1     M         1.203   1.224   1.278   1.360   1.389   1.464   1.287   1.317   1.397
2     P        -0.975  -1.074  -1.121  -0.718  -0.894  -1.029  -0.883  -0.998  -1.016
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    K        -1.722  -1.676  -1.557  -1.749  -1.631  -1.481  -1.462  -1.399  -1.225
13    I        -1.207  -1.153  -1.139  -1.343  -1.224  -1.244  -1.172  -1.096  -1.035
14    F        -1.207  -1.155  -1.138  -0.960  -0.910  -0.875  -1.172  -1.097  -1.033
15    C         0.429   0.545   0.208   0.726   0.877   0.355   0.419   0.587   0.034
16    L         0.429   0.258   0.172   0.520   0.323   0.198   0.419   0.146  -0.029
17    A         0.429   0.258   0.172   0.483   0.204   0.048   0.419   0.146  -0.029
18    D         1.203   1.224   1.278   1.185   1.229   1.304   1.287   1.317   1.397
19    V        -0.975  -1.105  -1.128  -0.981  -1.143  -1.148  -0.883  -1.031  -1.022
20    C         1.203   1.224   1.278   1.436   1.460   1.532   1.287   1.317   1.397
21    M        -0.086  -0.066   0.053  -0.222  -0.207  -0.031  -0.449  -0.424  -0.245
22    V        -0.086   0.029   0.097  -0.496  -0.249  -0.158  -0.449  -0.250  -0.163
23    P         1.203   1.224   1.278   1.360   1.397   1.464   1.287   1.317   1.397
24    I        -0.300  -0.364  -0.558  -0.271  -0.384  -0.710  -0.304  -0.407  -0.653
25    G         1.203   1.224   1.278   1.157   1.188   1.278   1.287   1.317   1.397
26    T         1.203   1.224   1.278   1.135   1.177   1.259   1.287   1.317   1.397
27    D        -0.975  -0.819  -1.073  -0.843  -0.621  -0.983  -0.883  -0.699  -0.964
28    S         0.074  -0.004   0.060   0.002  -0.112   0.009  -0.160  -0.310  -0.231
29    A        -0.975  -1.012  -1.105  -0.855  -0.985  -1.097  -0.883  -0.932  -0.998
30    S         1.203   1.224   1.278   1.135   1.162   1.259   1.287   1.317   1.397
31    I         0.074   0.237   0.151  -0.241   0.009  -0.109  -0.160   0.111  -0.065
32    S         0.429   0.258   0.172   0.439   0.195   0.063   0.419   0.146  -0.029
33    D        -0.975  -1.105  -1.125  -0.791  -0.978  -0.998  -0.883  -1.030  -1.020
34    F        -0.692  -0.646  -0.610  -0.548  -0.480  -0.406  -0.883  -0.801  -0.726
35    V         0.429   0.457   0.196   0.298   0.321  -0.031   0.419   0.458   0.014
36    A        -0.086  -0.051   0.055  -0.382  -0.324  -0.145  -0.449  -0.397  -0.240
37    L        -2.096  -2.016  -1.876  -1.930  -1.810  -1.615  -1.606  -1.525  -1.334
38    I         0.074  -0.004   0.060  -0.152  -0.323  -0.247  -0.160  -0.310  -0.231
39    E        -1.207  -1.283  -1.162  -1.271  -1.382  -1.217  -1.172  -1.229  -1.058
40    K        -0.601  -0.568  -0.619  -0.636  -0.607  -0.661  -0.738  -0.729  -0.740
41    K        -1.207  -1.182  -1.149  -1.326  -1.338  -1.220  -1.172  -1.138  -1.045
42    I        -0.601  -0.703  -0.625  -0.707  -0.844  -0.742  -0.738  -0.854  -0.745
43    R        -0.300  -0.476  -0.581  -0.059  -0.330  -0.530  -0.304  -0.545  -0.685
44    E        -0.601  -0.634  -0.629  -0.632  -0.712  -0.690  -0.738  -0.797  -0.752
45    S         1.203   1.224   1.278   1.135   1.162   1.259   1.287   1.317   1.397
46    P        -0.833  -0.799  -0.667  -0.873  -0.840  -0.643  -1.028  -0.979  -0.797
