1     M         1.377   1.404   1.526   1.558   1.587   1.762   1.469   1.507   1.698
2     S         0.631   0.604   0.421   0.587   0.562   0.283   0.639   0.596   0.257
3     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -0.504  -0.542  -0.466  -0.716  -0.811  -0.763  -0.656  -0.715  -0.612
5     -        -0.504  -0.461  -0.445  -0.588  -0.518  -0.533  -0.656  -0.596  -0.583
6     A         0.631   0.686   0.430   0.549   0.593   0.300   0.639   0.718   0.274
7     K        -1.024  -1.112  -1.007  -1.158  -1.268  -1.120  -1.021  -1.109  -0.937
8     S        -1.024  -1.065  -0.997  -0.997  -1.084  -0.943  -1.021  -1.069  -0.929
9     A         0.631   0.673   0.431   0.534   0.564   0.266   0.639   0.698   0.276
10    A        -0.079  -0.177  -0.363  -0.019  -0.157  -0.364  -0.072  -0.218  -0.469
11    N        -1.924  -1.957  -1.803  -1.558  -1.680  -1.528  -1.496  -1.510  -1.280
12    K         0.631   0.461   0.402   0.399   0.179   0.080   0.639   0.370   0.223
13    L        -0.552  -0.610  -0.467  -0.725  -0.746  -0.553  -0.784  -0.818  -0.619
14    D         0.631   0.718   0.434   0.756   0.867   0.515   0.639   0.764   0.280
15    W         0.631   0.678   0.431   1.008   1.062   0.737   0.639   0.706   0.275
16    A        -0.079  -0.020  -0.334   0.002   0.052  -0.282  -0.072   0.009  -0.429
17    K         0.631   0.461   0.402   0.408   0.201   0.104   0.639   0.370   0.223
18    V        -0.552  -0.500  -0.463  -0.641  -0.568  -0.506  -0.784  -0.715  -0.619
19    I        -1.238  -1.285  -1.045  -1.215  -1.313  -1.000  -1.258  -1.280  -0.976
20    S        -0.079  -0.082  -0.346   0.032   0.040  -0.310  -0.072  -0.077  -0.446
21    S        -0.748  -0.812  -0.949  -0.596  -0.710  -0.911  -0.665  -0.749  -0.870
22    L         1.377   1.404   1.526   1.219   1.261   1.446   1.469   1.507   1.698
23    R        -0.552  -0.477  -0.462  -0.602  -0.523  -0.475  -0.784  -0.698  -0.617
24    I         0.631   0.725   0.436   0.625   0.741   0.396   0.639   0.773   0.283
25    T        -0.079  -0.276  -0.384   0.138  -0.106  -0.271  -0.072  -0.344  -0.499
26    G         0.631   0.461   0.402   0.870   0.634   0.502   0.639   0.370   0.223
27    S        -2.054  -1.953  -1.793  -2.041  -1.882  -1.636  -1.614  -1.511  -1.274
28    T         1.377   1.404   1.526   1.321   1.356   1.541   1.469   1.507   1.698
29    A         0.631   0.673   0.431   0.536   0.565   0.270   0.639   0.698   0.276
30    T        -0.552  -0.508  -0.447  -0.725  -0.639  -0.574  -0.784  -0.698  -0.592
31    Q        -0.552  -0.610  -0.467  -0.642  -0.714  -0.531  -0.784  -0.818  -0.619
32    L         0.631   0.461   0.402   0.625   0.429   0.345   0.639   0.370   0.223
33    S        -1.238  -1.283  -1.046  -1.255  -1.312  -0.993  -1.258  -1.278  -0.977
34    S        -1.024  -1.023  -0.993  -1.057  -1.033  -0.983  -1.021  -0.996  -0.920
35    F         1.377   1.404   1.526   1.469   1.501   1.678   1.469   1.507   1.698
36    K         0.264   0.190   0.264  -0.018  -0.115   0.005   0.046  -0.097  -0.032
