1     M         1.554   1.554   1.577   1.715   1.716   1.749   1.643   1.643   1.670
2     M        -1.101  -1.101  -1.079  -0.893  -0.893  -0.854  -0.990  -0.990  -0.950
3     G         0.016   0.008  -0.023   0.012  -0.002  -0.061  -0.112  -0.125  -0.173
4     R        -1.101  -1.101  -1.079  -1.055  -1.058  -1.016  -0.990  -0.990  -0.950
5     N         0.016   0.008  -0.023   0.056   0.043  -0.011  -0.112  -0.125  -0.173
6     -        -0.121  -0.121  -0.099  -0.410  -0.410  -0.372  -0.332  -0.332  -0.295
7     -         1.554   1.554   1.577   1.569   1.569   1.603   1.643   1.643   1.670
8     -         1.554   1.554   1.577   1.337   1.337   1.371   1.643   1.643   1.670
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    G         1.554   1.554   1.577   1.556   1.555   1.590   1.643   1.643   1.670
11    I         0.016   0.020  -0.023   0.063   0.070  -0.017  -0.112  -0.106  -0.174
12    R        -1.101  -1.101  -1.079  -1.026  -1.029  -0.987  -0.990  -0.990  -0.950
13    L         0.016   0.020  -0.024  -0.253  -0.246  -0.312  -0.112  -0.106  -0.174
14    A         0.016   0.020  -0.024   0.005   0.012  -0.074  -0.112  -0.106  -0.174
15    L         0.016   0.020  -0.023  -0.107  -0.102  -0.144  -0.112  -0.106  -0.174
16    K        -1.101  -1.101  -1.079  -1.135  -1.136  -1.095  -0.990  -0.990  -0.950
17    R         0.016   0.020  -0.024  -0.069  -0.063  -0.134  -0.112  -0.106  -0.174
18    S        -1.101  -1.101  -1.079  -1.065  -1.065  -1.026  -0.990  -0.990  -0.950
19    F         0.016   0.020  -0.024  -0.003   0.006  -0.097  -0.112  -0.106  -0.174
20    S         0.016   0.020  -0.023   0.056   0.063  -0.011  -0.112  -0.106  -0.174
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -0.121  -0.121  -0.099  -0.258  -0.258  -0.220  -0.332  -0.332  -0.295
23    -        -0.121  -0.121  -0.099  -0.241  -0.242  -0.204  -0.332  -0.332  -0.295
24    -        -0.121  -0.121  -0.099  -0.160  -0.160  -0.122  -0.332  -0.332  -0.295
25    -        -0.121  -0.121  -0.099  -0.032  -0.033   0.005  -0.332  -0.332  -0.295
26    -         1.554   1.554   1.577   1.408   1.408   1.442   1.643   1.643   1.670
27    T         0.016   0.008  -0.023   0.178   0.163   0.110  -0.112  -0.125  -0.173
28    Y         1.554   1.554   1.577   1.604   1.605   1.638   1.643   1.643   1.670
29    Q        -1.101  -1.101  -1.079  -1.046  -1.043  -1.006  -0.990  -0.990  -0.950
30    P         1.554   1.554   1.577   1.684   1.684   1.717   1.643   1.643   1.670
31    P         1.554   1.554   1.577   1.684   1.684   1.717   1.643   1.643   1.670
32    V        -1.101  -1.101  -1.079  -0.940  -0.939  -0.901  -0.990  -0.990  -0.950
33    V        -1.101  -1.101  -1.079  -0.988  -0.987  -0.948  -0.990  -0.990  -0.950
34    E         0.016   0.020  -0.023  -0.145  -0.138  -0.205  -0.112  -0.106  -0.174
35    I         0.016   0.020  -0.023   0.070   0.077  -0.009  -0.112  -0.106  -0.174
36    T        -1.101  -1.101  -1.079  -1.125  -1.123  -1.085  -0.990  -0.990  -0.950
37    N        -0.121  -0.121  -0.099  -0.046  -0.046  -0.009  -0.332  -0.332  -0.295
38    I         0.016   0.008  -0.023   0.185   0.170   0.118  -0.112  -0.125  -0.173
39    T        -1.101  -1.101  -1.079  -0.856  -0.857  -0.817  -0.990  -0.990  -0.950
40    K        -1.101  -1.101  -1.079  -1.036  -1.038  -0.996  -0.990  -0.990  -0.950
41    L        -1.101  -1.101  -1.079  -1.342  -1.345  -1.302  -0.990  -0.990  -0.950
42    W         1.554   1.554   1.577   1.762   1.762   1.796   1.643   1.643   1.670
43    P        -1.101  -1.101  -1.079  -1.185  -1.183  -1.145  -0.990  -0.990  -0.950
44    T         0.016   0.020  -0.023   0.227   0.232   0.174  -0.112  -0.106  -0.174
45    L        -1.101  -1.101  -1.079  -1.185  -1.188  -1.145  -0.990  -0.990  -0.950
46    R        -1.101  -1.101  -1.079  -1.085  -1.086  -1.045  -0.990  -0.990  -0.950
47    P        -1.101  -1.101  -1.079  -1.095  -1.094  -1.055  -0.990  -0.990  -0.950
