1     M         1.272   1.274   1.302   1.552   1.557   1.594   1.352   1.356   1.394
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     K        -1.198  -1.220  -1.180  -1.187  -1.224  -1.158  -1.060  -1.084  -1.020
5     L         1.272   1.274   1.302   1.191   1.196   1.243   1.352   1.356   1.394
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     P         1.272   1.274   1.302   1.378   1.380   1.425   1.352   1.356   1.394
8     V        -1.198  -1.219  -1.202  -0.965  -0.987  -0.916  -1.060  -1.083  -1.041
9     A         1.272   1.274   1.302   1.402   1.409   1.448   1.352   1.356   1.394
10    Q        -1.713  -1.705  -1.625  -1.573  -1.587  -1.443  -1.328  -1.322  -1.221
11    Y         1.272   1.274   1.302   1.526   1.526   1.569   1.352   1.356   1.394
12    S        -1.198  -1.170  -1.178  -1.175  -1.139  -1.132  -1.060  -1.032  -1.017
13    A        -0.490  -0.556  -0.609  -0.322  -0.429  -0.526  -0.524  -0.611  -0.675
14    P         1.272   1.274   1.302   1.393   1.397   1.439   1.352   1.356   1.394
15    D         0.344   0.281   0.164   0.194   0.102  -0.091   0.280   0.179  -0.025
16    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    V        -1.713  -1.705  -1.625  -1.302  -1.307  -1.180  -1.328  -1.322  -1.221
18    E        -1.198  -1.176  -1.177  -1.360  -1.319  -1.335  -1.060  -1.038  -1.017
19    K        -1.713  -1.705  -1.625  -1.531  -1.504  -1.403  -1.328  -1.322  -1.221
20    S        -1.198  -1.198  -1.197  -1.107  -1.122  -1.130  -1.060  -1.062  -1.037
21    F        -0.490  -0.441  -0.607  -0.196  -0.116  -0.429  -0.524  -0.460  -0.673
22    A        -1.713  -1.705  -1.625  -1.495  -1.497  -1.367  -1.328  -1.322  -1.221
23    P        -1.198  -1.219  -1.202  -0.834  -0.871  -0.867  -1.060  -1.083  -1.041
24    I        -0.656  -0.706  -0.676  -0.569  -0.674  -0.651  -0.742  -0.808  -0.761
25    R        -0.656  -0.636  -0.648  -0.649  -0.612  -0.653  -0.742  -0.717  -0.726
26    D        -0.656  -0.639  -0.649  -0.727  -0.707  -0.744  -0.742  -0.721  -0.727
27    D        -0.656  -0.584  -0.658  -0.986  -0.859  -0.991  -0.742  -0.648  -0.738
28    P        -0.684  -0.670  -0.662  -0.672  -0.654  -0.624  -0.792  -0.777  -0.747
29    R        -0.684  -0.670  -0.662  -0.704  -0.681  -0.678  -0.792  -0.777  -0.747
30    Y        -0.656  -0.678  -0.658  -0.516  -0.578  -0.548  -0.742  -0.773  -0.738
31    M        -1.198  -1.219  -1.202  -0.885  -0.934  -0.915  -1.060  -1.083  -1.041
32    T         0.344   0.370   0.186   0.335   0.367   0.103   0.280   0.320   0.012
33    T         1.272   1.274   1.302   1.209   1.210   1.261   1.352   1.356   1.394
34    E        -0.684  -0.692  -0.670  -0.821  -0.843  -0.825  -0.792  -0.800  -0.755
35    G         1.272   1.274   1.302   1.302   1.308   1.351   1.352   1.356   1.394
36    R        -0.684  -0.692  -0.670  -0.710  -0.714  -0.662  -0.792  -0.800  -0.755
37    T         1.272   1.274   1.302   1.209   1.210   1.261   1.352   1.356   1.394
38    T         1.272   1.274   1.302   1.209   1.210   1.261   1.352   1.356   1.394
39    G         0.024   0.045   0.066  -0.114  -0.078  -0.048  -0.256  -0.221  -0.197
40    P        -0.684  -0.713  -0.676  -0.573  -0.612  -0.558  -0.792  -0.822  -0.763
41    S         1.272   1.274   1.302   1.402   1.402   1.448   1.352   1.356   1.394
42    D         0.344   0.324   0.181   0.232   0.208   0.000   0.280   0.248   0.004
43    H        -0.684  -0.659  -0.667  -0.442  -0.410  -0.405  -0.792  -0.765  -0.752
44    V         1.272   1.274   1.302   1.455   1.457   1.500   1.352   1.356   1.394
