1     M         1.724   1.725   1.748   2.126   2.127   2.166   1.841   1.842   1.871
2     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     M         1.724   1.725   1.748   2.128   2.130   2.167   1.841   1.842   1.871
4     R         1.724   1.725   1.748   1.966   1.968   2.005   1.841   1.842   1.871
5     E         1.724   1.725   1.748   1.520   1.521   1.558   1.841   1.842   1.871
6     E        -0.040  -0.040  -0.019  -0.740  -0.740  -0.705  -0.255  -0.255  -0.222
7     T        -0.040  -0.040  -0.019  -0.400  -0.399  -0.364  -0.255  -0.255  -0.222
8     I        -0.040  -0.040  -0.019  -0.117  -0.116  -0.081  -0.255  -0.255  -0.222
9     K        -0.040  -0.040  -0.019  -0.147  -0.146  -0.111  -0.255  -0.255  -0.222
10    S        -0.040  -0.040  -0.019  -0.465  -0.465  -0.430  -0.255  -0.255  -0.222
11    L        -0.040  -0.040  -0.019  -0.549  -0.549  -0.514  -0.255  -0.255  -0.222
12    E         1.724   1.725   1.748   1.520   1.521   1.558   1.841   1.842   1.871
13    D         1.724   1.725   1.748   1.841   1.843   1.880   1.841   1.842   1.871
14    P        -0.040  -0.040  -0.019  -0.056  -0.055  -0.020  -0.255  -0.255  -0.222
15    Y        -0.040  -0.040  -0.019   0.077   0.078   0.113  -0.255  -0.255  -0.222
16    K        -0.040  -0.040  -0.019  -0.209  -0.208  -0.173  -0.255  -0.255  -0.222
17    Y        -1.072  -1.071  -1.053  -1.007  -1.009  -0.973  -0.954  -0.953  -0.919
18    H        -1.072  -1.071  -1.053  -0.712  -0.721  -0.677  -0.954  -0.953  -0.919
19    Y         1.724   1.725   1.748   2.012   2.011   2.051   1.841   1.842   1.871
20    K         1.724   1.725   1.748   1.732   1.747   1.771   1.841   1.842   1.871
21    E        -1.072  -1.071  -1.053  -1.252  -1.221  -1.218  -0.954  -0.953  -0.919
22    E        -1.072  -1.071  -1.053  -0.848  -0.833  -0.813  -0.954  -0.953  -0.919
23    W         1.724   1.725   1.748   2.197   2.198   2.236   1.841   1.842   1.871
24    L         0.104   0.105   0.067  -0.171  -0.179  -0.204  -0.022  -0.020  -0.081
25    N        -0.040  -0.040  -0.019  -0.240  -0.239  -0.205  -0.255  -0.255  -0.222
26    T         0.104   0.105   0.067   0.317   0.328   0.267  -0.022  -0.020  -0.081
27    K         0.104   0.086   0.067   0.035   0.015  -0.027  -0.022  -0.051  -0.082
28    D         0.104   0.086   0.067  -0.049  -0.072  -0.133  -0.022  -0.051  -0.082
29    P        -1.072  -1.071  -1.053  -0.557  -0.561  -0.522  -0.954  -0.953  -0.919
30    D         0.104   0.105   0.067   0.185   0.194   0.135  -0.022  -0.020  -0.081
31    E         1.724   1.725   1.748   1.580   1.594   1.618   1.841   1.842   1.871
32    Q        -1.072  -1.071  -1.053  -0.814  -0.813  -0.779  -0.954  -0.953  -0.919
33    Q        -1.072  -1.071  -1.053  -0.980  -0.984  -0.946  -0.954  -0.953  -0.919
34    L         0.104   0.086   0.067  -0.266  -0.305  -0.313  -0.022  -0.051  -0.082
35    F        -1.072  -1.071  -1.053  -0.980  -0.985  -0.946  -0.954  -0.953  -0.919
36    E         0.104   0.105   0.067  -0.007   0.005  -0.050  -0.022  -0.020  -0.081
37    I         0.104   0.086   0.067  -0.127  -0.176  -0.225  -0.022  -0.051  -0.082
38    F         0.104   0.123   0.074  -0.178  -0.164  -0.205  -0.022   0.008  -0.071
39    A         0.104   0.105   0.067   0.471   0.470   0.416  -0.022  -0.020  -0.081
40    F         1.724   1.725   1.748   2.112   2.114   2.151   1.841   1.842   1.871
41    G         0.104   0.105   0.067   0.452   0.450   0.387  -0.022  -0.020  -0.081
