1     M         1.561   1.571   1.666   1.652   1.664   1.814   1.694   1.708   1.853
2     F        -1.411  -1.419  -1.324  -1.274  -1.267  -1.148  -1.131  -1.131  -0.998
3     K        -0.520  -0.521  -0.564  -0.580  -0.599  -0.668  -0.588  -0.593  -0.617
4     R        -0.110  -0.087  -0.097  -0.351  -0.321  -0.304  -0.371  -0.344  -0.332
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -0.249  -0.225  -0.156  -0.545  -0.514  -0.393  -0.532  -0.501  -0.405
21    -        -0.758  -0.769  -0.651  -0.838  -0.844  -0.672  -0.861  -0.864  -0.713
22    -        -1.097  -1.049  -1.011  -1.068  -1.002  -0.943  -1.003  -0.957  -0.874
23    -        -0.418  -0.499  -0.553  -0.397  -0.536  -0.666  -0.435  -0.537  -0.595
24    -        -1.777  -1.752  -1.625  -1.568  -1.560  -1.353  -1.287  -1.263  -1.109
25    -         0.535   0.514   0.537   0.463   0.413   0.394   0.274   0.229   0.213
26    -         0.195   0.093  -0.016   0.192   0.060  -0.093   0.133  -0.016  -0.194
27    -        -0.724  -0.752  -0.650  -0.941  -0.984  -0.834  -0.810  -0.841  -0.708
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    A        -0.724  -0.732  -0.653  -0.695  -0.711  -0.606  -0.810  -0.818  -0.711
36    M        -0.249  -0.205  -0.162  -0.437  -0.364  -0.295  -0.532  -0.478  -0.411
37    S        -0.078  -0.041  -0.083  -0.307  -0.245  -0.315  -0.293  -0.237  -0.300
38    T        -0.630  -0.612  -0.600  -0.758  -0.748  -0.708  -0.719  -0.704  -0.658
39    D        -0.418  -0.397  -0.547  -0.208  -0.190  -0.416  -0.435  -0.412  -0.588
40    G         0.535   0.514   0.534   0.490   0.447   0.431   0.274   0.230   0.206
41    P         1.561   1.571   1.666   1.674   1.689   1.835   1.694   1.708   1.853
42    V        -0.078  -0.134  -0.107  -0.074  -0.151  -0.117  -0.293  -0.367  -0.337
43    A        -1.002  -0.996  -0.983  -0.963  -0.944  -0.917  -0.914  -0.902  -0.849
44    R        -1.002  -0.912  -0.970  -0.922  -0.804  -0.883  -0.914  -0.830  -0.838
45    T        -1.114  -1.110  -1.017  -1.218  -1.204  -1.063  -1.023  -1.012  -0.881
46    I         0.915   0.911   0.726   1.033   1.034   0.783   0.933   0.925   0.578
47    L        -1.411  -1.434  -1.335  -1.285  -1.311  -1.161  -1.131  -1.141  -1.006
48    K        -0.705  -0.707  -0.632  -1.009  -0.997  -0.895  -0.805  -0.797  -0.693
49    R         0.017  -0.016  -0.066  -0.133  -0.174  -0.268  -0.154  -0.194  -0.278
50    L        -0.223  -0.207  -0.157  -0.354  -0.336  -0.281  -0.480  -0.460  -0.402
51    E        -1.002  -1.035  -0.986  -1.130  -1.180  -1.106  -0.914  -0.939  -0.852
52    C        -1.709  -1.660  -1.597  -1.383  -1.331  -1.210  -1.240  -1.199  -1.091
53    G        -1.709  -1.719  -1.605  -1.601  -1.608  -1.454  -1.240  -1.241  -1.096
54    F         0.426   0.407   0.501   0.262   0.211   0.333   0.064   0.019   0.139
55    P        -0.593  -0.603  -0.595  -0.662  -0.672  -0.654  -0.697  -0.702  -0.655
56    D        -0.110  -0.131  -0.100  -0.119  -0.143  -0.097  -0.371  -0.386  -0.334
57    Y        -1.411  -1.443  -1.325  -1.315  -1.354  -1.180  -1.131  -1.147  -0.999
58    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    A        -1.709  -1.709  -1.607  -1.558  -1.587  -1.419  -1.240  -1.235  -1.098
62    F        -0.110  -0.145  -0.101  -0.209  -0.263  -0.194  -0.371  -0.411  -0.338
63    G        -1.002  -1.048  -0.993  -1.008  -1.056  -0.961  -0.914  -0.949  -0.858
64    L        -0.295  -0.297  -0.179  -0.479  -0.487  -0.313  -0.588  -0.589  -0.434