48    E         0.016   0.008  -0.023  -0.032  -0.047  -0.115  -0.112  -0.125  -0.173
49    V        -1.101  -1.101  -1.079  -1.105  -1.104  -1.065  -0.990  -0.990  -0.950
50    R         0.016   0.020  -0.024  -0.122  -0.116  -0.194  -0.112  -0.106  -0.174
51    D         0.016   0.008  -0.023  -0.137  -0.149  -0.195  -0.112  -0.125  -0.173
52    E         1.554   1.554   1.577   1.425   1.426   1.459   1.643   1.643   1.670
53    I         1.554   1.554   1.577   1.715   1.715   1.749   1.643   1.643   1.670
54    K        -1.101  -1.101  -1.079  -1.016  -1.018  -0.977  -0.990  -0.990  -0.950
55    E         1.554   1.554   1.577   1.425   1.426   1.459   1.643   1.643   1.670
56    Y         1.554   1.554   1.577   1.604   1.605   1.638   1.643   1.643   1.670
57    L         1.554   1.554   1.577   1.325   1.326   1.360   1.643   1.643   1.670
58    R        -1.101  -1.101  -1.079  -1.226  -1.227  -1.186  -0.990  -0.990  -0.950
59    W         1.554   1.554   1.577   1.762   1.762   1.796   1.643   1.643   1.670
60    R         0.016   0.020  -0.024  -0.122  -0.116  -0.194  -0.112  -0.106  -0.174
61    M         0.016   0.020  -0.024   0.199   0.205   0.138  -0.112  -0.106  -0.174
62    Q         0.016   0.008  -0.023  -0.062  -0.073  -0.109  -0.112  -0.125  -0.173
63    E         0.016   0.020  -0.024  -0.137  -0.130  -0.197  -0.112  -0.106  -0.174
64    D        -1.101  -1.101  -1.079  -1.065  -1.065  -1.026  -0.990  -0.990  -0.950
65    W         1.554   1.554   1.577   1.762   1.762   1.796   1.643   1.643   1.670
66    R        -1.101  -1.101  -1.079  -1.007  -1.009  -0.967  -0.990  -0.990  -0.950
67    H        -1.101  -1.101  -1.079  -0.978  -0.975  -0.939  -0.990  -0.990  -0.950
68    I        -1.101  -1.101  -1.079  -1.115  -1.113  -1.075  -0.990  -0.990  -0.950
69    P        -1.101  -1.101  -1.079  -0.988  -0.986  -0.948  -0.990  -0.990  -0.950
70    L         0.016   0.020  -0.024  -0.198  -0.193  -0.249  -0.112  -0.106  -0.174
71    E        -1.101  -1.101  -1.079  -1.115  -1.117  -1.075  -0.990  -0.990  -0.950
72    E         0.016   0.020  -0.023  -0.137  -0.130  -0.196  -0.112  -0.106  -0.174
73    T        -1.101  -1.101  -1.079  -1.135  -1.134  -1.095  -0.990  -0.990  -0.950
74    K         0.016   0.008  -0.023  -0.122  -0.136  -0.193  -0.112  -0.125  -0.173
75    A         0.016   0.020  -0.023   0.185   0.190   0.134  -0.112  -0.106  -0.174
76    A         1.554   1.554   1.577   1.652   1.652   1.686   1.643   1.643   1.670
77    Y         1.554   1.554   1.577   1.604   1.605   1.638   1.643   1.643   1.670
78    F         0.016   0.008  -0.023   0.063   0.051   0.003  -0.112  -0.125  -0.173
79    L         0.016   0.008  -0.023  -0.017  -0.034  -0.109  -0.112  -0.125  -0.173
80    S         0.016   0.020  -0.023   0.056   0.063  -0.011  -0.112  -0.106  -0.174
81    Y         0.016   0.020  -0.024   0.063   0.070   0.002  -0.112  -0.106  -0.174
82    G         1.554   1.554   1.577   1.556   1.555   1.590   1.643   1.643   1.670
83    P         0.016   0.008  -0.023  -0.122  -0.134  -0.178  -0.112  -0.125  -0.173
84    C         0.016   0.008  -0.023   0.282   0.270   0.228  -0.112  -0.125  -0.173
85    G         1.554   1.554   1.577   1.556   1.555   1.590   1.643   1.643   1.670
86    G         0.016   0.008  -0.023   0.056   0.041  -0.019  -0.112  -0.125  -0.173
87    R         1.554   1.554   1.577   1.507   1.507   1.541   1.643   1.643   1.670
88    S        -1.101  -1.101  -1.079  -1.036  -1.035  -0.996  -0.990  -0.990  -0.950
89    K         0.016   0.020  -0.024  -0.025  -0.018  -0.085  -0.112  -0.106  -0.174
90    G         0.016   0.020  -0.023  -0.077  -0.070  -0.150  -0.112  -0.106  -0.174
91    N        -1.101  -1.101  -1.079  -0.959  -0.960  -0.920  -0.990  -0.990  -0.950
92    -        -0.121  -0.121  -0.099  -0.176  -0.176  -0.138  -0.332  -0.332  -0.295
