1     M         1.195   1.203   1.282   1.443   1.452   1.572   1.265   1.275   1.390
2     S         1.195   1.203   1.282   1.228   1.229   1.373   1.265   1.275   1.390
3     R         0.544   0.521   0.318   0.559   0.525   0.190   0.533   0.497   0.131
4     H         1.195   1.203   1.282   1.472   1.484   1.599   1.265   1.275   1.390
5     Q         0.051   0.090   0.175   0.055   0.128   0.241  -0.304  -0.236  -0.132
6     F        -0.975  -0.994  -0.943  -0.899  -0.929  -0.834  -1.037  -1.047  -0.932
7     D         1.195   1.203   1.282   1.216   1.230   1.362   1.265   1.275   1.390
8     L         1.195   1.203   1.282   1.265   1.283   1.407   1.265   1.275   1.390
9     I        -0.489  -0.520  -0.463  -0.592  -0.618  -0.507  -0.723  -0.747  -0.647
10    M        -0.602  -0.559  -0.475  -0.615  -0.537  -0.443  -0.828  -0.768  -0.656
11    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
12    L        -0.361  -0.323  -0.416  -0.289  -0.225  -0.425  -0.514  -0.460  -0.578
13    K        -0.077  -0.165  -0.371  -0.063  -0.184  -0.520  -0.095  -0.217  -0.511
14    Q        -0.077  -0.196  -0.383   0.211   0.042  -0.297  -0.095  -0.259  -0.529
15    P        -0.361  -0.347  -0.422  -0.294  -0.245  -0.397  -0.514  -0.476  -0.586
16    G         1.195   1.203   1.282   1.149   1.160   1.299   1.265   1.275   1.390
17    V        -0.975  -0.956  -0.923  -1.030  -1.002  -0.951  -1.037  -1.013  -0.914
18    Q        -2.100  -2.039  -1.888  -1.884  -1.816  -1.562  -1.560  -1.511  -1.304
19    T        -1.088  -1.038  -0.959  -1.142  -1.074  -0.920  -1.142  -1.092  -0.948
20    G         1.195   1.203   1.282   1.149   1.160   1.299   1.265   1.275   1.390
21    L        -1.501  -1.479  -1.331  -1.709  -1.674  -1.405  -1.351  -1.325  -1.117
22    L         0.544   0.486   0.312   0.653   0.581   0.293   0.533   0.443   0.119
23    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
24    E        -0.902  -0.851  -0.915  -0.854  -0.780  -0.902  -0.932  -0.877  -0.902
25    K        -0.902  -0.883  -0.921  -1.085  -1.073  -1.096  -0.932  -0.923  -0.909
26    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
27    D         1.195   1.203   1.282   1.216   1.230   1.362   1.265   1.275   1.390
28    G         0.544   0.521   0.318   0.551   0.523   0.235   0.533   0.497   0.131
29    K         0.223   0.157   0.182   0.016  -0.110  -0.104   0.009  -0.114  -0.121
30    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
31    P         1.195   1.203   1.282   1.384   1.394   1.518   1.265   1.275   1.390
32    I        -0.902  -0.939  -0.917  -0.921  -0.965  -0.968  -0.932  -0.956  -0.903
33    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
34    D         1.195   1.203   1.282   1.216   1.230   1.362   1.265   1.275   1.390
35    S         1.195   1.203   1.282   1.228   1.229   1.373   1.265   1.275   1.390
36    Y        -0.975  -1.013  -0.933  -0.847  -0.894  -0.776  -1.037  -1.064  -0.923
37    V         1.195   1.203   1.282   1.301   1.316   1.440   1.265   1.275   1.390
38    R         0.223   0.263   0.223   0.040   0.110  -0.002   0.009   0.076  -0.042
39    P         0.544   0.486   0.312   0.767   0.686   0.386   0.533   0.443   0.119
40    K        -0.661  -0.754  -0.894  -0.471  -0.624  -0.926  -0.618  -0.732  -0.875
41    R        -0.902  -0.927  -0.932  -0.878  -0.956  -0.962  -0.932  -0.971  -0.921
42    K        -0.975  -1.004  -0.936  -1.193  -1.226  -1.091  -1.037  -1.056  -0.926
43    V         1.195   1.203   1.282   1.301   1.316   1.440   1.265   1.275   1.390
44    R        -0.077  -0.078  -0.363  -0.033  -0.036  -0.490  -0.095  -0.103  -0.501
45    V         0.051   0.060   0.155  -0.121  -0.106   0.029  -0.304  -0.293  -0.171
46    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
47    E        -0.077  -0.059  -0.357   0.039   0.067  -0.361  -0.095  -0.072  -0.492
48    N        -1.201  -1.280  -1.294  -0.964  -1.091  -1.164  -1.037  -1.117  -1.082
49    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
50    S         0.544   0.521   0.318   0.640   0.602   0.327   0.533   0.497   0.131
51    F        -0.077  -0.132  -0.363   0.251   0.174  -0.228  -0.095  -0.172  -0.501
52    G         1.195   1.203   1.282   1.149   1.160   1.299   1.265   1.275   1.390
53    K        -1.088  -1.040  -0.956  -1.262  -1.214  -1.030  -1.142  -1.097  -0.945
54    Q        -1.088  -1.062  -0.965  -1.196  -1.176  -0.981  -1.142  -1.122  -0.955
55    A        -1.501  -1.460  -1.334  -1.499  -1.444  -1.247  -1.351  -1.313  -1.119
56    K        -1.388  -1.435  -1.321  -1.412  -1.490  -1.339  -1.246  -1.282  -1.107