65    Y        -1.002  -0.953  -0.974  -0.728  -0.655  -0.691  -0.914  -0.861  -0.840
66    N         1.561   1.571   1.666   1.668   1.690   1.829   1.694   1.708   1.853
67    D         1.561   1.571   1.666   1.620   1.632   1.782   1.694   1.708   1.853
68    S         1.561   1.571   1.666   1.431   1.449   1.596   1.694   1.708   1.853
69    H        -0.110  -0.108  -0.096  -0.138  -0.133  -0.098  -0.371  -0.365  -0.329
70    K         0.915   0.863   0.715   0.855   0.794   0.563   0.933   0.849   0.557
71    H         1.561   1.571   1.666   1.551   1.566   1.714   1.694   1.708   1.853
72    K        -0.295  -0.285  -0.182  -0.650  -0.632  -0.487  -0.588  -0.574  -0.437
73    G         0.426   0.450   0.520   0.253   0.293   0.388   0.064   0.105   0.178
74    H         1.561   1.571   1.666   1.551   1.566   1.714   1.694   1.708   1.853
75    A        -0.817  -0.840  -0.934  -0.684  -0.725  -0.908  -0.697  -0.723  -0.796
76    G        -0.110  -0.105  -0.102  -0.153  -0.155  -0.120  -0.371  -0.369  -0.340
77    V        -0.223  -0.170  -0.150  -0.252  -0.166  -0.162  -0.480  -0.405  -0.391
78    Q        -0.705  -0.693  -0.633  -0.798  -0.794  -0.695  -0.805  -0.792  -0.694
79    G         0.017   0.055  -0.057   0.084   0.142  -0.046  -0.154  -0.096  -0.265
80    N        -0.520  -0.542  -0.578  -0.474  -0.514  -0.567  -0.588  -0.624  -0.633
81    -        -1.512  -1.487  -1.364  -1.451  -1.397  -1.239  -1.204  -1.179  -1.027
82    V        -0.281  -0.377  -0.512   0.002  -0.132  -0.359  -0.262  -0.383  -0.545
83    S        -0.295  -0.296  -0.185  -0.684  -0.685  -0.522  -0.588  -0.587  -0.441
84    A        -1.002  -1.045  -0.983  -0.957  -1.011  -0.917  -0.914  -0.945  -0.849
85    E         1.561   1.571   1.666   1.508   1.523   1.672   1.694   1.708   1.853
86    T         0.426   0.407   0.501   0.083   0.041   0.184   0.064   0.019   0.140
87    H         1.561   1.571   1.666   1.551   1.566   1.714   1.694   1.708   1.853
88    F         0.915   0.933   0.732   1.092   1.123   0.838   0.933   0.961   0.588
89    R         0.915   0.911   0.726   0.976   0.967   0.706   0.933   0.925   0.578
90    I        -0.281  -0.345  -0.507  -0.166  -0.255  -0.481  -0.262  -0.342  -0.539
91    E         0.299   0.272   0.024   0.382   0.346  -0.016   0.281   0.240  -0.134
92    M         0.915   0.909   0.731   1.033   1.032   0.790   0.933   0.923   0.586
93    V         0.915   0.863   0.715   1.044   0.974   0.736   0.933   0.849   0.557
94    S         0.915   0.933   0.732   0.856   0.883   0.600   0.933   0.961   0.588
95    K        -0.817  -0.808  -0.928  -0.588  -0.581  -0.785  -0.697  -0.687  -0.789
96    K        -1.114  -1.049  -1.016  -1.256  -1.168  -1.100  -1.023  -0.968  -0.880
97    F         1.561   1.571   1.666   1.657   1.677   1.819   1.694   1.708   1.853
98    E        -0.593  -0.618  -0.584  -0.807  -0.837  -0.781  -0.697  -0.716  -0.645
99    G         0.915   0.863   0.715   1.066   1.000   0.778   0.933   0.849   0.557
100   L         0.017  -0.021  -0.060  -0.136  -0.182  -0.253  -0.154  -0.202  -0.270
101   K        -0.281  -0.326  -0.505  -0.233  -0.291  -0.557  -0.262  -0.320  -0.537
102   L        -0.817  -0.882  -0.946  -0.669  -0.762  -0.845  -0.697  -0.766  -0.808
103   P         0.299   0.328   0.056   0.538   0.578   0.167   0.281   0.317  -0.086
104   Q        -1.299  -1.254  -1.287  -1.126  -1.057  -1.130  -1.023  -0.977  -0.966
