1     M         1.285   1.287   1.300   1.543   1.545   1.564   1.336   1.337   1.353
2     S         1.285   1.287   1.300   1.224   1.226   1.247   1.336   1.337   1.353
3     K         1.285   1.287   1.300   1.263   1.266   1.285   1.336   1.337   1.353
4     L        -0.102  -0.084  -0.141  -0.113  -0.086  -0.170  -0.239  -0.212  -0.299
5     G        -1.110  -1.108  -1.090  -1.020  -1.022  -0.986  -1.027  -1.024  -0.992
6     P        -0.102  -0.119  -0.153  -0.061  -0.083  -0.126  -0.239  -0.265  -0.318
7     L         1.285   1.287   1.300   1.263   1.264   1.285   1.336   1.337   1.353
8     A        -1.110  -1.108  -1.090  -0.975  -0.974  -0.941  -1.027  -1.024  -0.992
9     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    K        -1.110  -1.108  -1.090  -1.161  -1.160  -1.126  -1.027  -1.024  -0.992
13    W        -0.102  -0.119  -0.153   0.108   0.079   0.019  -0.239  -0.265  -0.318
14    T         1.285   1.287   1.300   1.339   1.339   1.361   1.336   1.337   1.353
15    L        -0.102  -0.100  -0.143  -0.157  -0.154  -0.223  -0.239  -0.235  -0.301
16    S        -1.110  -1.108  -1.090  -1.374  -1.366  -1.338  -1.027  -1.024  -0.992
17    V        -0.102  -0.119  -0.153  -0.337  -0.369  -0.448  -0.239  -0.265  -0.318
18    G        -0.102  -0.100  -0.143  -0.069  -0.069  -0.140  -0.239  -0.235  -0.301
19    V        -0.102  -0.100  -0.143  -0.412  -0.406  -0.474  -0.239  -0.235  -0.301
20    I        -1.110  -1.108  -1.090  -1.235  -1.223  -1.199  -1.027  -1.024  -0.992
21    G        -0.102  -0.084  -0.141  -0.018   0.007  -0.078  -0.239  -0.212  -0.299
22    S        -1.110  -1.108  -1.090  -1.323  -1.322  -1.287  -1.027  -1.024  -0.992
23    V        -0.102  -0.119  -0.153  -0.337  -0.369  -0.448  -0.239  -0.265  -0.318
24    F        -1.110  -1.108  -1.090  -0.821  -0.820  -0.788  -1.027  -1.024  -0.992
25    Y         1.285   1.287   1.300   1.263   1.266   1.285   1.336   1.337   1.353
26    L        -0.102  -0.119  -0.153  -0.192  -0.220  -0.282  -0.239  -0.265  -0.318
27    Y         1.285   1.287   1.300   1.263   1.266   1.285   1.336   1.337   1.353
28    R        -1.110  -1.108  -1.090  -1.161  -1.160  -1.126  -1.027  -1.024  -0.992
29    Y        -0.102  -0.119  -0.153  -0.035  -0.066  -0.134  -0.239  -0.265  -0.318
30    S        -0.102  -0.119  -0.153  -0.210  -0.240  -0.304  -0.239  -0.265  -0.318
31    N        -0.102  -0.119  -0.153  -0.078  -0.104  -0.155  -0.239  -0.265  -0.318
32    N        -1.110  -1.108  -1.090  -0.919  -0.916  -0.885  -1.027  -1.024  -0.992
33    G         1.285   1.287   1.300   1.320   1.322   1.343   1.336   1.337   1.353
34    Y         1.285   1.287   1.300   1.270   1.270   1.292   1.336   1.337   1.353
35    F        -1.110  -1.108  -1.090  -0.875  -0.873  -0.841  -1.027  -1.024  -0.992
36    Y         1.285   1.287   1.300   1.263   1.266   1.285   1.336   1.337   1.353
37    D        -1.110  -1.108  -1.090  -1.114  -1.112  -1.079  -1.027  -1.024  -0.992
38    H        -1.110  -1.108  -1.090  -0.919  -0.912  -0.885  -1.027  -1.024  -0.992
