1     M         1.319   1.349   1.420   1.517   1.562   1.659   1.398   1.442   1.549
2     A         0.025   0.081   0.159  -0.204  -0.120  -0.005  -0.300  -0.214  -0.122
3     V        -1.265  -1.260  -1.113  -1.281  -1.285  -1.040  -1.206  -1.190  -0.990
4     P        -0.239  -0.274  -0.503   0.153   0.094  -0.312  -0.229  -0.279  -0.589
5     G        -0.551  -0.595  -0.557  -0.422  -0.459  -0.417  -0.672  -0.708  -0.662
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     Y         1.319   1.349   1.420   1.471   1.510   1.617   1.398   1.442   1.549
10    Y         1.319   1.349   1.420   1.471   1.510   1.617   1.398   1.442   1.549
11    E        -0.120  -0.280  -0.493   0.133  -0.069  -0.467  -0.074  -0.286  -0.576
12    L         0.582   0.448   0.282   0.503   0.331   0.086   0.606   0.402   0.100
13    Y         1.319   1.349   1.420   1.471   1.510   1.617   1.398   1.442   1.549
14    R         1.319   1.349   1.420   1.350   1.378   1.504   1.398   1.442   1.549
15    R        -0.120  -0.280  -0.493   0.141  -0.092  -0.370  -0.074  -0.286  -0.576
16    S         0.582   0.566   0.296   0.643   0.629   0.265   0.606   0.581   0.123
17    T        -0.442  -0.550  -0.562  -0.498  -0.695  -0.695  -0.527  -0.680  -0.673
18    I         0.219   0.240   0.175   0.099   0.121  -0.054   0.040   0.065  -0.092
19    G         1.319   1.349   1.420   1.417   1.455   1.566   1.398   1.442   1.549
20    N        -1.713  -1.668  -1.538  -1.665  -1.629  -1.440  -1.412  -1.362  -1.175
21    S        -0.587  -0.655  -0.566  -0.769  -0.852  -0.704  -0.753  -0.811  -0.679
22    L         1.319   1.349   1.420   1.135   1.181   1.304   1.398   1.442   1.549
23    V        -0.715  -0.590  -0.557  -0.817  -0.640  -0.577  -0.866  -0.701  -0.662
24    D         0.582   0.448   0.282   0.512   0.362   0.122   0.606   0.402   0.100
25    A         0.582   0.644   0.306   0.706   0.782   0.296   0.606   0.692   0.141
26    L         1.319   1.349   1.420   1.135   1.181   1.304   1.398   1.442   1.549
27    D         1.319   1.349   1.420   1.129   1.184   1.299   1.398   1.442   1.549
28    T        -0.442  -0.588  -0.562  -0.536  -0.759  -0.741  -0.527  -0.710  -0.671
29    L         1.319   1.349   1.420   1.135   1.181   1.304   1.398   1.442   1.549
30    I         1.319   1.349   1.420   1.297   1.337   1.455   1.398   1.442   1.549
31    S        -0.120  -0.280  -0.493   0.030  -0.186  -0.486  -0.074  -0.286  -0.576
32    D        -0.120  -0.191  -0.477  -0.078  -0.151  -0.524  -0.074  -0.166  -0.554
33    G        -0.587  -0.655  -0.566  -0.545  -0.628  -0.521  -0.753  -0.811  -0.679
34    R        -0.587  -0.658  -0.563  -0.715  -0.819  -0.675  -0.753  -0.815  -0.675
35    I         1.319   1.349   1.420   1.297   1.337   1.455   1.398   1.442   1.549
36    E        -1.604  -1.683  -1.544  -1.287  -1.384  -1.243  -1.319  -1.369  -1.180
37    A         0.025   0.107   0.181   0.064   0.201   0.280  -0.300  -0.166  -0.081
38    S         0.025   0.107   0.181   0.000   0.150   0.219  -0.300  -0.166  -0.081
39    L         1.319   1.349   1.420   1.135   1.181   1.304   1.398   1.442   1.549
40    A         1.319   1.349   1.420   1.344   1.384   1.499   1.398   1.442   1.549
41    M        -0.120  -0.186  -0.471   0.248   0.139  -0.330  -0.074  -0.170  -0.546
42    R        -0.587  -0.552  -0.557  -0.715  -0.704  -0.673  -0.753  -0.721  -0.669
