.079   1.176
27    V        -1.397  -1.474  -1.197  -1.515  -1.609  -1.191  -1.394  -1.493  -1.141
28    K        -0.524  -0.561  -0.351  -1.066  -1.031  -0.655  -0.782  -0.864  -0.567
29    P        -1.041  -1.088  -1.167  -0.729  -0.833  -1.002  -0.986  -1.055  -1.109
30    H        -1.041  -1.179  -1.178  -0.712  -0.982  -1.083  -0.986  -1.171  -1.121
31    D         1.028   1.043   1.108   1.366   1.360   1.436   1.054   1.079   1.176
32    E        -1.041  -1.236  -1.173  -0.696  -0.939  -0.882  -0.986  -1.211  -1.114
33    G         1.028   1.043   1.108   1.121   1.126   1.232   1.054   1.079   1.176
34    S        -0.647  -0.553  -0.347  -0.729  -0.614  -0.326  -0.986  -0.851  -0.562
35    K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
36    S        -1.256  -1.325  -1.166  -1.157  -1.239  -1.080  -1.292  -1.330  -1.109
37    H         1.028   1.043   1.108   1.268   1.281   1.355   1.054   1.079   1.176
38    P         1.028   1.043   1.108   1.184   1.189   1.285   1.054   1.079   1.176
39    F         0.178  -0.037  -0.264   0.449   0.198  -0.147   0.238  -0.054  -0.425
40    G        -1.397  -1.226  -1.184  -1.292  -1.053  -1.093  -1.394  -1.193  -1.126
41    H         1.028   1.043   1.108   1.268   1.281   1.355   1.054   1.079   1.176
42    A         1.028   1.043   1.108   0.959   0.999   1.098   1.054   1.079   1.176
43    L        -1.558  -1.506  -1.189  -1.598  -1.558  -1.143  -1.598  -1.533  -1.132
44    V         1.028   1.043   1.108   0.799   0.841   0.964   1.054   1.079   1.176
45    A         0.178   0.283  -0.244   0.241   0.386  -0.424   0.238   0.369  -0.393
46    G         1.028   1.043   1.108   1.121   1.126   1.232   1.054   1.079   1.176
47    I        -0.524  -0.523  -0.348  -0.596  -0.657  -0.473  -0.782  -0.801  -0.563
48    E         1.028   1.043   1.108   1.094   1.116   1.210   1.054   1.079   1.176
49    R         1.028   1.043   1.108   1.084   1.076   1.201   1.054   1.079   1.176
50    Y         0.178   0.242  -0.246   0.600   0.652  -0.106   0.238   0.317  -0.397
51    P         1.028   1.043   1.108   1.184   1.189   1.285   1.054   1.079   1.176
52    L         0.178  -0.037  -0.264   0.440   0.162  -0.188   0.238  -0.054  -0.425
53    K         0.178   0.132  -0.254  -0.216  -0.217  -0.613   0.238   0.176  -0.409
54    V         0.178  -0.037  -0.264   0.134  -0.098  -0.405   0.238  -0.054  -0.425
55    T         0.178   0.132  -0.254   0.430   0.351  -0.180   0.238   0.176  -0.409
56    K        -0.639  -0.886  -1.136  -0.953  -1.226  -1.540  -0.476  -0.778  -1.070
57    K        -2.684  -2.584  -2.267  -2.689  -2.479  -1.946  -2.107  -2.002  -1.607
58    H        -1.773  -1.294  -1.733  -1.068  -0.506  -1.139  -1.496  -0.984  -1.371
59    G        -1.041  -1.205  -1.166  -0.680  -0.910  -0.885  -0.986  -1.170  -1.108
60    A         0.178  -0.037  -0.264   0.197  -0.087  -0.615   0.238  -0.054  -0.425
61    K         0.178  -0.037  -0.264  -0.250  -0.468  -0.735   0.238  -0.054  -0.425
62    K        -0.524  -0.561  -0.351  -1.199  -1.212  -0.819  -0.782  -0.864  -0.567
63    V        -1.933  -1.937  -1.787  -1.824  -1.749  -1.519  -1.699  -1.681  -1.421