47    L         1.203   1.224   1.278   1.171   1.215   1.291   1.287   1.317   1.397
48    K        -0.975  -0.965  -1.112  -0.759  -0.733  -0.928  -0.883  -0.864  -1.006
49    S        -0.975  -0.965  -1.112  -0.797  -0.772  -0.945  -0.883  -0.864  -1.006
50    T         0.429   0.413   0.192   0.404   0.392   0.018   0.419   0.391   0.007
51    L         0.429   0.258   0.172   0.500   0.291   0.152   0.419   0.146  -0.029
52    H         1.203   1.224   1.278   1.319   1.354   1.426   1.287   1.317   1.397
53    S         1.203   1.224   1.278   1.135   1.162   1.259   1.287   1.317   1.397
54    A         1.203   1.224   1.278   1.214   1.228   1.330   1.287   1.317   1.397
55    G         1.203   1.224   1.278   1.157   1.188   1.278   1.287   1.317   1.397
56    T         1.203   1.224   1.278   1.135   1.177   1.259   1.287   1.317   1.397
57    T         1.203   1.224   1.278   1.135   1.177   1.259   1.287   1.317   1.397
58    I         0.429   0.258   0.172   0.426   0.182  -0.002   0.419   0.146  -0.029
59    E         0.074   0.107   0.100   0.002   0.054   0.014  -0.160  -0.110  -0.159
60    G         1.203   1.224   1.278   1.157   1.188   1.278   1.287   1.317   1.397
61    P         0.429   0.258   0.172   0.651   0.409   0.223   0.419   0.146  -0.029
62    W         1.203   1.224   1.278   1.490   1.515   1.581   1.287   1.317   1.397
63    D         0.429   0.458   0.196   0.476   0.533   0.118   0.419   0.461   0.014
64    D        -0.601  -0.459  -0.566  -0.616  -0.365  -0.541  -0.738  -0.528  -0.666
65    V         1.203   1.224   1.278   1.004   1.013   1.139   1.287   1.317   1.397
66    M         0.429   0.413   0.192   0.700   0.685   0.370   0.419   0.391   0.007
67    G        -1.722  -1.661  -1.548  -1.742  -1.625  -1.461  -1.462  -1.380  -1.218
68    L        -0.300  -0.476  -0.581  -0.264  -0.542  -0.758  -0.304  -0.545  -0.685
69    I         1.203   1.224   1.278   1.157   1.206   1.278   1.287   1.317   1.397
70    G         1.203   1.224   1.278   1.157   1.188   1.278   1.287   1.317   1.397
71    E        -0.692  -0.646  -0.610  -0.743  -0.647  -0.588  -0.883  -0.801  -0.726
72    I        -1.722  -1.694  -1.563  -1.702  -1.683  -1.488  -1.462  -1.413  -1.230
73    H         1.203   1.224   1.278   1.319   1.354   1.426   1.287   1.317   1.397
74    E        -0.300  -0.439  -0.569  -0.124  -0.332  -0.528  -0.304  -0.499  -0.668
75    Y        -1.207  -1.266  -1.156  -1.062  -1.228  -1.083  -1.172  -1.215  -1.053
76    G        -1.581  -1.442  -1.532  -1.584  -1.419  -1.562  -1.317  -1.183  -1.204
77    H         1.203   1.224   1.278   1.319   1.354   1.426   1.287   1.317   1.397
78    E        -0.300  -0.438  -0.567  -0.129  -0.322  -0.536  -0.304  -0.497  -0.666
79    K        -1.207  -1.225  -1.130  -1.209  -1.213  -1.052  -1.172  -1.167  -1.026
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    G         1.203   1.224   1.278   1.157   1.188   1.278   1.287   1.317   1.397
82    Y        -0.086   0.029   0.097  -0.320  -0.185  -0.037  -0.449  -0.250  -0.163
83    V         0.429   0.258   0.172   0.303   0.045  -0.061   0.419   0.146  -0.029
84    R         1.203   1.224   1.278   1.326   1.351   1.432   1.287   1.317   1.397