37    K         0.631   0.461   0.402   0.408   0.201   0.104   0.639   0.370   0.223
38    R         1.377   1.404   1.526   1.447   1.476   1.658   1.469   1.507   1.698
39    N         0.067   0.061   0.233   0.147   0.137   0.372  -0.310  -0.336  -0.092
40    D        -0.405  -0.498  -0.437  -0.403  -0.529  -0.523  -0.547  -0.651  -0.578
41    E        -0.079  -0.276  -0.384   0.011  -0.220  -0.375  -0.072  -0.344  -0.499
42    A         1.377   1.404   1.526   1.158   1.167   1.389   1.469   1.507   1.698
43    R        -0.405  -0.516  -0.443  -0.352  -0.509  -0.508  -0.547  -0.676  -0.586
44    R        -0.552  -0.635  -0.471  -0.709  -0.827  -0.623  -0.784  -0.856  -0.627
45    Q        -1.238  -1.202  -1.041  -1.281  -1.282  -1.052  -1.258  -1.211  -0.972
46    L        -0.748  -0.640  -0.922  -0.553  -0.412  -0.792  -0.665  -0.531  -0.839
47    L        -1.924  -1.973  -1.790  -1.423  -1.448  -1.200  -1.496  -1.522  -1.271
48    E        -1.367  -1.445  -1.418  -1.152  -1.248  -1.237  -1.140  -1.216  -1.119
49    L         1.377   1.404   1.526   1.219   1.261   1.446   1.469   1.507   1.698
50    Q        -1.108  -1.148  -1.009  -1.019  -1.044  -0.878  -1.140  -1.157  -0.941
51    S        -1.238  -1.201  -1.036  -1.247  -1.203  -0.950  -1.258  -1.210  -0.968
52    Q         0.631   0.604   0.421   0.828   0.802   0.511   0.639   0.596   0.257
53    P        -0.405  -0.496  -0.435  -0.225  -0.358  -0.362  -0.547  -0.647  -0.573
54    T         0.631   0.686   0.430   0.700   0.771   0.416   0.639   0.718   0.274
55    E        -1.108  -0.951  -0.988  -1.153  -0.923  -0.968  -1.140  -0.975  -0.921
56    V         0.631   0.678   0.431   0.636   0.698   0.399   0.639   0.706   0.275
57    D         1.377   1.404   1.526   1.347   1.390   1.565   1.469   1.507   1.698
58    F         1.377   1.404   1.526   1.469   1.501   1.678   1.469   1.507   1.698
59    S        -0.681  -0.525  -0.453  -0.876  -0.659  -0.555  -0.903  -0.686  -0.595
60    H        -0.079  -0.276  -0.384   0.374   0.100  -0.147  -0.072  -0.344  -0.499
61    Y         1.377   1.404   1.526   1.548   1.582   1.752   1.469   1.507   1.698
62    R         1.377   1.404   1.526   1.447   1.476   1.658   1.469   1.507   1.698
63    S         0.631   0.673   0.431   0.570   0.634   0.259   0.639   0.698   0.276
64    V        -0.079  -0.082  -0.346   0.039   0.042  -0.310  -0.072  -0.077  -0.446
65    L         1.377   1.404   1.526   1.219   1.261   1.446   1.469   1.507   1.698
66    K        -0.748  -0.805  -0.940  -0.795  -0.893  -1.069  -0.665  -0.741  -0.860
67    N         1.377   1.404   1.526   1.443   1.473   1.654   1.469   1.507   1.698
68    T        -1.238  -1.255  -1.031  -1.287  -1.310  -1.025  -1.258  -1.249  -0.962
69    S        -1.108  -1.058  -1.002  -1.427  -1.343  -1.260  -1.140  -1.075  -0.934
70    V         0.264   0.162   0.257   0.163   0.007   0.133   0.046  -0.147  -0.046
71    I         0.264   0.367   0.304   0.163   0.311   0.206   0.046   0.213   0.044