64    A        -0.639  -0.788  -1.125  -0.396  -0.576  -1.089  -0.476  -0.669  -1.057
65    K         0.178   0.130  -0.245  -0.252  -0.264  -0.717   0.238   0.173  -0.395
66    R         1.028   1.043   1.108   1.084   1.076   1.201   1.054   1.079   1.176
67    T        -0.524  -0.561  -0.351  -0.533  -0.649  -0.337  -0.782  -0.864  -0.567
68    K        -0.263  -0.288  -0.296  -0.815  -0.821  -0.785  -0.374  -0.424  -0.478
69    I        -0.524  -0.247  -0.279  -0.791  -0.379  -0.426  -0.782  -0.363  -0.450
70    K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
71    P         1.028   1.043   1.108   1.184   1.189   1.285   1.054   1.079   1.176
72    F         1.028   1.043   1.108   1.105   1.125   1.219   1.054   1.079   1.176
73    I        -0.263  -0.154  -0.292  -0.116   0.026  -0.326  -0.374  -0.223  -0.472
74    K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
75    V        -1.041  -0.766  -1.132  -1.112  -0.754  -1.258  -0.986  -0.679  -1.066
76    V        -0.647  -0.577  -0.352  -0.959  -0.848  -0.503  -0.986  -0.891  -0.569
77    N         1.028   1.043   1.108   1.309   1.308   1.389   1.054   1.079   1.176
78    Y         1.028   1.043   1.108   1.299   1.294   1.381   1.054   1.079   1.176
79    N         1.028   1.043   1.108   1.309   1.308   1.389   1.054   1.079   1.176
80    H         1.028   1.043   1.108   1.268   1.281   1.355   1.054   1.079   1.176
81    L         0.178   0.132  -0.254   0.464   0.396  -0.097   0.238   0.176  -0.409
82    L        -0.524  -0.247  -0.279  -0.319   0.093  -0.053  -0.782  -0.363  -0.450
83    P         1.028   1.043   1.108   1.184   1.189   1.285   1.054   1.079   1.176
84    T         1.028   1.043   1.108   1.100   1.094   1.215   1.054   1.079   1.176
85    R         1.028   1.043   1.108   1.084   1.076   1.201   1.054   1.079   1.176
86    Y         1.028   1.043   1.108   1.299   1.294   1.381   1.054   1.079   1.176
87    T        -1.397  -1.323  -1.174  -1.309  -1.251  -1.091  -1.394  -1.311  -1.115
88    L         1.028   1.043   1.108   1.110   1.111   1.223   1.054   1.079   1.176
89    D        -0.524  -0.561  -0.351  -0.335  -0.471  -0.226  -0.782  -0.864  -0.567
90    V        -0.647  -0.573  -0.339  -1.035  -0.873  -0.521  -0.986  -0.884  -0.548
91    E        -1.041  -1.102  -1.157  -0.716  -0.805  -0.923  -0.986  -1.064  -1.095
92    A        -2.075  -2.031  -1.788  -1.746  -1.680  -1.445  -1.801  -1.733  -1.421
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    F        -0.647  -0.573  -0.339  -0.789  -0.692  -0.358  -0.986  -0.884  -0.548
95    K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
96    S        -1.256  -1.286  -1.186  -1.038  -1.127  -0.950  -1.292  -1.325  -1.130
97    V        -1.773  -1.887  -1.786  -1.716  -1.858  -1.720  -1.496  -1.609  -1.420
98    V        -0.263  -0.309  -0.330  -0.412  -0.466  -0.492  -0.374  -0.457  -0.534
99    S        -1.256  -1.256  -1.170  -1.081  -1.125  -1.010  -1.292  -1.282  -1.113
100   T        -2.075  -2.044  -1.797  -1.859  -1.884  -1.550  -1.801  -1.763  -1.430
101   E        -0.639  -0.700  -1.126  -0.222  -0.296  -0.894  -0.476  -0.551  -1.059
102   T         0.178   0.242  -0.246   0.401   0.452  -0.258   0.238   0.317  -0.397
