1     M         1.464   1.468   1.481   1.913   1.921   1.935   1.540   1.544   1.560
2     -         1.464   1.468   1.481   1.561   1.569   1.587   1.540   1.544   1.560
3     -        -0.335  -0.332  -0.309  -0.061  -0.055  -0.018  -0.498  -0.492  -0.455
4     -        -0.335  -0.332  -0.309  -0.142  -0.136  -0.099  -0.498  -0.492  -0.455
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    N        -1.388  -1.380  -1.355  -1.368  -1.348  -1.312  -1.178  -1.166  -1.126
16    L        -0.188  -0.231  -0.242  -0.481  -0.544  -0.555  -0.272  -0.335  -0.351
17    Q        -0.188  -0.177  -0.244  -0.211  -0.182  -0.315  -0.272  -0.254  -0.355
18    N        -1.388  -1.380  -1.355  -1.655  -1.649  -1.596  -1.178  -1.166  -1.126
19    N        -0.188  -0.177  -0.244  -0.233  -0.195  -0.342  -0.272  -0.254  -0.355
20    V        -0.188  -0.177  -0.244   0.251   0.269   0.169  -0.272  -0.254  -0.355
21    L        -0.188  -0.177  -0.244  -0.449  -0.436  -0.521  -0.272  -0.254  -0.355
22    N        -1.388  -1.380  -1.355  -1.471  -1.459  -1.414  -1.178  -1.166  -1.126
23    Q        -0.188  -0.231  -0.242  -0.144  -0.203  -0.232  -0.272  -0.335  -0.351
24    I         1.464   1.468   1.481   1.442   1.446   1.469   1.540   1.544   1.560
25    H         1.464   1.468   1.481   1.744   1.747   1.768   1.540   1.544   1.560
26    Q        -1.388  -1.380  -1.355  -1.368  -1.356  -1.312  -1.178  -1.166  -1.126
27    I         1.464   1.468   1.481   1.442   1.446   1.469   1.540   1.544   1.560
28    L        -0.188  -0.177  -0.244  -0.561  -0.548  -0.654  -0.272  -0.254  -0.355
29    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    T        -0.335  -0.332  -0.309  -0.460  -0.445  -0.413  -0.498  -0.492  -0.455
32    N         1.464   1.468   1.481   1.439   1.464   1.467   1.540   1.544   1.560
33    P        -0.335  -0.332  -0.309  -0.044  -0.041  -0.002  -0.498  -0.492  -0.455
34    T        -0.335  -0.332  -0.309  -0.179  -0.161  -0.134  -0.498  -0.492  -0.455
35    L         1.464   1.468   1.481   1.214   1.213   1.243   1.540   1.544   1.560
36    D        -0.335  -0.332  -0.309  -0.444  -0.429  -0.397  -0.498  -0.492  -0.455
37    K        -0.335  -0.332  -0.309  -0.541  -0.527  -0.494  -0.498  -0.492  -0.455
38    P        -0.335  -0.332  -0.309  -0.270  -0.269  -0.225  -0.498  -0.492  -0.455
39    N        -0.335  -0.332  -0.309  -0.224  -0.207  -0.180  -0.498  -0.492  -0.455
40    A        -0.335  -0.332  -0.309  -0.492  -0.494  -0.445  -0.498  -0.492  -0.455
41    E        -0.335  -0.332  -0.309  -0.575  -0.578  -0.526  -0.498  -0.492  -0.455
42    A        -0.335  -0.332  -0.309  -0.364  -0.364  -0.318  -0.498  -0.492  -0.455
43    T        -0.335  -0.332  -0.309  -0.444  -0.412  -0.397  -0.498  -0.492  -0.455
44    K        -0.335  -0.332  -0.309  -0.591  -0.594  -0.543  -0.498  -0.492  -0.455
45    E        -0.335  -0.332  -0.309  -0.460  -0.445  -0.413  -0.498  -0.492  -0.455
46    E        -0.335  -0.332  -0.309  -0.762  -0.767  -0.712  -0.498  -0.492  -0.455
47    F        -0.335  -0.332  -0.309  -0.428  -0.429  -0.381  -0.498  -0.492  -0.455
48    S        -0.335  -0.332  -0.309  -0.348  -0.348  -0.302  -0.498  -0.492  -0.455
49    S         1.464   1.468   1.481   1.373   1.374   1.401   1.540   1.544   1.560