72    D         0.264   0.162   0.257   0.284   0.133   0.237   0.046  -0.147  -0.046
73    K        -0.552  -0.610  -0.467  -0.869  -0.871  -0.675  -0.784  -0.818  -0.619
74    I         1.377   1.404   1.526   1.417   1.439   1.631   1.469   1.507   1.698
75    E         1.377   1.404   1.526   1.193   1.230   1.421   1.469   1.507   1.698
76    S        -1.238  -1.171  -1.032  -1.377  -1.289  -1.046  -1.258  -1.179  -0.965
77    Y        -2.054  -2.013  -1.809  -1.577  -1.564  -1.246  -1.614  -1.563  -1.285
78    V        -1.024  -1.027  -0.996  -0.795  -0.793  -0.686  -1.021  -1.033  -0.926
79    K        -0.405  -0.381  -0.420  -0.668  -0.605  -0.673  -0.547  -0.499  -0.552
80    Q        -0.748  -0.596  -0.908  -0.545  -0.347  -0.758  -0.665  -0.478  -0.824
81    Y         0.067   0.174   0.281   0.135   0.299   0.424  -0.310  -0.125   0.000
82    K         0.631   0.686   0.430   0.408   0.487   0.150   0.639   0.718   0.274
83    P         1.377   1.404   1.526   1.523   1.554   1.729   1.469   1.507   1.698
84    V         0.631   0.604   0.421   0.599   0.570   0.293   0.639   0.596   0.257
85    K        -0.405  -0.316  -0.435  -0.477  -0.407  -0.611  -0.547  -0.473  -0.578
86    I        -0.765  -0.678  -0.501  -0.710  -0.578  -0.365  -1.021  -0.909  -0.663
87    D         1.377   1.404   1.526   1.347   1.390   1.565   1.469   1.507   1.698
88    A        -0.748  -0.800  -0.945  -0.618  -0.702  -0.960  -0.665  -0.736  -0.866
89    S         0.264   0.162   0.257   0.161   0.015   0.138   0.046  -0.147  -0.046
90    K        -0.079  -0.276  -0.384  -0.173  -0.419  -0.560  -0.072  -0.344  -0.499
91    Q        -0.079   0.022  -0.339   0.260   0.389  -0.108  -0.072   0.064  -0.437
92    L         1.377   1.404   1.526   1.219   1.261   1.446   1.469   1.507   1.698
93    Q        -0.748  -0.508  -0.912  -0.719  -0.415  -0.893  -0.665  -0.377  -0.828
94    V        -1.108  -1.000  -0.982  -1.151  -1.033  -0.955  -1.140  -1.012  -0.914
95    I         1.377   1.404   1.526   1.417   1.439   1.631   1.469   1.507   1.698
96    E        -1.024  -1.077  -0.987  -1.002  -1.047  -0.951  -1.021  -1.064  -0.916
97    S        -1.024  -0.896  -0.967  -1.005  -0.852  -0.872  -1.021  -0.863  -0.893
98    F         1.377   1.404   1.526   1.469   1.501   1.678   1.469   1.507   1.698
99    E         1.377   1.404   1.526   1.193   1.230   1.421   1.469   1.507   1.698
100   K        -1.711  -1.639  -1.453  -1.912  -1.811  -1.515  -1.496  -1.411  -1.152
101   H        -1.367  -1.191  -1.379  -1.272  -1.058  -1.254  -1.140  -0.951  -1.083
102   A         1.377   1.404   1.526   1.158   1.167   1.389   1.469   1.507   1.698
103   M        -1.367  -1.359  -1.395  -0.960  -0.987  -1.080  -1.140  -1.132  -1.098
104   T        -0.079  -0.040  -0.339  -0.065  -0.014  -0.469  -0.072  -0.022  -0.436
105   N        -0.079  -0.217  -0.370   0.267   0.098  -0.132  -0.072  -0.268  -0.480
106   A         1.377   1.404   1.526   1.158   1.167   1.389   1.469   1.507   1.698
107   K        -0.079   0.040  -0.328  -0.230  -0.078  -0.598  -0.072   0.077  -0.421