43    V         0.025   0.108   0.164  -0.219  -0.096  -0.013  -0.300  -0.166  -0.113
44    L         0.582   0.448   0.282   0.498   0.323   0.074   0.606   0.402   0.100
45    E        -1.393  -1.338  -1.487  -0.957  -0.873  -1.112  -1.093  -1.035  -1.131
46    T        -1.137  -1.213  -1.111  -1.085  -1.181  -0.996  -1.093  -1.146  -0.987
47    F         1.319   1.349   1.420   1.448   1.484   1.596   1.398   1.442   1.549
48    D         1.319   1.349   1.420   1.129   1.184   1.299   1.398   1.442   1.549
49    K         0.025   0.075   0.166  -0.177  -0.107   0.023  -0.300  -0.225  -0.110
50    V        -0.442  -0.395  -0.505  -0.478  -0.409  -0.588  -0.527  -0.447  -0.593
51    V        -0.715  -0.702  -0.579  -0.772  -0.751  -0.566  -0.866  -0.858  -0.692
52    A        -0.798  -0.781  -0.603  -1.028  -1.014  -0.737  -0.980  -0.956  -0.721
53    E         0.219   0.171   0.159   0.201   0.115  -0.011   0.040  -0.053  -0.122
54    T        -1.054  -0.958  -1.080  -1.050  -0.944  -1.102  -0.980  -0.892  -0.956
55    L         1.319   1.349   1.420   1.135   1.181   1.304   1.398   1.442   1.549
56    K        -1.054  -1.140  -1.092  -1.036  -1.173  -1.091  -0.980  -1.070  -0.970
57    D        -0.798  -0.781  -0.612  -1.007  -0.951  -0.705  -0.980  -0.956  -0.732
58    N        -1.265  -1.253  -1.101  -1.324  -1.304  -1.108  -1.206  -1.170  -0.975
59    T        -1.604  -1.413  -1.501  -1.585  -1.316  -1.445  -1.319  -1.132  -1.145
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    Q        -1.265  -1.217  -1.115  -1.244  -1.202  -1.037  -1.206  -1.157  -0.992
64    S        -0.120  -0.280  -0.493   0.022  -0.188  -0.504  -0.074  -0.286  -0.576
65    K         0.025   0.003   0.135  -0.217  -0.272  -0.050  -0.300  -0.357  -0.165
66    L         0.582   0.448   0.282   0.536   0.381   0.174   0.606   0.402   0.100
67    T        -0.120  -0.186  -0.471  -0.020  -0.127  -0.549  -0.074  -0.170  -0.546
68    V         0.219   0.333   0.251   0.288   0.453   0.292   0.040   0.219   0.045
69    K         1.319   1.349   1.420   1.238   1.290   1.400   1.398   1.442   1.549
70    G         1.319   1.349   1.420   1.431   1.474   1.580   1.398   1.442   1.549
71    N        -1.732  -1.754  -1.541  -1.554  -1.542  -1.268  -1.433  -1.430  -1.178
72    L         1.319   1.349   1.420   1.135   1.181   1.304   1.398   1.442   1.549
73    D         0.219   0.194   0.172   0.096   0.070   0.067   0.040  -0.014  -0.098
74    T         1.319   1.349   1.420   1.244   1.282   1.405   1.398   1.442   1.549
75    Y         1.319   1.349   1.420   1.471   1.510   1.617   1.398   1.442   1.549
76    G         0.219   0.333   0.251   0.246   0.397   0.274   0.040   0.219   0.045
77    F         0.582   0.448   0.282   0.835   0.661   0.410   0.606   0.402   0.100
78    C         0.582   0.448   0.282   0.891   0.707   0.387   0.606   0.402   0.100
79    D         0.582   0.448   0.282   0.512   0.362   0.122   0.606   0.402   0.100
80    D         0.219   0.189   0.178   0.023  -0.013  -0.041   0.040  -0.023  -0.086
81    V         1.319   1.349   1.420   1.268   1.297   1.428   1.398   1.442   1.549
82    W         1.319   1.349   1.420   1.606   1.648   1.743   1.398   1.442   1.549
83    T         1.319   1.349   1.420   1.244   1.282   1.405   1.398   1.442   1.549
84    F         1.319   1.349   1.420   1.448   1.484   1.596   1.398   1.442   1.549
