1     M         1.443   1.446   1.469   1.730   1.732   1.767   1.521   1.524   1.551
2     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -0.114  -0.075  -0.140  -0.210  -0.154  -0.234  -0.235  -0.175  -0.274
5     E         1.443   1.446   1.469   1.300   1.303   1.342   1.521   1.524   1.551
6     D        -0.114  -0.137  -0.160  -0.542  -0.581  -0.600  -0.235  -0.270  -0.304
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    T        -1.244  -1.239  -1.205  -1.096  -1.086  -1.026  -1.113  -1.105  -1.046
19    S        -1.244  -1.239  -1.205  -1.231  -1.217  -1.158  -1.113  -1.105  -1.046
20    V        -1.244  -1.239  -1.205  -0.940  -0.934  -0.871  -1.113  -1.105  -1.046
21    I        -0.114  -0.118  -0.154  -0.256  -0.254  -0.334  -0.235  -0.241  -0.296
22    L        -1.244  -1.239  -1.205  -1.339  -1.346  -1.266  -1.113  -1.105  -1.046
23    Q         1.443   1.446   1.469   1.543   1.547   1.582   1.521   1.524   1.551
24    G        -0.114  -0.137  -0.160  -0.142  -0.173  -0.203  -0.235  -0.270  -0.304
25    I        -0.114  -0.137  -0.160  -0.530  -0.565  -0.586  -0.235  -0.270  -0.304
26    D        -0.114  -0.137  -0.160  -0.054  -0.093  -0.144  -0.235  -0.270  -0.304
27    T        -0.114  -0.075  -0.140  -0.043   0.030  -0.102  -0.235  -0.175  -0.274
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    I        -1.244  -1.239  -1.205  -0.968  -0.956  -0.898  -1.113  -1.105  -1.046
30    N        -1.244  -1.239  -1.205  -1.024  -1.001  -0.954  -1.113  -1.105  -1.046
31    S         1.443   1.446   1.469   1.275   1.277   1.318   1.521   1.524   1.551
32    V        -0.114  -0.137  -0.160  -0.109  -0.139  -0.163  -0.235  -0.270  -0.304
33    E        -1.244  -1.239  -1.205  -1.436  -1.441  -1.361  -1.113  -1.105  -1.046
34    G        -0.114  -0.137  -0.160  -0.444  -0.479  -0.483  -0.235  -0.270  -0.304
35    L        -1.244  -1.239  -1.205  -1.469  -1.482  -1.393  -1.113  -1.105  -1.046
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    E        -0.114  -0.137  -0.160  -0.267  -0.306  -0.353  -0.235  -0.270  -0.304
57    E        -0.114  -0.137  -0.160  -0.361  -0.400  -0.440  -0.235  -0.270  -0.304
58    D        -0.114  -0.118  -0.154  -0.267  -0.271  -0.342  -0.235  -0.241  -0.296
59    G        -1.244  -1.239  -1.205  -1.339  -1.319  -1.266  -1.113  -1.105  -1.046
60    Y        -0.114  -0.118  -0.154  -0.021  -0.024  -0.110  -0.235  -0.241  -0.296
61    L        -0.114  -0.137  -0.160  -0.131  -0.180  -0.255  -0.235  -0.270  -0.304
62    S        -1.244  -1.239  -1.205  -1.246  -1.243  -1.173  -1.113  -1.105  -1.046
63    D        -0.114  -0.118  -0.154  -0.279  -0.283  -0.356  -0.235  -0.241  -0.296
64    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    D         1.443   1.446   1.469   1.374   1.379   1.415   1.521   1.524   1.551
66    T        -1.244  -1.239  -1.205  -1.096  -1.073  -1.026  -1.113  -1.105  -1.046
67    S        -1.244  -1.239  -1.205  -1.277  -1.270  -1.204  -1.113  -1.105  -1.046
68    L        -1.244  -1.239  -1.205  -1.639  -1.638  -1.562  -1.113  -1.105  -1.046
69    S        -0.114  -0.137  -0.160  -0.349  -0.389  -0.432  -0.235  -0.270  -0.304
70    N        -0.114  -0.137  -0.160   0.129   0.099   0.058  -0.235  -0.270  -0.304
71    E         1.443   1.446   1.469   1.300   1.303   1.342   1.521   1.524   1.551
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    L         1.443   1.446   1.469   1.046   1.042   1.091   1.521   1.524   1.551
75    A        -1.244  -1.239  -1.205  -1.096  -1.087  -1.026  -1.113  -1.105  -1.046
76    D         1.443   1.446   1.469   1.361   1.364   1.402   1.521   1.524   1.551
77    A         1.443   1.446   1.469   1.637   1.639   1.675   1.521   1.524   1.551
78    Q         1.443   1.446   1.469   1.543   1.547   1.582   1.521   1.524   1.551
79    R        -0.114  -0.075  -0.140  -0.109  -0.038  -0.165  -0.235  -0.175  -0.274