85    V        -0.692  -0.589  -0.623  -1.031  -0.883  -0.875  -0.883  -0.763  -0.746
86    H         0.074   0.234   0.145   0.115   0.355   0.207  -0.160   0.106  -0.076
87    T        -0.086  -0.055   0.052  -0.431  -0.375  -0.201  -0.449  -0.405  -0.247
88    D        -0.300  -0.359  -0.553  -0.224  -0.316  -0.640  -0.304  -0.402  -0.646
89    I         0.074   0.042   0.070  -0.015  -0.049  -0.019  -0.160  -0.227  -0.212
90    R         1.203   1.224   1.278   1.326   1.351   1.432   1.287   1.317   1.397
91    V         0.429   0.413   0.192   0.298   0.263  -0.039   0.419   0.391   0.007
92    G         1.203   1.224   1.278   1.157   1.188   1.278   1.287   1.317   1.397
93    T         0.429   0.458   0.196   0.426   0.481   0.075   0.419   0.461   0.014
94    R         1.203   1.224   1.278   1.326   1.351   1.432   1.287   1.317   1.397
95    T        -0.601  -0.703  -0.625  -0.828  -0.981  -0.879  -0.738  -0.854  -0.745
96    D         1.203   1.224   1.278   1.185   1.229   1.304   1.287   1.317   1.397
97    K         1.203   1.224   1.278   1.185   1.219   1.304   1.287   1.317   1.397
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    H        -2.096  -2.065  -1.894  -1.873  -1.834  -1.615  -1.606  -1.557  -1.346
100   Q         1.203   1.224   1.278   1.312   1.327   1.419   1.287   1.317   1.397
101   T        -0.601  -0.577  -0.620  -0.763  -0.718  -0.794  -0.738  -0.707  -0.740
102   A        -0.086  -0.055   0.052  -0.226  -0.180  -0.002  -0.449  -0.405  -0.247
103   Q         0.074   0.040   0.069   0.083   0.003   0.024  -0.160  -0.230  -0.215
104   D         1.203   1.224   1.278   1.185   1.229   1.304   1.287   1.317   1.397
105   K         1.203   1.224   1.278   1.185   1.219   1.304   1.287   1.317   1.397
106   I        -0.086  -0.057   0.052  -0.496  -0.454  -0.268  -0.449  -0.408  -0.245
107   D        -0.601  -0.675  -0.616  -0.565  -0.656  -0.567  -0.738  -0.813  -0.735
108   V        -0.601  -0.692  -0.623  -0.811  -0.940  -0.781  -0.738  -0.837  -0.744
109   V         1.203   1.224   1.278   1.004   1.013   1.139   1.287   1.317   1.397
110   L        -1.207  -1.205  -1.144  -1.148  -1.119  -1.004  -1.172  -1.158  -1.041
111   K        -1.348  -1.340  -1.160  -1.431  -1.398  -1.128  -1.317  -1.280  -1.056
112   K        -0.300  -0.476  -0.581  -0.182  -0.431  -0.606  -0.304  -0.545  -0.685
113   I        -0.300  -0.050  -0.513  -0.188   0.155  -0.492  -0.304   0.025  -0.593
114   -        -1.311  -1.194  -1.145  -1.462  -1.276  -1.208  -1.265  -1.125  -1.040
115   -        -1.311  -1.298  -1.166  -1.210  -1.190  -1.001  -1.265  -1.239  -1.061
116   -        -0.759  -0.631  -0.631  -0.873  -0.641  -0.685  -0.928  -0.752  -0.750
117   -        -0.759  -0.750  -0.644  -0.741  -0.736  -0.566  -0.928  -0.917  -0.767
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   S        -1.722  -1.670  -1.544  -1.749  -1.661  -1.466  -1.462  -1.389  -1.215
123   Q        -2.096  -2.063  -1.892  -1.691  -1.686  -1.409  -1.606  -1.556  -1.345
* 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/P35195
Output conservation file - output/P35195
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