45    L         0.024   0.045   0.066  -0.135  -0.103  -0.062  -0.256  -0.221  -0.197
46    N         0.024   0.030   0.061  -0.090  -0.081  -0.027  -0.256  -0.247  -0.205
47    A         0.344   0.281   0.164   0.511   0.418   0.218   0.280   0.179  -0.025
48    G         1.272   1.274   1.302   1.302   1.308   1.351   1.352   1.356   1.394
49    Q        -0.684  -0.713  -0.676  -0.678  -0.710  -0.635  -0.792  -0.822  -0.763
50    I        -1.198  -1.219  -1.202  -1.114  -1.148  -1.086  -1.060  -1.083  -1.041
51    D         1.272   1.274   1.302   1.105   1.113   1.160   1.352   1.356   1.394
52    R         0.344   0.281   0.164   0.520   0.430   0.247   0.280   0.179  -0.025
53    D         1.272   1.274   1.302   1.105   1.113   1.160   1.352   1.356   1.394
54    K         0.344   0.324   0.181   0.376   0.350   0.130   0.280   0.248   0.004
55    P         1.272   1.274   1.302   1.393   1.397   1.439   1.352   1.356   1.394
56    S         0.344   0.324   0.181   0.524   0.492   0.270   0.280   0.248   0.004
57    E         0.024   0.030   0.061  -0.373  -0.360  -0.309  -0.256  -0.247  -0.205
58    P        -0.684  -0.670  -0.662  -0.579  -0.562  -0.529  -0.792  -0.777  -0.747
59    E        -0.490  -0.477  -0.606  -0.498  -0.473  -0.693  -0.524  -0.508  -0.671
60    R        -1.198  -1.219  -1.202  -1.294  -1.326  -1.266  -1.060  -1.083  -1.041
61    T         0.092   0.133   0.084   0.040   0.116  -0.002  -0.137  -0.066  -0.165
62    K        -0.765  -0.758  -0.696  -0.965  -0.960  -0.852  -0.882  -0.873  -0.785
63    D        -0.765  -0.758  -0.696  -0.946  -0.916  -0.834  -0.882  -0.873  -0.785
64    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    Q         0.092   0.100   0.080  -0.000   0.010  -0.036  -0.137  -0.124  -0.172
73    L        -0.765  -0.758  -0.696  -0.809  -0.786  -0.700  -0.882  -0.873  -0.785
74    T         1.272   1.274   1.302   1.209   1.210   1.261   1.352   1.356   1.394
75    Y        -1.198  -1.198  -1.197  -0.983  -1.003  -1.020  -1.060  -1.062  -1.037
76    L         1.272   1.274   1.302   1.191   1.196   1.243   1.352   1.356   1.394
77    G         0.344   0.281   0.164   0.426   0.335   0.152   0.280   0.179  -0.025
78    Q         0.344   0.370   0.186   0.484   0.517   0.250   0.280   0.320   0.012
79    L         1.272   1.274   1.302   1.191   1.196   1.243   1.352   1.356   1.394
80    R         1.272   1.274   1.302   1.384   1.390   1.431   1.352   1.356   1.394
81    T        -1.198  -1.219  -1.202  -0.976  -0.997  -0.984  -1.060  -1.083  -1.041
82    Q        -0.490  -0.441  -0.607  -0.451  -0.373  -0.676  -0.524  -0.460  -0.673
83    L         1.272   1.274   1.302   1.191   1.196   1.243   1.352   1.356   1.394
84    T         1.272   1.274   1.302   1.209   1.210   1.261   1.352   1.356   1.394
85    G         0.024   0.045   0.066  -0.193  -0.152  -0.129  -0.256  -0.221  -0.197
86    L         1.272   1.274   1.302   1.191   1.196   1.243   1.352   1.356   1.394
87    Q         1.272   1.274   1.302   1.348   1.349   1.395   1.352   1.356   1.394
88    D         1.272   1.274   1.302   1.105   1.113   1.160   1.352   1.356   1.394
89    D        -0.490  -0.441  -0.607  -0.546  -0.476  -0.688  -0.524  -0.460  -0.673
90    I         0.024   0.045   0.066  -0.054  -0.005   0.002  -0.256  -0.221  -0.197
91    N         1.272   1.274   1.302   1.455   1.459   1.500   1.352   1.356   1.394
92    E         0.024   0.045   0.066  -0.127  -0.095  -0.055  -0.256  -0.221  -0.197