108   E        -1.238  -1.283  -1.046  -1.530  -1.629  -1.302  -1.258  -1.278  -0.977
109   T         0.631   0.461   0.402   0.730   0.531   0.444   0.639   0.370   0.223
110   E        -0.079  -0.276  -0.384  -0.080  -0.347  -0.583  -0.072  -0.344  -0.499
111   S        -1.581  -1.549  -1.433  -1.678  -1.614  -1.422  -1.377  -1.338  -1.135
112   L        -1.238  -1.173  -1.031  -1.466  -1.363  -1.163  -1.258  -1.179  -0.962
113   V         1.377   1.404   1.526   1.231   1.269   1.457   1.469   1.507   1.698
114   S        -2.054  -2.013  -1.809  -2.027  -1.989  -1.715  -1.614  -1.563  -1.285
115   K        -2.054  -2.045  -1.804  -2.014  -2.038  -1.700  -1.614  -1.581  -1.281
116   E         1.377   1.404   1.526   1.193   1.230   1.421   1.469   1.507   1.698
117   L        -0.405  -0.308  -0.422  -0.425  -0.289  -0.459  -0.547  -0.419  -0.557
118   K        -0.748  -0.848  -0.949  -0.719  -0.825  -0.937  -0.665  -0.788  -0.870
119   D        -1.367  -1.391  -1.405  -1.015  -1.044  -1.128  -1.140  -1.163  -1.107
120   L         1.377   1.404   1.526   1.219   1.261   1.446   1.469   1.507   1.698
121   Q        -1.024  -1.096  -0.993  -0.949  -1.022  -0.996  -1.021  -1.074  -0.921
122   S        -1.108  -1.125  -1.003  -1.427  -1.459  -1.272  -1.140  -1.137  -0.935
123   T         1.377   1.404   1.526   1.321   1.356   1.541   1.469   1.507   1.698
124   L         1.377   1.404   1.526   1.219   1.261   1.446   1.469   1.507   1.698
125   D        -1.924  -1.760  -1.763  -1.889  -1.670  -1.671  -1.496  -1.336  -1.250
126   N        -0.079   0.022  -0.339   0.217   0.343  -0.188  -0.072   0.064  -0.437
127   I         1.377   1.404   1.526   1.417   1.439   1.631   1.469   1.507   1.698
128   Q         0.631   0.725   0.436   0.603   0.716   0.383   0.639   0.773   0.283
129   S        -0.748  -0.869  -0.953  -0.513  -0.658  -0.760  -0.665  -0.814  -0.875
130   A         1.377   1.404   1.526   1.158   1.167   1.389   1.469   1.507   1.698
131   R         1.377   1.404   1.526   1.447   1.476   1.658   1.469   1.507   1.698
132   P         1.377   1.404   1.526   1.523   1.554   1.729   1.469   1.507   1.698
133   F         0.631   0.461   0.402   0.860   0.647   0.529   0.639   0.370   0.223
134   D         0.631   0.461   0.402   0.721   0.510   0.378   0.639   0.370   0.223
135   E         0.067   0.058   0.230  -0.063  -0.110   0.107  -0.310  -0.343  -0.096
136   L         0.631   0.461   0.402   0.625   0.429   0.345   0.639   0.370   0.223
137   T         0.631   0.673   0.431   0.698   0.755   0.414   0.639   0.698   0.276
138   V         0.631   0.461   0.402   0.636   0.437   0.355   0.639   0.370   0.223
139   D         0.631   0.461   0.402   0.721   0.510   0.378   0.639   0.370   0.223
140   D         0.067   0.132   0.254  -0.155  -0.033   0.092  -0.310  -0.204  -0.051
141   L        -0.552  -0.610  -0.467  -0.694  -0.697  -0.497  -0.784  -0.818  -0.619
142   T        -1.581  -1.568  -1.438  -1.581  -1.612  -1.404  -1.377  -1.340  -1.138