103   F        -0.263  -0.154  -0.292  -0.145  -0.000  -0.275  -0.374  -0.223  -0.472
104   E        -1.773  -1.885  -1.791  -1.684  -1.990  -1.915  -1.496  -1.620  -1.425
105   Q         0.178   0.389  -0.240   0.443   0.661  -0.104   0.238   0.496  -0.387
106   P         0.178  -0.037  -0.264   0.467   0.170  -0.291   0.238  -0.054  -0.425
107   S        -0.647  -0.571  -0.352  -0.729  -0.651  -0.336  -0.986  -0.881  -0.569
108   Q         0.178   0.132  -0.254   0.654   0.581  -0.036   0.238   0.176  -0.409
109   R         1.028   1.043   1.108   1.084   1.076   1.201   1.054   1.079   1.176
110   E        -0.263  -0.288  -0.296  -0.133  -0.184  -0.254  -0.374  -0.424  -0.478
111   E        -1.397  -1.474  -1.197  -1.249  -1.367  -1.024  -1.394  -1.493  -1.141
112   A         1.028   1.043   1.108   0.959   0.999   1.098   1.054   1.079   1.176
113   K         0.178   0.130  -0.245  -0.252  -0.264  -0.717   0.238   0.173  -0.395
114   K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
115   V        -0.647  -0.573  -0.339  -1.042  -0.888  -0.528  -0.986  -0.884  -0.548
116   V        -0.524  -0.371  -0.323  -0.791  -0.557  -0.484  -0.782  -0.554  -0.522
117   K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
118   K        -0.639  -0.698  -1.114  -0.853  -0.872  -1.249  -0.476  -0.549  -1.044
119   A        -1.041  -1.236  -1.173  -0.984  -1.272  -1.285  -0.986  -1.211  -1.114
120   F        -0.263  -0.332  -0.339  -0.145  -0.268  -0.359  -0.374  -0.493  -0.548
121   E         1.028   1.043   1.108   1.094   1.116   1.210   1.054   1.079   1.176
122   E         1.028   1.043   1.108   1.094   1.116   1.210   1.054   1.079   1.176
123   R        -0.647  -0.580  -0.352  -1.238  -1.149  -0.801  -0.986  -0.896  -0.570
124   H        -0.524  -0.561  -0.351  -0.333  -0.431  -0.172  -0.782  -0.864  -0.567
125   Q        -0.639  -0.886  -1.136  -0.108  -0.470  -1.100  -0.476  -0.778  -1.070
126   A        -1.256  -1.261  -1.169  -1.238  -1.240  -1.080  -1.292  -1.305  -1.111
127   G         1.028   1.043   1.108   1.121   1.126   1.232   1.054   1.079   1.176
128   K         1.028   1.043   1.108   0.435   0.500   0.661   1.054   1.079   1.176
129   N        -0.263  -0.288  -0.296   0.074  -0.001  -0.101  -0.374  -0.424  -0.478
130   Q        -2.167  -2.153  -1.796  -2.359  -2.382  -1.873  -1.903  -1.848  -1.429
131   W         1.028   1.043   1.108   1.437   1.431   1.496   1.054   1.079   1.176
132   F         1.028   1.043   1.108   1.105   1.125   1.219   1.054   1.079   1.176
133   F         1.028   1.043   1.108   1.105   1.125   1.219   1.054   1.079   1.176
134   S        -1.041  -0.746  -1.114  -0.734  -0.376  -0.853  -0.986  -0.614  -1.044
135   K        -0.524  -0.561  -0.351  -1.145  -1.133  -0.753  -0.782  -0.864  -0.567
136   L         1.028   1.043   1.108   1.110   1.111   1.223   1.054   1.079   1.176
137   R        -1.041  -0.804  -1.137  -0.721  -0.448  -0.873  -0.986  -0.689  -1.073
138   F         1.028   1.043   1.108   1.105   1.125   1.219   1.054   1.079   1.176
* 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/P0C2H6
Output conservation file - output/P0C2H6
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