85    I         0.582   0.566   0.296   0.642   0.621   0.192   0.606   0.581   0.123
86    V         0.025   0.107   0.181  -0.208  -0.077   0.028  -0.300  -0.166  -0.081
87    K         0.582   0.448   0.282   0.613   0.449   0.197   0.606   0.402   0.100
88    N        -0.781  -0.805  -1.029  -0.514  -0.554  -0.963  -0.640  -0.675  -0.898
89    C        -0.587  -0.571  -0.549  -0.527  -0.508  -0.417  -0.753  -0.711  -0.654
90    Q        -2.071  -2.087  -1.883  -1.877  -1.943  -1.697  -1.546  -1.541  -1.297
91    V        -0.798  -0.712  -0.587  -0.923  -0.787  -0.599  -0.980  -0.873  -0.701
92    T        -0.442  -0.396  -0.497  -0.509  -0.417  -0.587  -0.527  -0.447  -0.582
93    V        -1.265  -1.266  -1.119  -1.322  -1.284  -1.043  -1.206  -1.196  -0.995
94    E        -1.054  -0.857  -1.041  -1.103  -0.820  -1.067  -0.980  -0.753  -0.913
95    D        -0.037   0.002   0.137  -0.372  -0.302  -0.088  -0.413  -0.357  -0.162
96    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   G        -0.540  -0.527  -0.564  -0.620  -0.599  -0.615  -0.631  -0.619  -0.670
110   D        -1.287  -1.236  -1.134  -1.570  -1.500  -1.341  -1.211  -1.151  -1.008
111   S        -1.713  -1.601  -1.526  -1.381  -1.252  -1.120  -1.412  -1.312  -1.167
112   Q        -1.265  -1.217  -1.119  -1.160  -1.084  -0.960  -1.206  -1.157  -0.995
113   S        -1.943  -1.915  -1.849  -1.822  -1.807  -1.749  -1.433  -1.405  -1.272
114   V        -0.798  -0.758  -0.602  -0.979  -0.937  -0.706  -0.980  -0.927  -0.719
115   I        -0.798  -0.709  -0.608  -1.141  -1.006  -0.841  -0.980  -0.869  -0.726
116   S        -1.265  -1.202  -1.118  -1.330  -1.241  -1.136  -1.206  -1.138  -0.994
117   V        -1.054  -1.105  -1.094  -0.964  -1.079  -1.000  -0.980  -1.044  -0.972
118   D         0.582   0.547   0.302   0.511   0.486   0.149   0.606   0.553   0.134
119   K         1.319   1.349   1.420   1.238   1.290   1.400   1.398   1.442   1.549
120   L        -1.265  -1.257  -1.126  -1.393  -1.396  -1.166  -1.206  -1.189  -1.002
121   R        -0.587  -0.521  -0.551  -0.660  -0.579  -0.528  -0.753  -0.671  -0.659
122   I         1.319   1.349   1.420   1.297   1.337   1.455   1.398   1.442   1.549
123   V         1.319   1.349   1.420   1.268   1.297   1.428   1.398   1.442   1.549
124   A        -0.120  -0.280  -0.493   0.072  -0.161  -0.525  -0.074  -0.286  -0.576
125   C         1.319   1.349   1.420   1.545   1.590   1.686   1.398   1.442   1.549
126   N        -0.120  -0.191  -0.477   0.134   0.045  -0.419  -0.074  -0.166  -0.554
127   S        -0.587  -0.614  -0.552  -0.727  -0.768  -0.651  -0.753  -0.780  -0.663
128   K         0.025   0.016   0.137  -0.217  -0.249  -0.050  -0.300  -0.333  -0.162
129   K        -0.120  -0.191  -0.477  -0.038  -0.128  -0.592  -0.074  -0.166  -0.554
130   S        -0.587  -0.540  -0.560  -0.696  -0.644  -0.615  -0.753  -0.701  -0.671
131   E        -1.604  -1.543  -1.515  -1.499  -1.413  -1.421  -1.319  -1.256  -1.158
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -0.660  -0.662  -0.566  -0.766  -0.772  -0.642  -0.816  -0.814  -0.677
134   -        -1.287  -1.333  -1.143  -1.208  -1.335  -1.072  -1.211  -1.253  -1.016
* 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/P32774
Output conservation file - output/P32774
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