105   R         1.561   1.571   1.666   1.551   1.561   1.714   1.694   1.708   1.853
106   H         1.561   1.571   1.666   1.551   1.566   1.714   1.694   1.708   1.853
107   R         1.561   1.571   1.666   1.551   1.561   1.714   1.694   1.708   1.853
108   M        -0.110  -0.099  -0.095  -0.250  -0.234  -0.202  -0.371  -0.349  -0.329
109   V         1.561   1.571   1.666   1.631   1.644   1.793   1.694   1.708   1.853
110   Y         1.561   1.571   1.666   1.741   1.755   1.901   1.694   1.708   1.853
111   S        -0.520  -0.483  -0.568  -0.485  -0.413  -0.578  -0.588  -0.537  -0.621
112   L         0.915   0.983   0.736   0.920   1.001   0.690   0.933   1.037   0.596
113   L         0.915   0.945   0.726   0.920   0.958   0.677   0.933   0.979   0.578
114   Q        -1.299  -1.213  -1.286  -1.167  -1.040  -1.132  -1.023  -0.939  -0.965
115   D        -0.110  -0.027  -0.089  -0.204  -0.087  -0.144  -0.371  -0.266  -0.320
116   E         1.561   1.571   1.666   1.508   1.523   1.672   1.694   1.708   1.853
117   M        -0.110  -0.053  -0.099  -0.125  -0.054  -0.107  -0.371  -0.312  -0.335
118   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   Q        -0.174  -0.175  -0.131  -0.305  -0.303  -0.220  -0.431  -0.430  -0.371
120   A        -1.002  -1.009  -0.991  -0.840  -0.850  -0.825  -0.914  -0.913  -0.855
121   N        -1.114  -1.094  -1.020  -1.009  -0.976  -0.874  -1.023  -0.998  -0.883
122   G         1.561   1.571   1.666   1.636   1.651   1.798   1.694   1.708   1.853
123   I        -0.223  -0.187  -0.152  -0.403  -0.353  -0.303  -0.480  -0.432  -0.395
124   H         1.561   1.571   1.666   1.551   1.566   1.714   1.694   1.708   1.853
125   A         1.561   1.571   1.666   1.567   1.584   1.730   1.694   1.708   1.853
126   L         1.561   1.571   1.666   1.475   1.488   1.640   1.694   1.708   1.853
127   Q         0.299   0.315   0.041   0.571   0.593   0.153   0.281   0.303  -0.110
128   L         0.017   0.010  -0.057  -0.042  -0.045  -0.143  -0.154  -0.152  -0.261
129   S        -0.520  -0.542  -0.568  -0.636  -0.662  -0.733  -0.588  -0.604  -0.619
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   L         0.299   0.244   0.042   0.352   0.270  -0.056   0.281   0.202  -0.107
132   K         0.915   0.863   0.715   0.881   0.825   0.621   0.933   0.849   0.557
133   T         1.561   1.571   1.666   1.519   1.528   1.682   1.694   1.708   1.853
134   P         0.299   0.240   0.026   0.534   0.453   0.108   0.281   0.196  -0.132
135   Q        -0.281  -0.311  -0.497  -0.150  -0.190  -0.466  -0.262  -0.301  -0.527
136   E         1.561   1.571   1.666   1.508   1.523   1.672   1.694   1.708   1.853
137   Y        -1.002  -1.030  -0.994  -0.724  -0.764  -0.706  -0.914  -0.933  -0.858
138   E        -0.758  -0.771  -0.656  -0.844  -0.856  -0.685  -0.861  -0.866  -0.717
139   S        -0.418  -0.438  -0.548  -0.486  -0.516  -0.714  -0.435  -0.460  -0.589
140   K        -1.437  -1.421  -1.339  -1.510  -1.479  -1.364  -1.145  -1.127  -1.008
141   A        -1.097  -1.083  -1.010  -1.023  -1.016  -0.909  -1.003  -0.985  -0.873
142   -        -1.200  -1.183  -1.055  -1.144  -1.115  -0.936  -1.088  -1.069  -0.911
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   K        -0.705  -0.703  -0.627  -0.844  -0.839  -0.727  -0.805  -0.794  -0.688
* 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/Q3E793
Output conservation file - output/Q3E793
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