57    N        -0.975  -0.992  -0.935  -1.199  -1.205  -1.058  -1.037  -1.046  -0.925
58    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
59    I         0.544   0.622   0.327   0.707   0.810   0.368   0.533   0.647   0.147
60    I        -0.489  -0.430  -0.456  -0.640  -0.560  -0.566  -0.723  -0.661  -0.639
61    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
62    N        -0.661  -0.589  -0.854  -0.618  -0.515  -0.895  -0.618  -0.532  -0.830
63    L        -1.501  -1.478  -1.336  -1.627  -1.587  -1.345  -1.351  -1.322  -1.120
64    N        -1.388  -1.355  -1.312  -1.209  -1.180  -1.087  -1.246  -1.221  -1.101
65    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    G         0.544   0.617   0.324   0.561   0.652   0.267   0.533   0.638   0.142
67    V        -1.201  -1.241  -1.280  -1.053  -1.122  -1.206  -1.037  -1.079  -1.069
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    N        -1.388  -1.380  -1.309  -1.342  -1.341  -1.174  -1.246  -1.240  -1.099
74    D        -1.201  -1.248  -1.297  -1.080  -1.155  -1.208  -1.037  -1.087  -1.084
75    A         0.544   0.521   0.318   0.806   0.774   0.379   0.533   0.497   0.131
76    F        -0.361  -0.366  -0.425  -0.207  -0.203  -0.336  -0.514  -0.506  -0.592
77    Y         1.195   1.203   1.282   1.425   1.435   1.556   1.265   1.275   1.390
78    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
79    W        -1.088  -1.044  -0.955  -0.986  -0.897  -0.806  -1.142  -1.082  -0.943
80    E         0.544   0.486   0.312   0.772   0.696   0.380   0.533   0.443   0.119
81    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
82    C        -1.088  -1.110  -0.970  -1.274  -1.314  -1.082  -1.142  -1.155  -0.959
83    R         0.544   0.476   0.301   0.559   0.460   0.158   0.533   0.427   0.101
84    L        -0.077  -0.156  -0.366   0.063  -0.048  -0.386  -0.095  -0.204  -0.505
85    G         0.223   0.196   0.198   0.237   0.185   0.112   0.009  -0.042  -0.089
86    K        -0.077  -0.156  -0.366  -0.056  -0.166  -0.497  -0.095  -0.204  -0.505
87    D        -0.661  -0.768  -0.890  -0.547  -0.708  -0.887  -0.618  -0.748  -0.870
88    K         0.544   0.565   0.315   0.559   0.587   0.185   0.533   0.563   0.126
89    D        -0.361  -0.388  -0.436  -0.446  -0.478  -0.585  -0.514  -0.538  -0.605
90    G         1.195   1.203   1.282   1.149   1.160   1.299   1.265   1.275   1.390
91    C         1.195   1.203   1.282   0.991   1.004   1.153   1.265   1.275   1.390
92    P         1.195   1.203   1.282   1.384   1.394   1.518   1.265   1.275   1.390
93    R         0.223   0.312   0.231   0.040   0.196   0.014   0.009   0.160  -0.028
94    I         0.544   0.521   0.318   0.707   0.677   0.352   0.533   0.497   0.131
95    L        -0.361  -0.327  -0.431  -0.372  -0.335  -0.511  -0.514  -0.483  -0.602
96    N         1.195   1.203   1.282   1.384   1.395   1.518   1.265   1.275   1.390
97    L        -0.489  -0.523  -0.457  -0.651  -0.683  -0.573  -0.723  -0.752  -0.640
98    G         1.195   1.203   1.282   1.149   1.160   1.299   1.265   1.275   1.390
99    S         0.223   0.266   0.205   0.074   0.139  -0.014   0.009   0.081  -0.077
100   N        -0.489  -0.493  -0.463  -0.624  -0.635  -0.536  -0.723  -0.732  -0.648
101   R        -0.003   0.012   0.148  -0.442  -0.414  -0.174  -0.409  -0.385  -0.184
102   L        -0.661  -0.653  -0.870  -0.375  -0.368  -0.705  -0.618  -0.612  -0.848
103   D         1.195   1.203   1.282   1.216   1.230   1.362   1.265   1.275   1.390
104   R        -1.088  -1.044  -0.955  -1.184  -1.107  -0.930  -1.142  -1.082  -0.943
105   H        -1.501  -1.528  -1.338  -1.359  -1.389  -1.115  -1.351  -1.362  -1.122
106   F        -0.489  -0.435  -0.450  -0.414  -0.341  -0.332  -0.723  -0.664  -0.632
107   E        -1.501  -1.506  -1.332  -1.414  -1.425  -1.168  -1.351  -1.344  -1.118
108   K        -0.361  -0.399  -0.428  -0.541  -0.582  -0.637  -0.514  -0.555  -0.596
109   K         1.195   1.203   1.282   1.155   1.172   1.305   1.265   1.275   1.390
110   K         0.223   0.231   0.198   0.078   0.094   0.025   0.009   0.020  -0.089
111   -        -1.503  -1.458  -1.335  -1.347  -1.272  -1.119  -1.339  -1.293  -1.118
112   -        -1.503  -1.489  -1.347  -1.658  -1.644  -1.484  -1.339  -1.323  -1.128
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   K        -1.801  -1.755  -1.630  -1.883  -1.834  -1.631  -1.456  -1.416  -1.224
123   V        -1.801  -1.771  -1.627  -1.617  -1.572  -1.365  -1.456  -1.427  -1.222
* 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/Q06835
Output conservation file - output/Q06835
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