80    Q        -0.114  -0.118  -0.154  -0.109  -0.114  -0.193  -0.235  -0.241  -0.296
81    W         1.443   1.446   1.469   1.614   1.618   1.652   1.521   1.524   1.551
82    E         1.443   1.446   1.469   1.300   1.303   1.342   1.521   1.524   1.551
83    E        -0.114  -0.118  -0.154  -0.221  -0.226  -0.271  -0.235  -0.241  -0.296
84    S         1.443   1.446   1.469   1.275   1.277   1.318   1.521   1.524   1.551
85    L         1.443   1.446   1.469   1.046   1.042   1.091   1.521   1.524   1.551
86    Q        -1.244  -1.239  -1.205  -1.082  -1.078  -1.011  -1.113  -1.105  -1.046
87    Q         1.443   1.446   1.469   1.543   1.547   1.582   1.521   1.524   1.551
88    L        -0.114  -0.075  -0.140  -0.530  -0.472  -0.557  -0.235  -0.175  -0.274
89    N        -0.114  -0.118  -0.154   0.118   0.117   0.054  -0.235  -0.241  -0.296
90    K        -1.244  -1.239  -1.205  -0.885  -0.870  -0.816  -1.113  -1.105  -1.046
91    L        -0.114  -0.118  -0.154  -0.408  -0.418  -0.435  -0.235  -0.241  -0.296
92    L        -1.244  -1.239  -1.205  -1.371  -1.368  -1.297  -1.113  -1.105  -1.046
93    N        -0.114  -0.118  -0.154   0.118   0.116   0.054  -0.235  -0.241  -0.296
94    W        -0.114  -0.075  -0.140  -0.153  -0.074  -0.229  -0.235  -0.175  -0.274
95    V        -0.114  -0.137  -0.160  -0.087  -0.111  -0.142  -0.235  -0.270  -0.304
96    L        -0.114  -0.137  -0.160  -0.361  -0.403  -0.472  -0.235  -0.270  -0.304
97    L        -0.114  -0.075  -0.140  -0.361  -0.316  -0.365  -0.235  -0.175  -0.274
98    P         1.443   1.446   1.469   1.776   1.780   1.812   1.521   1.524   1.551
99    L         1.443   1.446   1.469   1.046   1.042   1.091   1.521   1.524   1.551
100   L        -1.244  -1.239  -1.205  -1.371  -1.368  -1.297  -1.113  -1.105  -1.046
101   G         1.443   1.446   1.469   1.567   1.569   1.606   1.521   1.524   1.551
102   K         1.443   1.446   1.469   1.707   1.709   1.744   1.521   1.524   1.551
103   Y        -1.244  -1.239  -1.205  -1.215  -1.210  -1.143  -1.113  -1.105  -1.046
104   I        -0.114  -0.118  -0.154  -0.361  -0.363  -0.459  -0.235  -0.241  -0.296
105   G         1.443   1.446   1.469   1.567   1.569   1.606   1.521   1.524   1.551
106   R         1.443   1.446   1.469   1.543   1.546   1.582   1.521   1.524   1.551
107   R         1.443   1.446   1.469   1.543   1.546   1.582   1.521   1.524   1.551
108   M        -1.244  -1.239  -1.205  -0.777  -0.765  -0.710  -1.113  -1.105  -1.046
109   A        -0.114  -0.075  -0.140  -0.032   0.040  -0.093  -0.235  -0.175  -0.274
110   K        -1.244  -1.239  -1.205  -0.777  -0.770  -0.710  -1.113  -1.105  -1.046
111   T        -0.114  -0.137  -0.160  -0.098  -0.122  -0.156  -0.235  -0.270  -0.304
112   L        -0.114  -0.137  -0.160  -0.361  -0.403  -0.472  -0.235  -0.270  -0.304
113   W         1.443   1.446   1.469   1.614   1.618   1.652   1.521   1.524   1.551
114   S        -0.114  -0.137  -0.160  -0.120  -0.163  -0.217  -0.235  -0.270  -0.304
115   R        -0.114  -0.118  -0.154   0.076   0.072   0.025  -0.235  -0.241  -0.296
116   F        -0.114  -0.118  -0.154   0.212   0.209   0.144  -0.235  -0.241  -0.296
117   I        -1.244  -1.239  -1.205  -0.954  -0.945  -0.885  -1.113  -1.105  -1.046
118   E        -0.114  -0.137  -0.160  -0.021  -0.062  -0.122  -0.235  -0.270  -0.304
119   -        -0.252  -0.250  -0.218   0.001   0.007   0.058  -0.454  -0.450  -0.397
120   H        -1.244  -1.239  -1.205  -1.126  -1.115  -1.055  -1.113  -1.105  -1.046
121   F        -0.114  -0.118  -0.154   0.212   0.212   0.144  -0.235  -0.241  -0.296
122   V        -0.114  -0.118  -0.154  -0.032  -0.041  -0.123  -0.235  -0.241  -0.296
* 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/Q3E798
Output conservation file - output/Q3E798
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