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    E         0.016   0.020  -0.024  -0.198  -0.191  -0.268  -0.112  -0.106  -0.174
99    W        -1.101  -1.101  -1.079  -0.921  -0.920  -0.882  -0.990  -0.990  -0.950
100   N         0.016   0.020  -0.024   0.070   0.077   0.002  -0.112  -0.106  -0.174
101   V        -1.101  -1.101  -1.079  -0.968  -0.969  -0.929  -0.990  -0.990  -0.950
102   G        -1.101  -1.101  -1.079  -1.046  -1.047  -1.006  -0.990  -0.990  -0.950
103   Y         0.016   0.020  -0.023  -0.077  -0.069  -0.159  -0.112  -0.106  -0.174
104   T        -1.101  -1.101  -1.079  -1.105  -1.104  -1.065  -0.990  -0.990  -0.950
105   G        -1.101  -1.101  -1.079  -0.978  -0.980  -0.939  -0.990  -0.990  -0.950
106   M         0.016   0.008  -0.023  -0.198  -0.210  -0.248  -0.112  -0.125  -0.173
107   R         0.016   0.020  -0.023  -0.122  -0.116  -0.193  -0.112  -0.106  -0.174
108   I        -1.101  -1.101  -1.079  -1.016  -1.016  -0.977  -0.990  -0.990  -0.950
109   V        -1.101  -1.101  -1.079  -1.095  -1.093  -1.055  -0.990  -0.990  -0.950
110   F         1.554   1.554   1.577   1.731   1.731   1.764   1.643   1.643   1.670
111   N         0.016   0.020  -0.023   0.063   0.070  -0.006  -0.112  -0.106  -0.174
112   L         1.554   1.554   1.577   1.325   1.326   1.360   1.643   1.643   1.670
113   V        -1.101  -1.101  -1.079  -0.875  -0.875  -0.835  -0.990  -0.990  -0.950
114   L         1.554   1.554   1.577   1.325   1.326   1.360   1.643   1.643   1.670
115   F         1.554   1.554   1.577   1.731   1.731   1.764   1.643   1.643   1.670
116   G        -1.101  -1.101  -1.079  -1.268  -1.267  -1.228  -0.990  -0.990  -0.950
117   G        -1.101  -1.101  -1.079  -1.065  -1.066  -1.026  -0.990  -0.990  -0.950
118   A         0.016   0.020  -0.023  -0.077  -0.069  -0.168  -0.112  -0.106  -0.174
119   A         0.016   0.008  -0.023  -0.017  -0.031  -0.081  -0.112  -0.125  -0.173
120   T        -1.101  -1.101  -1.079  -0.884  -0.884  -0.845  -0.990  -0.990  -0.950
121   A         1.554   1.554   1.577   1.652   1.652   1.686   1.643   1.643   1.670
122   F         1.554   1.554   1.577   1.731   1.731   1.764   1.643   1.643   1.670
123   Y         0.016   0.020  -0.023   0.041   0.048  -0.022  -0.112  -0.106  -0.174
124   N         1.554   1.554   1.577   1.652   1.652   1.686   1.643   1.643   1.670
125   W        -1.101  -1.101  -1.079  -1.155  -1.152  -1.115  -0.990  -0.990  -0.950
126   K         1.554   1.554   1.577   1.524   1.524   1.557   1.643   1.643   1.670
127   Q         0.016   0.008  -0.023   0.027   0.015  -0.024  -0.112  -0.125  -0.173
128   D         1.554   1.554   1.577   1.652   1.653   1.686   1.643   1.643   1.670
129   K         1.554   1.554   1.577   1.524   1.524   1.557   1.643   1.643   1.670
130   K        -1.101  -1.101  -1.079  -1.185  -1.186  -1.145  -0.990  -0.990  -0.950
131   L         0.016   0.020  -0.024  -0.198  -0.192  -0.249  -0.112  -0.106  -0.174
132   E        -1.101  -1.101  -1.079  -1.115  -1.117  -1.075  -0.990  -0.990  -0.950
133   E         0.016   0.020  -0.024  -0.198  -0.191  -0.268  -0.112  -0.106  -0.174
134   Q        -1.101  -1.101  -1.079  -0.978  -0.976  -0.939  -0.990  -0.990  -0.950
135   L         0.016   0.020  -0.024  -0.198  -0.193  -0.249  -0.112  -0.106  -0.174
136   R        -1.101  -1.101  -1.079  -1.085  -1.086  -1.045  -0.990  -0.990  -0.950
137   D         0.016   0.020  -0.023   0.012   0.020  -0.065  -0.112  -0.106  -0.174
138   L         1.554   1.554   1.577   1.325   1.326   1.360   1.643   1.643   1.670
139   -        -0.121  -0.121  -0.099  -0.275  -0.275  -0.237  -0.332  -0.332  -0.295
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   V        -1.101  -1.101  -1.079  -1.046  -1.045  -1.006  -0.990  -0.990  -0.950
* 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/P53077
Output conservation file - output/P53077
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
