1     M         1.166   1.172   1.225   1.375   1.381   1.454   1.279   1.289   1.363
2     S         0.576   0.543   0.335   0.755   0.708   0.399   0.585   0.531   0.147
3     E        -1.636  -1.620  -1.491  -1.616  -1.592  -1.397  -1.365  -1.347  -1.183
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    M         0.576   0.616   0.335   0.787   0.833   0.458   0.585   0.646   0.147
11    Q        -1.171  -1.180  -1.179  -1.144  -1.173  -1.190  -1.100  -1.107  -1.052
12    P         1.166   1.172   1.225   1.309   1.317   1.391   1.279   1.289   1.363
13    V        -0.358  -0.366  -0.379  -0.531  -0.543  -0.538  -0.604  -0.611  -0.598
14    N         1.166   1.172   1.225   1.122   1.131   1.213   1.279   1.289   1.363
15    P         1.166   1.172   1.225   1.309   1.317   1.391   1.279   1.289   1.363
16    K         0.015  -0.054  -0.294   0.096   0.007  -0.324  -0.009  -0.110  -0.464
17    P         1.166   1.172   1.225   1.309   1.317   1.391   1.279   1.289   1.363
18    F         1.166   1.172   1.225   1.284   1.291   1.368   1.279   1.289   1.363
19    L         1.166   1.172   1.225   1.038   1.052   1.133   1.279   1.289   1.363
20    K        -0.358  -0.386  -0.389  -0.423  -0.449  -0.393  -0.604  -0.637  -0.610
21    G        -1.544  -1.545  -1.463  -1.406  -1.405  -1.279  -1.298  -1.293  -1.164
22    L         1.166   1.172   1.225   1.038   1.052   1.133   1.279   1.289   1.363
23    V        -0.358  -0.367  -0.385  -0.531  -0.545  -0.548  -0.604  -0.612  -0.606
24    N        -0.460  -0.471  -0.428  -0.592  -0.614  -0.567  -0.704  -0.719  -0.658
25    H         0.015  -0.021  -0.300   0.123   0.070  -0.276  -0.009  -0.064  -0.473
26    R        -1.815  -1.830  -1.708  -1.420  -1.447  -1.273  -1.398  -1.403  -1.246
27    V         0.286   0.314   0.228   0.137   0.180   0.020   0.090   0.139  -0.058
28    G        -1.171  -1.164  -1.169  -1.246  -1.227  -1.245  -1.100  -1.091  -1.043
29    V         0.576   0.504   0.325   0.560   0.463   0.194   0.585   0.468   0.129
30    K        -0.731  -0.715  -0.812  -0.520  -0.495  -0.645  -0.803  -0.782  -0.862
31    L         1.166   1.172   1.225   1.038   1.052   1.133   1.279   1.289   1.363
32    K         1.166   1.172   1.225   1.103   1.109   1.195   1.279   1.289   1.363
33    F         0.131   0.146   0.190   0.220   0.246   0.283  -0.208  -0.181  -0.133
34    N         0.131   0.123   0.184  -0.098  -0.112  -0.022  -0.208  -0.226  -0.147
35    S        -0.513  -0.506  -0.752  -0.425  -0.429  -0.773  -0.505  -0.499  -0.787
36    T         0.524   0.500   0.315   0.630   0.597   0.299   0.502   0.462   0.109
37    E         0.131   0.136   0.185  -0.070  -0.064   0.018  -0.208  -0.200  -0.144
38    Y         1.166   1.172   1.225   1.321   1.326   1.402   1.279   1.289   1.363
39    R        -0.731  -0.766  -0.818  -0.725  -0.775  -0.835  -0.803  -0.831  -0.867
40    G         1.166   1.172   1.225   1.198   1.208   1.285   1.279   1.289   1.363
41    T        -0.242  -0.253  -0.368  -0.168  -0.200  -0.377  -0.406  -0.443  -0.579
42    L         1.166   1.172   1.225   1.038   1.052   1.133   1.279   1.289   1.363
43    V         0.015   0.095  -0.276   0.060   0.160  -0.348  -0.009   0.103  -0.437
44    S         1.166   1.172   1.225   1.272   1.275   1.356   1.279   1.289   1.363
45    T        -0.527  -0.502  -0.430  -0.770  -0.736  -0.609  -0.803  -0.770  -0.661
46    D         1.166   1.172   1.225   1.235   1.237   1.321   1.279   1.289   1.363
47    N        -0.358  -0.386  -0.389  -0.466  -0.499  -0.474  -0.604  -0.637  -0.610
48    Y         1.166   1.172   1.225   1.321   1.326   1.402   1.279   1.289   1.363
49    F         0.131   0.146   0.190   0.169   0.194   0.238  -0.208  -0.181  -0.133
50    N         1.166   1.172   1.225   1.122   1.131   1.213   1.279   1.289   1.363
51    L         0.576   0.504   0.325   0.514   0.426   0.152   0.585   0.468   0.129
52    Q         1.166   1.172   1.225   1.290   1.297   1.373   1.279   1.289   1.363