50    A         1.464   1.468   1.481   1.742   1.748   1.766   1.540   1.544   1.560
51    E        -0.335  -0.332  -0.309  -0.642  -0.645  -0.593  -0.498  -0.492  -0.455
52    N        -0.335  -0.332  -0.309  -0.444  -0.429  -0.397  -0.498  -0.492  -0.455
53    R         1.464   1.468   1.481   1.549   1.553   1.575   1.540   1.544   1.560
54    D        -0.335  -0.332  -0.309  -0.476  -0.478  -0.429  -0.498  -0.492  -0.455
55    E        -0.335  -0.332  -0.309  -0.412  -0.412  -0.365  -0.498  -0.492  -0.455
56    K        -0.335  -0.332  -0.309  -0.575  -0.578  -0.526  -0.498  -0.492  -0.455
57    D        -0.335  -0.332  -0.309  -0.194  -0.192  -0.149  -0.498  -0.492  -0.455
58    Y        -0.335  -0.332  -0.309  -0.209  -0.207  -0.165  -0.498  -0.492  -0.455
59    L         1.464   1.468   1.481   1.214   1.213   1.243   1.540   1.544   1.560
60    T        -0.335  -0.332  -0.309  -0.460  -0.445  -0.413  -0.498  -0.492  -0.455
61    N        -0.335  -0.332  -0.309  -0.541  -0.527  -0.494  -0.498  -0.492  -0.455
62    Q        -0.335  -0.332  -0.309  -0.301  -0.285  -0.256  -0.498  -0.492  -0.455
63    Q        -0.335  -0.332  -0.309  -0.412  -0.412  -0.365  -0.498  -0.492  -0.455
64    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    K        -0.335  -0.332  -0.309  -0.428  -0.429  -0.381  -0.498  -0.492  -0.455
66    N         1.464   1.468   1.481   1.439   1.464   1.467   1.540   1.544   1.560
67    L        -0.335  -0.332  -0.309  -0.779  -0.785  -0.729  -0.498  -0.492  -0.455
68    S         1.464   1.468   1.481   1.373   1.374   1.401   1.540   1.544   1.560
69    T        -0.188  -0.177  -0.244  -0.189  -0.174  -0.303  -0.272  -0.254  -0.355
70    P        -1.388  -1.380  -1.355  -1.210  -1.215  -1.155  -1.178  -1.166  -1.126
71    S        -1.388  -1.380  -1.355  -1.348  -1.323  -1.292  -1.178  -1.166  -1.126
72    T        -0.188  -0.231  -0.242  -0.189  -0.275  -0.299  -0.272  -0.335  -0.351
73    S        -0.188  -0.177  -0.244  -0.294  -0.281  -0.375  -0.272  -0.254  -0.355
74    S        -1.388  -1.380  -1.355  -1.268  -1.251  -1.213  -1.178  -1.166  -1.126
75    N        -1.388  -1.380  -1.355  -1.210  -1.178  -1.155  -1.178  -1.166  -1.126
76    G        -1.388  -1.380  -1.355  -0.948  -0.954  -0.896  -1.178  -1.166  -1.126
77    E         1.464   1.468   1.481   1.409   1.416   1.437   1.540   1.544   1.560
78    F         1.464   1.468   1.481   1.852   1.862   1.875   1.540   1.544   1.560
79    I         1.464   1.468   1.481   1.442   1.446   1.469   1.540   1.544   1.560
80    P         1.464   1.468   1.481   1.729   1.737   1.753   1.540   1.544   1.560
81    H        -1.388  -1.380  -1.355  -1.503  -1.525  -1.445  -1.178  -1.166  -1.126
82    I        -0.188  -0.231  -0.242  -0.402  -0.494  -0.520  -0.272  -0.335  -0.351
83    F        -0.188  -0.231  -0.242   0.291   0.232   0.210  -0.272  -0.335  -0.351
84    Y        -1.388  -1.380  -1.355  -0.790  -0.786  -0.740  -1.178  -1.166  -1.126
85    S         1.464   1.468   1.481   1.360   1.365   1.388   1.540   1.544   1.560
86    L         1.464   1.468   1.481   1.192   1.196   1.222   1.540   1.544   1.560
87    H        -0.188  -0.231  -0.242  -0.028  -0.120  -0.144  -0.272  -0.335  -0.351
88    Q        -0.188  -0.177  -0.244  -0.233  -0.207  -0.342  -0.272  -0.254  -0.355