39    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    A        -1.110  -1.108  -1.090  -1.055  -1.049  -1.020  -1.027  -1.024  -0.992
41    T        -1.110  -1.108  -1.090  -1.173  -1.165  -1.138  -1.027  -1.024  -0.992
42    W        -0.102  -0.100  -0.143  -0.035  -0.033  -0.114  -0.239  -0.235  -0.301
43    L        -1.110  -1.108  -1.090  -1.020  -1.019  -0.986  -1.027  -1.024  -0.992
44    K        -0.102  -0.084  -0.141  -0.130  -0.102  -0.190  -0.239  -0.212  -0.299
45    Q        -1.110  -1.108  -1.090  -1.210  -1.200  -1.175  -1.027  -1.024  -0.992
46    D        -1.110  -1.108  -1.090  -1.032  -1.035  -0.997  -1.027  -1.024  -0.992
47    H        -1.110  -1.108  -1.090  -1.161  -1.151  -1.126  -1.027  -1.024  -0.992
48    Q        -0.102  -0.084  -0.141  -0.001   0.027  -0.065  -0.239  -0.212  -0.299
49    V         1.285   1.287   1.300   1.027   1.031   1.051   1.336   1.337   1.353
50    Q        -0.102  -0.100  -0.143  -0.001   0.002  -0.067  -0.239  -0.235  -0.301
51    D        -1.110  -1.108  -1.090  -1.067  -1.066  -1.032  -1.027  -1.024  -0.992
52    L        -1.110  -1.108  -1.090  -1.235  -1.228  -1.199  -1.027  -1.024  -0.992
53    V        -0.102  -0.119  -0.153  -0.139  -0.174  -0.259  -0.239  -0.265  -0.318
54    D         1.285   1.287   1.300   1.263   1.264   1.285   1.336   1.337   1.353
55    R        -0.102  -0.100  -0.143  -0.078  -0.074  -0.139  -0.239  -0.235  -0.301
56    K         1.285   1.287   1.300   1.263   1.266   1.285   1.336   1.337   1.353
57    E        -1.110  -1.108  -1.090  -0.821  -0.822  -0.788  -1.027  -1.024  -0.992
58    V        -1.110  -1.108  -1.090  -1.284  -1.286  -1.249  -1.027  -1.024  -0.992
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -         1.285   1.287   1.300   1.479   1.481   1.500   1.336   1.337   1.353
71    -        -0.226  -0.225  -0.208  -0.331  -0.330  -0.300  -0.436  -0.435  -0.406
72    -         1.285   1.287   1.300   1.213   1.214   1.235   1.336   1.337   1.353
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    V         1.285   1.287   1.300   0.981   0.980   1.005   1.336   1.337   1.353
77    P        -0.226  -0.225  -0.208  -0.240  -0.240  -0.210  -0.436  -0.435  -0.406
78    G         1.285   1.287   1.300   1.320   1.322   1.343   1.336   1.337   1.353
79    E         1.285   1.287   1.300   1.414   1.416   1.436   1.336   1.337   1.353
80    T        -1.110  -1.108  -1.090  -0.952  -0.951  -0.918  -1.027  -1.024  -0.992
81    R        -1.110  -1.108  -1.090  -1.137  -1.128  -1.102  -1.027  -1.024  -0.992
82    N        -1.110  -1.108  -1.090  -1.020  -1.019  -0.986  -1.027  -1.024  -0.992
83    R         1.285   1.287   1.300   1.301   1.304   1.323   1.336   1.337   1.353
84    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    V         1.285   1.287   1.300   0.981   0.980   1.005   1.336   1.337   1.353
87    V        -0.226  -0.225  -0.208  -0.387  -0.387  -0.356  -0.436  -0.435  -0.406
88    T        -0.226  -0.225  -0.208  -0.482  -0.483  -0.451  -0.436  -0.435  -0.406