42    N        -1.072  -1.071  -1.053  -0.953  -0.945  -0.919  -0.954  -0.953  -0.919
43    I         0.104   0.086   0.067   0.083   0.044   0.016  -0.022  -0.051  -0.082
44    K        -1.072  -1.071  -1.053  -1.331  -1.311  -1.297  -0.954  -0.953  -0.919
45    D         1.724   1.725   1.748   1.792   1.802   1.831   1.841   1.842   1.871
46    L         1.724   1.725   1.748   1.375   1.366   1.413   1.841   1.842   1.871
47    P         0.104   0.086   0.067   0.304   0.271   0.211  -0.022  -0.051  -0.082
48    E         0.104   0.086   0.067  -0.077  -0.096  -0.131  -0.022  -0.051  -0.082
49    N        -1.072  -1.071  -1.053  -0.944  -0.938  -0.910  -0.954  -0.953  -0.919
50    I         0.104   0.123   0.074   0.165   0.207   0.107  -0.022   0.008  -0.071
51    I        -0.040  -0.040  -0.019  -0.132  -0.131  -0.096  -0.255  -0.255  -0.222
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    L         1.724   1.725   1.748   1.375   1.366   1.413   1.841   1.842   1.871
55    T        -1.072  -1.071  -1.053  -0.953  -0.942  -0.919  -0.954  -0.953  -0.919
56    S        -1.072  -1.071  -1.053  -0.953  -0.945  -0.919  -0.954  -0.953  -0.919
57    L        -1.072  -1.071  -1.053  -1.016  -1.010  -0.982  -0.954  -0.953  -0.919
58    M        -1.072  -1.071  -1.053  -0.918  -0.925  -0.883  -0.954  -0.953  -0.919
59    R         0.104   0.105   0.067   0.000  -0.006  -0.099  -0.022  -0.020  -0.081
60    S        -1.072  -1.071  -1.053  -0.971  -0.967  -0.937  -0.954  -0.953  -0.919
61    K         0.104   0.086   0.067   0.014  -0.010  -0.051  -0.022  -0.051  -0.082
62    L         1.724   1.725   1.748   1.375   1.366   1.413   1.841   1.842   1.871
63    E        -1.072  -1.071  -1.053  -1.165  -1.161  -1.131  -0.954  -0.953  -0.919
64    K         0.104   0.105   0.067   0.014   0.024  -0.050  -0.022  -0.020  -0.081
65    L         1.724   1.725   1.748   1.375   1.366   1.413   1.841   1.842   1.871
66    T         0.104   0.123   0.074   0.185   0.219   0.133  -0.022   0.008  -0.071
67    L         0.104   0.086   0.067  -0.334  -0.374  -0.390  -0.022  -0.051  -0.082
68    V         0.104   0.123   0.074  -0.319  -0.305  -0.362  -0.022   0.008  -0.071
69    T        -1.072  -1.071  -1.053  -0.900  -0.896  -0.866  -0.954  -0.953  -0.919
70    L         0.104   0.086   0.067  -0.229  -0.266  -0.271  -0.022  -0.051  -0.082
71    S        -1.072  -1.071  -1.053  -0.857  -0.865  -0.822  -0.954  -0.953  -0.919
72    E         0.104   0.086   0.067  -0.042  -0.059  -0.090  -0.022  -0.051  -0.082
73    I        -1.072  -1.071  -1.053  -1.184  -1.186  -1.150  -0.954  -0.953  -0.919
74    Y        -1.072  -1.071  -1.053  -0.998  -0.998  -0.964  -0.954  -0.953  -0.919
75    N        -1.072  -1.071  -1.053  -0.779  -0.774  -0.745  -0.954  -0.953  -0.919
76    E         0.104   0.086   0.067  -0.127  -0.151  -0.188  -0.022  -0.051  -0.082
77    L         0.104   0.123   0.074  -0.099  -0.072  -0.180  -0.022   0.008  -0.071
78    S        -1.072  -1.071  -1.053  -0.900  -0.896  -0.866  -0.954  -0.953  -0.919
79    Y         0.104   0.086   0.067   0.395   0.364   0.339  -0.022  -0.051  -0.082
80    E        -1.072  -1.071  -1.053  -1.099  -1.084  -1.065  -0.954  -0.953  -0.919
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    L         0.104   0.105   0.067  -0.449  -0.451  -0.520  -0.022  -0.020  -0.081
83    I         0.104   0.086   0.067  -0.127  -0.176  -0.225  -0.022  -0.051  -0.082
84    K         1.724   1.725   1.748   1.732   1.747   1.771   1.841   1.842   1.871