89    I         1.464   1.468   1.481   1.442   1.446   1.469   1.540   1.544   1.560
90    R        -0.188  -0.231  -0.242  -0.189  -0.270  -0.299  -0.272  -0.335  -0.351
91    K         1.464   1.468   1.481   1.393   1.392   1.421   1.540   1.544   1.560
92    D        -0.188  -0.231  -0.242   0.043  -0.019  -0.038  -0.272  -0.335  -0.351
93    P         1.464   1.468   1.481   1.729   1.737   1.753   1.540   1.544   1.560
94    N         1.464   1.468   1.481   1.523   1.555   1.550   1.540   1.544   1.560
95    N         1.464   1.468   1.481   1.523   1.555   1.550   1.540   1.544   1.560
96    L        -1.388  -1.380  -1.355  -1.461  -1.449  -1.404  -1.178  -1.166  -1.126
97    S         1.464   1.468   1.481   1.360   1.365   1.388   1.540   1.544   1.560
98    N        -0.188  -0.177  -0.244  -0.248  -0.207  -0.360  -0.272  -0.254  -0.355
99    Q        -0.188  -0.231  -0.242  -0.248  -0.319  -0.356  -0.272  -0.335  -0.351
100   L         1.464   1.468   1.481   1.192   1.196   1.222   1.540   1.544   1.560
101   E        -0.188  -0.231  -0.242  -0.218  -0.280  -0.294  -0.272  -0.335  -0.351
102   T        -0.188  -0.231  -0.242  -0.021  -0.090  -0.100  -0.272  -0.335  -0.351
103   L        -1.388  -1.380  -1.355  -1.514  -1.480  -1.456  -1.178  -1.166  -1.126
104   T         1.464   1.468   1.481   1.587   1.591   1.613   1.540   1.544   1.560
105   G        -0.188  -0.231  -0.242   0.100   0.012  -0.027  -0.272  -0.335  -0.351
106   S        -0.188  -0.177  -0.244  -0.166  -0.152  -0.224  -0.272  -0.254  -0.355
107   I         1.464   1.468   1.481   1.442   1.446   1.469   1.540   1.544   1.560
108   R         1.464   1.468   1.481   1.587   1.596   1.613   1.540   1.544   1.560
109   H         1.464   1.468   1.481   1.744   1.747   1.768   1.540   1.544   1.560
110   R         1.464   1.468   1.481   1.587   1.596   1.613   1.540   1.544   1.560
111   L        -0.188  -0.177  -0.244  -0.521  -0.509  -0.606  -0.272  -0.254  -0.355
112   K         1.464   1.468   1.481   1.393   1.392   1.421   1.540   1.544   1.560
113   L        -1.388  -1.380  -1.355  -1.461  -1.436  -1.404  -1.178  -1.166  -1.126
114   C        -0.188  -0.231  -0.242   0.298   0.226   0.198  -0.272  -0.335  -0.351
115   K         1.464   1.468   1.481   1.393   1.392   1.421   1.540   1.544   1.560
116   S        -1.388  -1.380  -1.355  -1.268  -1.254  -1.213  -1.178  -1.166  -1.126
117   L         1.464   1.468   1.481   1.192   1.196   1.222   1.540   1.544   1.560
118   I        -0.188  -0.140  -0.226  -0.521  -0.448  -0.576  -0.272  -0.198  -0.327
119   S        -0.188  -0.140  -0.226  -0.248  -0.151  -0.323  -0.272  -0.198  -0.327
120   E        -0.188  -0.231  -0.242  -0.279  -0.344  -0.365  -0.272  -0.335  -0.351
121   N        -0.188  -0.231  -0.242  -0.115  -0.157  -0.197  -0.272  -0.335  -0.351
122   E        -0.188  -0.231  -0.242  -0.181  -0.242  -0.250  -0.272  -0.335  -0.351
123   D        -1.388  -1.380  -1.355  -1.200  -1.182  -1.145  -1.178  -1.166  -1.126
124   T        -1.388  -1.380  -1.355  -1.003  -0.990  -0.950  -1.178  -1.166  -1.126
125   K        -1.388  -1.380  -1.355  -1.430  -1.423  -1.373  -1.178  -1.166  -1.126
126   D        -1.388  -1.380  -1.355  -1.328  -1.309  -1.272  -1.178  -1.166  -1.126
127   L         1.464   1.468   1.481   1.192   1.196   1.222   1.540   1.544   1.560