89    D         1.285   1.287   1.300   1.263   1.264   1.285   1.336   1.337   1.353
90    D        -1.110  -1.108  -1.090  -1.043  -1.047  -1.009  -1.027  -1.024  -0.992
91    G        -1.110  -1.108  -1.090  -1.055  -1.053  -1.020  -1.027  -1.024  -0.992
92    T        -1.110  -1.108  -1.090  -0.952  -0.953  -0.918  -1.027  -1.024  -0.992
93    A        -1.110  -1.108  -1.090  -1.222  -1.214  -1.187  -1.027  -1.024  -0.992
94    W        -0.102  -0.119  -0.153  -0.328  -0.350  -0.390  -0.239  -0.265  -0.318
95    S        -1.110  -1.108  -1.090  -1.137  -1.137  -1.102  -1.027  -1.024  -0.992
96    R         1.285   1.287   1.300   1.301   1.304   1.323   1.336   1.337   1.353
97    T        -1.110  -1.108  -1.090  -0.975  -0.973  -0.941  -1.027  -1.024  -0.992
98    M        -1.110  -1.108  -1.090  -0.778  -0.775  -0.745  -1.027  -1.024  -0.992
99    G        -1.110  -1.108  -1.090  -1.043  -1.040  -1.009  -1.027  -1.024  -0.992
100   E         1.285   1.287   1.300   1.414   1.416   1.436   1.336   1.337   1.353
101   S        -0.102  -0.119  -0.153  -0.139  -0.171  -0.237  -0.239  -0.265  -0.318
102   I        -1.110  -1.108  -1.090  -1.055  -1.054  -1.020  -1.027  -1.024  -0.992
103   K         1.285   1.287   1.300   1.263   1.266   1.285   1.336   1.337   1.353
104   D         1.285   1.287   1.300   1.263   1.264   1.285   1.336   1.337   1.353
105   I        -0.102  -0.084  -0.141  -0.035  -0.005  -0.111  -0.239  -0.212  -0.299
106   W         1.285   1.287   1.300   1.433   1.432   1.454   1.336   1.337   1.353
107   N         1.285   1.287   1.300   1.433   1.433   1.454   1.336   1.337   1.353
108   E        -0.102  -0.119  -0.153  -0.121  -0.146  -0.198  -0.239  -0.265  -0.318
109   Q        -0.102  -0.119  -0.153   0.007  -0.020  -0.079  -0.239  -0.265  -0.318
110   I        -0.102  -0.119  -0.153  -0.328  -0.349  -0.390  -0.239  -0.265  -0.318
111   R         1.285   1.287   1.300   1.301   1.304   1.323   1.336   1.337   1.353
112   N        -0.102  -0.084  -0.141   0.049   0.076  -0.014  -0.239  -0.212  -0.299
113   S        -1.110  -1.108  -1.090  -1.173  -1.174  -1.138  -1.027  -1.024  -0.992
114   V        -0.102  -0.100  -0.143  -0.319  -0.313  -0.366  -0.239  -0.235  -0.301
115   D         1.285   1.287   1.300   1.263   1.264   1.285   1.336   1.337   1.353
116   W         1.285   1.287   1.300   1.433   1.432   1.454   1.336   1.337   1.353
117   I        -1.110  -1.108  -1.090  -1.235  -1.223  -1.199  -1.027  -1.024  -0.992
118   Y         1.285   1.287   1.300   1.263   1.266   1.285   1.336   1.337   1.353
119   S         1.285   1.287   1.300   1.224   1.226   1.247   1.336   1.337   1.353
120   W         1.285   1.287   1.300   1.406   1.407   1.428   1.336   1.337   1.353
121   G         1.285   1.287   1.300   1.351   1.352   1.374   1.336   1.337   1.353
122   K        -0.102  -0.084  -0.141  -0.174  -0.143  -0.241  -0.239  -0.212  -0.299
123   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P38341
Output conservation file - output/P38341
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