53    L         1.166   1.172   1.225   1.038   1.052   1.133   1.279   1.289   1.363
54    N        -1.815  -1.809  -1.717  -1.673  -1.660  -1.547  -1.398  -1.389  -1.252
55    E        -1.002  -0.917  -1.117  -0.838  -0.708  -1.060  -0.902  -0.805  -0.990
56    A         0.131   0.124   0.183   0.149   0.125   0.198  -0.208  -0.225  -0.147
57    E        -1.442  -1.449  -1.451  -1.353  -1.380  -1.356  -1.199  -1.203  -1.153
58    E         1.166   1.172   1.225   1.096   1.102   1.188   1.279   1.289   1.363
59    F        -1.171  -1.109  -1.158  -1.076  -0.983  -1.089  -1.100  -1.042  -1.034
60    V         0.082   0.091   0.176  -0.225  -0.206  -0.064  -0.307  -0.290  -0.161
61    A        -1.273  -1.250  -1.190  -1.139  -1.128  -1.006  -1.199  -1.174  -1.061
62    G        -1.171  -1.232  -1.177  -1.102  -1.173  -1.070  -1.100  -1.150  -1.049
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -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    V        -0.900  -0.901  -0.847  -1.159  -1.162  -1.055  -1.001  -0.999  -0.901
70    S        -1.171  -1.195  -1.180  -1.201  -1.224  -1.208  -1.100  -1.120  -1.053
71    H        -1.273  -1.268  -1.195  -1.279  -1.270  -1.105  -1.199  -1.190  -1.066
72    G         0.286   0.308   0.249   0.219   0.258   0.117   0.090   0.128  -0.018
73    T        -1.815  -1.825  -1.716  -1.739  -1.751  -1.619  -1.398  -1.400  -1.250
74    L        -0.242  -0.256  -0.347  -0.417  -0.427  -0.584  -0.406  -0.417  -0.543
75    G         1.166   1.172   1.225   1.198   1.208   1.285   1.279   1.289   1.363
76    E        -0.242  -0.326  -0.371  -0.300  -0.420  -0.473  -0.406  -0.521  -0.583
77    I        -0.242  -0.245  -0.368  -0.322  -0.351  -0.573  -0.406  -0.428  -0.577
78    F         0.286   0.271   0.224   0.286   0.257   0.111   0.090   0.060  -0.067
79    I         1.166   1.172   1.225   1.185   1.190   1.273   1.279   1.289   1.363
80    R         1.166   1.172   1.225   1.339   1.344   1.420   1.279   1.289   1.363
81    C         1.166   1.172   1.225   1.429   1.435   1.505   1.279   1.289   1.363
82    N         1.166   1.172   1.225   1.122   1.131   1.213   1.279   1.289   1.363
83    N         1.166   1.172   1.225   1.122   1.131   1.213   1.279   1.289   1.363
84    V         1.166   1.172   1.225   1.083   1.090   1.176   1.279   1.289   1.363
85    L         1.166   1.172   1.225   1.038   1.052   1.133   1.279   1.289   1.363
86    Y        -0.460  -0.434  -0.402  -0.336  -0.296  -0.255  -0.704  -0.665  -0.621
87    I         0.286   0.295   0.230   0.203   0.213   0.061   0.090   0.103  -0.055
88    R        -0.358  -0.397  -0.387  -0.389  -0.439  -0.428  -0.604  -0.641  -0.606
89    E         0.576   0.504   0.325   0.560   0.461   0.176   0.585   0.468   0.129
90    -        -0.777  -0.800  -0.814  -0.685  -0.718  -0.735  -0.836  -0.862  -0.859
91    -        -1.275  -1.295  -1.205  -1.431  -1.461  -1.318  -1.188  -1.204  -1.074
92    -        -0.777  -0.781  -0.826  -0.897  -0.906  -0.980  -0.836  -0.839  -0.873
93    -        -0.777  -0.754  -0.819  -0.794  -0.749  -0.839  -0.836  -0.807  -0.866
94    -         0.082   0.089   0.175  -0.166  -0.158  -0.019  -0.307  -0.296  -0.163
95    -        -1.636  -1.623  -1.491  -1.629  -1.601  -1.410  -1.365  -1.349  -1.183
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -0.484  -0.473  -0.414  -0.686  -0.648  -0.553  -0.751  -0.732  -0.639
111   -        -1.351  -1.336  -1.214  -1.401  -1.381  -1.192  -1.259  -1.241  -1.081
112   -         0.113   0.140   0.189  -0.169  -0.113  -0.059  -0.243  -0.194  -0.136
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   L        -1.544  -1.516  -1.467  -1.463  -1.420  -1.335  -1.298  -1.273  -1.166
132   P        -2.086  -2.070  -1.927  -1.802  -1.777  -1.575  -1.497  -1.481  -1.310
133   N        -0.900  -0.878  -0.845  -1.015  -0.993  -0.931  -1.001  -0.981  -0.898
* 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/P54999
Output conservation file - output/P54999
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