128   L        -0.188  -0.231  -0.242  -0.340  -0.395  -0.389  -0.272  -0.335  -0.351
129   S        -0.188  -0.177  -0.244  -0.226  -0.213  -0.295  -0.272  -0.254  -0.355
130   K        -0.188  -0.177  -0.244  -0.294  -0.273  -0.383  -0.272  -0.254  -0.355
131   S        -0.188  -0.231  -0.242  -0.294  -0.364  -0.372  -0.272  -0.335  -0.351
132   P        -0.188  -0.177  -0.244  -0.021  -0.001  -0.136  -0.272  -0.254  -0.355
133   S        -0.188  -0.140  -0.226  -0.355  -0.272  -0.425  -0.272  -0.198  -0.327
134   E        -0.188  -0.231  -0.242  -0.279  -0.344  -0.365  -0.272  -0.335  -0.351
135   W         1.464   1.468   1.481   1.928   1.936   1.950   1.540   1.544   1.560
136   Q        -0.188  -0.177  -0.244  -0.226  -0.196  -0.333  -0.272  -0.254  -0.355
137   D        -1.388  -1.380  -1.355  -1.461  -1.455  -1.404  -1.178  -1.166  -1.126
138   I        -0.188  -0.231  -0.242  -0.144  -0.210  -0.214  -0.272  -0.335  -0.351
139   I         1.464   1.468   1.481   1.442   1.446   1.469   1.540   1.544   1.560
140   H        -1.388  -1.380  -1.355  -1.077  -1.073  -1.023  -1.178  -1.166  -1.126
141   Q        -1.388  -1.380  -1.355  -1.328  -1.313  -1.272  -1.178  -1.166  -1.126
142   R        -0.188  -0.140  -0.226  -0.264  -0.195  -0.318  -0.272  -0.198  -0.327
143   E        -0.188  -0.231  -0.242  -0.340  -0.422  -0.438  -0.272  -0.335  -0.351
144   Q        -0.188  -0.231  -0.242  -0.211  -0.278  -0.311  -0.272  -0.335  -0.351
145   E        -0.188  -0.177  -0.244  -0.279  -0.256  -0.369  -0.272  -0.254  -0.355
146   L         1.464   1.468   1.481   1.192   1.196   1.222   1.540   1.544   1.560
147   Q        -1.388  -1.380  -1.355  -1.368  -1.356  -1.312  -1.178  -1.166  -1.126
148   I        -1.388  -1.380  -1.355  -1.288  -1.289  -1.232  -1.178  -1.166  -1.126
149   K         1.464   1.468   1.481   1.393   1.392   1.421   1.540   1.544   1.560
150   R        -1.388  -1.380  -1.355  -1.133  -1.126  -1.079  -1.178  -1.166  -1.126
151   D        -0.188  -0.140  -0.226  -0.233  -0.165  -0.284  -0.272  -0.198  -0.327
152   V        -0.188  -0.231  -0.242   0.183   0.112   0.092  -0.272  -0.335  -0.351
153   L         1.464   1.468   1.481   1.192   1.196   1.222   1.540   1.544   1.560
154   D        -1.388  -1.380  -1.355  -1.219  -1.202  -1.164  -1.178  -1.166  -1.126
155   D        -0.188  -0.231  -0.242  -0.028  -0.094  -0.122  -0.272  -0.335  -0.351
156   L         1.464   1.468   1.481   1.192   1.196   1.222   1.540   1.544   1.560
157   Y        -1.388  -1.380  -1.355  -0.994  -0.990  -0.941  -1.178  -1.166  -1.126
158   R        -1.388  -1.380  -1.355  -1.239  -1.239  -1.184  -1.178  -1.166  -1.126
159   K        -1.388  -1.380  -1.355  -1.482  -1.479  -1.424  -1.178  -1.166  -1.126
160   L        -0.188  -0.140  -0.226  -0.402  -0.314  -0.485  -0.272  -0.198  -0.327
161   Q        -0.188  -0.177  -0.244  -0.226  -0.196  -0.333  -0.272  -0.254  -0.355
162   R        -0.188  -0.140  -0.226  -0.264  -0.195  -0.318  -0.272  -0.198  -0.327
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -0.335  -0.332  -0.309  -0.327  -0.321  -0.281  -0.498  -0.492  -0.455
* 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/P33308
Output conservation file - output/P33308
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