85    E         0.104   0.086   0.067  -0.049  -0.066  -0.098  -0.022  -0.051  -0.082
86    E        -1.072  -1.071  -1.053  -1.184  -1.161  -1.150  -0.954  -0.953  -0.919
87    C         0.104   0.086   0.067   0.497   0.463   0.435  -0.022  -0.051  -0.082
88    Q         0.104   0.105   0.067   0.317   0.322   0.240  -0.022  -0.020  -0.081
89    I        -1.072  -1.071  -1.053  -1.213  -1.216  -1.179  -0.954  -0.953  -0.919
90    E        -1.072  -1.071  -1.053  -1.108  -1.084  -1.074  -0.954  -0.953  -0.919
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    D         0.104   0.123   0.074   0.158   0.205   0.099  -0.022   0.008  -0.071
95    D         1.724   1.725   1.748   1.792   1.802   1.831   1.841   1.842   1.871
96    G         0.104   0.086   0.067   0.446   0.410   0.379  -0.022  -0.051  -0.082
97    I        -1.072  -1.071  -1.053  -1.281  -1.268  -1.247  -0.954  -0.953  -0.919
98    I         0.104   0.105   0.067   0.083   0.079   0.017  -0.022  -0.020  -0.081
99    E         1.724   1.725   1.748   1.580   1.594   1.618   1.841   1.842   1.871
100   S        -1.072  -1.071  -1.053  -0.927  -0.915  -0.892  -0.954  -0.953  -0.919
101   H        -1.072  -1.071  -1.053  -1.118  -1.132  -1.084  -0.954  -0.953  -0.919
102   L         1.724   1.725   1.748   1.375   1.366   1.413   1.841   1.842   1.871
103   I         0.104   0.086   0.067  -0.127  -0.176  -0.225  -0.022  -0.051  -0.082
104   Q        -1.072  -1.071  -1.053  -1.007  -1.013  -0.973  -0.954  -0.953  -0.919
105   L         0.104   0.105   0.067  -0.193  -0.203  -0.229  -0.022  -0.020  -0.081
106   Q        -1.072  -1.071  -1.053  -0.883  -0.876  -0.848  -0.954  -0.953  -0.919
107   N         0.104   0.105   0.067   0.056   0.051  -0.045  -0.022  -0.020  -0.081
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   I         0.104   0.105   0.067   0.212   0.212   0.163  -0.022  -0.020  -0.081
111   F        -1.072  -1.071  -1.053  -0.729  -0.733  -0.694  -0.954  -0.953  -0.919
112   K         0.104   0.123   0.074   0.021   0.069  -0.039  -0.022   0.008  -0.071
113   A        -1.072  -1.071  -1.053  -1.194  -1.213  -1.160  -0.954  -0.953  -0.919
114   E        -1.072  -1.071  -1.053  -1.271  -1.250  -1.237  -0.954  -0.953  -0.919
115   M         0.104   0.123   0.074   0.219   0.244   0.180  -0.022   0.008  -0.071
116   D         1.724   1.725   1.748   1.792   1.802   1.831   1.841   1.842   1.871
117   S         1.724   1.725   1.748   1.881   1.880   1.920   1.841   1.842   1.871
118   V         1.724   1.725   1.748   1.837   1.829   1.876   1.841   1.842   1.871
119   S         0.104   0.123   0.074   0.356   0.386   0.298  -0.022   0.008  -0.071
120   K         0.104   0.123   0.074   0.158   0.195   0.095  -0.022   0.008  -0.071
121   S        -1.072  -1.071  -1.053  -1.137  -1.138  -1.103  -0.954  -0.953  -0.919
122   M        -1.072  -1.071  -1.053  -0.746  -0.759  -0.711  -0.954  -0.953  -0.919
123   K         0.104   0.105   0.067   0.049   0.068  -0.010  -0.022  -0.020  -0.081
124   F         0.104   0.123   0.074   0.239   0.258   0.199  -0.022   0.008  -0.071
125   S         0.104   0.123   0.074  -0.296  -0.279  -0.337  -0.022   0.008  -0.071
126   R        -1.072  -1.071  -1.053  -1.007  -1.000  -0.973  -0.954  -0.953  -0.919
127   R        -1.072  -1.071  -1.053  -1.175  -1.197  -1.140  -0.954  -0.953  -0.919
128   F        -1.072  -1.071  -1.053  -0.936  -0.933  -0.901  -0.954  -0.953  -0.919