93    F         0.024   0.004   0.050   0.211   0.171   0.237  -0.256  -0.293  -0.226
94    L         1.272   1.274   1.302   1.191   1.196   1.243   1.352   1.356   1.394
95    T         1.272   1.274   1.302   1.209   1.210   1.261   1.352   1.356   1.394
96    G        -1.198  -1.170  -1.178  -1.343  -1.299  -1.316  -1.060  -1.032  -1.017
97    R         0.344   0.281   0.164   0.471   0.375   0.164   0.280   0.179  -0.025
98    M         0.344   0.281   0.164   0.688   0.598   0.403   0.280   0.179  -0.025
99    E        -1.198  -1.198  -1.197  -1.310  -1.296  -1.309  -1.060  -1.062  -1.037
100   L        -0.684  -0.692  -0.659  -0.672  -0.671  -0.621  -0.792  -0.799  -0.743
101   A        -0.684  -0.713  -0.676  -0.736  -0.766  -0.696  -0.792  -0.822  -0.763
102   K         1.272   1.274   1.302   1.256   1.262   1.306   1.352   1.356   1.394
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   N        -0.684  -0.712  -0.660  -0.628  -0.680  -0.598  -0.792  -0.822  -0.745
115   K        -1.198  -1.198  -1.197  -1.088  -1.090  -1.067  -1.060  -1.062  -1.037
116   K        -0.490  -0.512  -0.602  -0.433  -0.468  -0.599  -0.524  -0.556  -0.666
117   K        -1.713  -1.705  -1.625  -1.592  -1.580  -1.462  -1.328  -1.322  -1.221
118   A        -1.713  -1.705  -1.625  -1.559  -1.549  -1.430  -1.328  -1.322  -1.221
119   G        -1.198  -1.219  -1.202  -1.335  -1.376  -1.346  -1.060  -1.083  -1.041
120   A        -0.684  -0.664  -0.664  -0.704  -0.675  -0.678  -0.792  -0.771  -0.748
121   D         1.272   1.274   1.302   1.102   1.110   1.156   1.352   1.356   1.394
122   E        -0.013  -0.009   0.042  -0.382  -0.375  -0.285  -0.323  -0.316  -0.240
123   K        -0.656  -0.685  -0.676  -0.800  -0.844  -0.827  -0.742  -0.780  -0.761
124   R         1.272   1.274   1.302   1.366   1.367   1.413   1.352   1.356   1.394
125   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   Q         0.092   0.133   0.084  -0.062   0.008  -0.083  -0.137  -0.066  -0.165
127   E        -0.765  -0.758  -0.696  -0.946  -0.935  -0.834  -0.882  -0.873  -0.785
128   E         1.272   1.274   1.302   1.241   1.245   1.292   1.352   1.356   1.394
129   I         1.272   1.274   1.302   1.490   1.496   1.533   1.352   1.356   1.394
130   N         1.272   1.274   1.302   1.447   1.448   1.492   1.352   1.356   1.394
131   Q        -1.198  -1.225  -1.180  -1.234  -1.303  -1.229  -1.060  -1.089  -1.020
132   L        -0.490  -0.441  -0.607  -0.448  -0.381  -0.595  -0.524  -0.460  -0.673
133   L         1.272   1.274   1.302   1.191   1.196   1.243   1.352   1.356   1.394
134   D         1.272   1.274   1.302   1.105   1.113   1.160   1.352   1.356   1.394
135   G        -0.013  -0.009   0.042  -0.304  -0.296  -0.208  -0.323  -0.316  -0.240
136   G         1.272   1.274   1.302   1.302   1.308   1.351   1.352   1.356   1.394
137   D        -0.684  -0.713  -0.676  -0.781  -0.825  -0.753  -0.792  -0.822  -0.763
138   G        -0.684  -0.663  -0.659  -1.011  -0.978  -0.953  -0.792  -0.770  -0.743
139   D         0.024   0.049   0.059  -0.345  -0.288  -0.294  -0.256  -0.213  -0.209
140   E         0.092   0.130   0.086  -0.208  -0.126  -0.245  -0.137  -0.073  -0.162
141   D        -0.765  -0.751  -0.696  -1.041  -1.038  -0.926  -0.882  -0.864  -0.785
142   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   V        -1.198  -1.192  -1.175  -1.331  -1.330  -1.298  -1.060  -1.055  -1.015
* 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/P46984
Output conservation file - output/P46984
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