143   K        -0.405  -0.545  -0.454  -0.666  -0.837  -0.709  -0.547  -0.719  -0.602
144   I         0.631   0.725   0.436   0.564   0.647   0.341   0.639   0.773   0.283
145   K        -1.151  -1.207  -1.022  -1.190  -1.262  -1.066  -1.164  -1.200  -0.952
146   P         0.631   0.678   0.431   0.900   0.959   0.593   0.639   0.706   0.275
147   E        -0.552  -0.540  -0.466  -0.717  -0.676  -0.584  -0.784  -0.750  -0.620
148   I         0.067   0.126   0.258  -0.078   0.014   0.171  -0.310  -0.215  -0.044
149   D         0.067   0.061   0.233  -0.155  -0.181   0.040  -0.310  -0.336  -0.092
150   A        -0.681  -0.626  -0.489  -1.061  -1.000  -0.834  -0.903  -0.835  -0.645
151   K        -0.079  -0.205  -0.370  -0.137  -0.285  -0.462  -0.072  -0.253  -0.480
152   V        -0.079  -0.087  -0.351   0.039   0.037  -0.317  -0.072  -0.083  -0.453
153   E        -1.024  -0.980  -0.979  -1.069  -0.995  -1.041  -1.021  -0.954  -0.905
154   E        -1.024  -1.129  -1.005  -0.963  -1.097  -0.968  -1.021  -1.115  -0.934
155   M         0.264   0.278   0.282   0.416   0.428   0.338   0.046   0.060   0.001
156   V         1.377   1.404   1.526   1.231   1.269   1.457   1.469   1.507   1.698
157   K        -0.079  -0.276  -0.384  -0.196  -0.439  -0.612  -0.072  -0.344  -0.499
158   K         0.067   0.130   0.251  -0.297  -0.202  -0.011  -0.310  -0.207  -0.056
159   G         0.631   0.718   0.434   0.878   0.979   0.579   0.639   0.764   0.280
160   K         0.067   0.128   0.252  -0.295  -0.203  -0.008  -0.310  -0.211  -0.055
161   W         1.377   1.404   1.526   1.597   1.627   1.798   1.469   1.507   1.698
162   D        -1.238  -1.255  -1.031  -1.368  -1.375  -1.088  -1.258  -1.249  -0.962
163   V         0.264   0.196   0.263   0.163   0.059   0.142   0.046  -0.087  -0.034
164   P         1.377   1.404   1.526   1.523   1.554   1.729   1.469   1.507   1.698
165   G        -0.079   0.030  -0.329   0.274   0.408  -0.122  -0.072   0.074  -0.422
166   Y         1.377   1.404   1.526   1.548   1.582   1.752   1.469   1.507   1.698
167   K        -1.024  -1.017  -0.989  -1.007  -0.982  -0.857  -1.021  -1.023  -0.920
168   D        -0.079   0.036  -0.332   0.011   0.158  -0.302  -0.072   0.082  -0.427
169   R         0.264   0.298   0.287  -0.018   0.037   0.032   0.046   0.095   0.011
170   F         1.377   1.404   1.526   1.469   1.501   1.678   1.469   1.507   1.698
171   G         1.377   1.404   1.526   1.501   1.528   1.708   1.469   1.507   1.698
172   N        -0.405  -0.316  -0.402  -0.297  -0.158  -0.319  -0.547  -0.418  -0.528
173   L        -0.079  -0.012  -0.331   0.037   0.130  -0.279  -0.072   0.019  -0.425
174   N        -1.581  -1.421  -1.405  -1.500  -1.262  -1.273  -1.377  -1.198  -1.110
175   V        -1.024  -0.994  -0.981  -0.987  -0.950  -0.956  -1.021  -0.987  -0.912
176   M         0.631   0.604   0.421   0.935   0.902   0.607   0.639   0.596   0.257
* 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/P30902
Output conservation file - output/P30902
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