129   D        -1.072  -1.071  -1.053  -1.053  -1.048  -1.019  -0.954  -0.953  -0.919
130   C        -1.072  -1.071  -1.053  -0.754  -0.760  -0.719  -0.954  -0.953  -0.919
131   R         1.724   1.725   1.748   1.940   1.937   1.979   1.841   1.842   1.871
132   D         1.724   1.725   1.748   1.792   1.802   1.831   1.841   1.842   1.871
133   V         1.724   1.725   1.748   1.837   1.829   1.876   1.841   1.842   1.871
134   Y         1.724   1.725   1.748   2.012   2.011   2.051   1.841   1.842   1.871
135   C         0.104   0.105   0.067   0.408   0.408   0.335  -0.022  -0.020  -0.081
136   H         0.104   0.123   0.074   0.547   0.573   0.505  -0.022   0.008  -0.071
137   E         1.724   1.725   1.748   1.580   1.594   1.618   1.841   1.842   1.871
138   K         0.104   0.086   0.067   0.063   0.043   0.005  -0.022  -0.051  -0.082
139   E         0.104   0.105   0.067   0.014   0.026  -0.026  -0.022  -0.020  -0.081
140   L         0.104   0.105   0.067  -0.319  -0.332  -0.372  -0.022  -0.020  -0.081
141   T        -1.072  -1.071  -1.053  -1.090  -1.100  -1.056  -0.954  -0.953  -0.919
142   I        -1.072  -1.071  -1.053  -0.918  -0.924  -0.883  -0.954  -0.953  -0.919
143   I        -1.072  -1.071  -1.053  -0.848  -0.854  -0.813  -0.954  -0.953  -0.919
144   K        -1.072  -1.071  -1.053  -0.989  -0.972  -0.955  -0.954  -0.953  -0.919
145   N         0.104   0.123   0.074   0.484   0.515   0.429  -0.022   0.008  -0.071
146   P        -1.072  -1.071  -1.053  -0.822  -0.825  -0.788  -0.954  -0.953  -0.919
147   R         0.104   0.086   0.067   0.158   0.125   0.080  -0.022  -0.051  -0.082
148   V         1.724   1.725   1.748   1.834   1.825   1.872   1.841   1.842   1.871
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   T         0.104   0.105   0.067   0.199   0.209   0.132  -0.022  -0.020  -0.081
151   K         0.104   0.086   0.067   0.090   0.072   0.036  -0.022  -0.051  -0.082
152   E         0.104   0.123   0.074  -0.035   0.005  -0.104  -0.022   0.008  -0.071
153   Y        -1.072  -1.071  -1.053  -1.016  -1.021  -0.982  -0.954  -0.953  -0.919
154   L         0.104   0.123   0.074  -0.127  -0.094  -0.208  -0.022   0.008  -0.071
155   V        -1.072  -1.071  -1.053  -1.381  -1.395  -1.347  -0.954  -0.953  -0.919
156   Q        -1.072  -1.071  -1.053  -0.918  -0.921  -0.883  -0.954  -0.953  -0.919
157   N        -1.072  -1.071  -1.053  -0.779  -0.779  -0.745  -0.954  -0.953  -0.919
158   L         1.724   1.725   1.748   1.375   1.366   1.413   1.841   1.842   1.871
159   R        -1.072  -1.071  -1.053  -0.874  -0.876  -0.840  -0.954  -0.953  -0.919
160   S        -1.072  -1.071  -1.053  -0.796  -0.798  -0.762  -0.954  -0.953  -0.919
161   W         0.104   0.086   0.067   0.516   0.482   0.447  -0.022  -0.051  -0.082
162   E        -1.072  -1.071  -1.053  -1.137  -1.127  -1.103  -0.954  -0.953  -0.919
163   T        -1.072  -1.071  -1.053  -1.026  -1.017  -0.991  -0.954  -0.953  -0.919
164   K         0.104   0.105   0.067   0.035   0.048  -0.026  -0.022  -0.020  -0.081
165   L         1.724   1.725   1.748   1.375   1.366   1.413   1.841   1.842   1.871
166   K        -0.040  -0.040  -0.019  -0.209  -0.208  -0.173  -0.255  -0.255  -0.222
167   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   E        -0.040  -0.040  -0.019  -0.383  -0.383  -0.348  -0.255  -0.255  -0.222
* 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/Q03981
Output conservation file - output/Q03981
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
