1     M         2.046   2.056   2.212   2.342   2.344   2.597   2.258   2.273   2.541
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -         0.047   0.127   0.041  -0.015   0.103  -0.062  -0.098   0.017  -0.123
24    -        -0.173  -0.178  -0.065  -0.614  -0.623  -0.465  -0.434  -0.435  -0.290
25    S        -0.224  -0.222  -0.119  -0.406  -0.391  -0.262  -0.489  -0.489  -0.357
26    T        -1.631  -1.618  -1.577  -1.504  -1.461  -1.414  -1.176  -1.160  -1.078
27    V        -0.641  -0.702  -0.653  -0.450  -0.544  -0.476  -0.661  -0.715  -0.642
28    T        -0.798  -0.761  -0.703  -0.706  -0.672  -0.581  -0.833  -0.793  -0.698
29    K         0.035   0.035   0.011  -0.043  -0.055  -0.036  -0.146  -0.163  -0.184
30    Y        -0.641  -0.547  -0.613  -0.512  -0.392  -0.463  -0.661  -0.548  -0.596
31    F         0.371   0.228   0.117   0.719   0.558   0.429   0.369   0.162  -0.010
32    Y         2.046   2.056   2.212   2.271   2.291   2.525   2.258   2.273   2.541
33    K         1.183   1.063   1.027   1.091   0.930   0.901   1.228   1.027   0.927
34    G         1.183   1.063   1.027   1.159   1.024   0.975   1.228   1.027   0.927
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    E        -1.057  -1.008  -1.100  -1.043  -0.964  -1.134  -0.833  -0.779  -0.844
37    N         0.371   0.331   0.162   0.406   0.331   0.101   0.369   0.302   0.056
38    T        -0.381  -0.353  -0.562  -0.198  -0.163  -0.499  -0.317  -0.283  -0.526
39    D         1.183   1.063   1.027   1.282   1.112   1.064   1.228   1.027   0.927
40    L         0.787   0.856   0.859   0.756   0.877   0.835   0.541   0.663   0.606
41    I         0.035  -0.010  -0.005  -0.026  -0.117  -0.101  -0.146  -0.211  -0.206
42    V         0.787   0.812   0.812   0.690   0.715   0.675   0.541   0.581   0.513
43    F         0.371   0.296   0.158   0.642   0.542   0.355   0.369   0.256   0.051
44    A        -0.224  -0.208  -0.100  -0.406  -0.376  -0.232  -0.489  -0.468  -0.332
45    A        -1.214  -1.199  -1.162  -1.176  -1.166  -1.109  -1.004  -0.986  -0.908
46    S         0.035  -0.025   0.008  -0.029  -0.104  -0.075  -0.146  -0.215  -0.181
47    E        -1.631  -1.633  -1.579  -1.611  -1.645  -1.540  -1.176  -1.171  -1.080
48    E        -0.641  -0.654  -0.644  -0.626  -0.619  -0.606  -0.661  -0.666  -0.632
49    L        -0.641  -0.611  -0.639  -0.673  -0.645  -0.694  -0.661  -0.639  -0.630
50    V        -0.381  -0.348  -0.524  -0.165  -0.120  -0.361  -0.317  -0.276  -0.481
51    D        -1.631  -1.631  -1.582  -1.287  -1.254  -1.199  -1.176  -1.170  -1.082
52    E        -0.641  -0.640  -0.644  -0.781  -0.766  -0.762  -0.661  -0.655  -0.632
53    Y         0.787   0.716   0.785   1.032   0.926   1.018   0.541   0.399   0.458
54    L        -0.641  -0.663  -0.636  -0.685  -0.705  -0.652  -0.661  -0.679  -0.622
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    K         0.371   0.373   0.157   0.284   0.285  -0.047   0.369   0.370   0.050
61    N        -0.798  -0.752  -0.706  -0.968  -0.872  -0.827  -0.833  -0.781  -0.701
62    P        -0.641  -0.616  -0.663  -0.572  -0.604  -0.670  -0.661  -0.643  -0.656
63    S         0.787   0.745   0.798   0.660   0.572   0.629   0.541   0.455   0.485
64    I        -0.641  -0.640  -0.644  -0.500  -0.527  -0.503  -0.661  -0.655  -0.632
65    G        -0.173  -0.158  -0.098  -0.503  -0.478  -0.407  -0.434  -0.412  -0.331
66    K         0.035   0.124   0.021   0.106   0.250   0.060  -0.146  -0.016  -0.161
67    L         1.183   1.231   1.043   1.289   1.339   1.097   1.228   1.301   0.957
68    S        -0.798  -0.745  -0.700  -0.843  -0.761  -0.699  -0.833  -0.779  -0.696
69    E        -0.641  -0.644  -0.648  -0.641  -0.662  -0.644  -0.661  -0.666  -0.639
70    V        -0.641  -0.601  -0.632  -0.645  -0.621  -0.631  -0.661  -0.624  -0.622
71    V         2.046   2.056   2.212   2.008   2.003   2.255   2.258   2.273   2.541
72    E        -0.641  -0.659  -0.620  -0.779  -0.800  -0.757  -0.661  -0.672  -0.603
73    L        -0.798  -0.820  -0.708  -0.893  -0.942  -0.765  -0.833  -0.843  -0.703
74    F         1.183   1.221   1.040   1.384   1.442   1.217   1.228   1.286   0.951
75    E         0.035  -0.040  -0.006  -0.220  -0.325  -0.280  -0.146  -0.238  -0.208
76    V         1.183   1.232   1.041   1.245   1.290   1.050   1.228   1.304   0.954
77    F         2.046   2.056   2.212   2.112   2.133   2.362   2.258   2.273   2.541
78    T         0.035   0.105   0.031   0.029   0.128   0.023  -0.146  -0.047  -0.146
79    P         0.035   0.044  -0.007   0.078   0.066   0.020  -0.146  -0.164  -0.209
80    Q        -1.214  -1.240  -1.180  -0.787  -0.838  -0.734  -1.004  -1.019  -0.923
81    D        -0.641  -0.711  -0.676  -0.579  -0.685  -0.653  -0.661  -0.727  -0.666
82    G        -0.141  -0.175  -0.093  -0.337  -0.347  -0.282  -0.371  -0.426  -0.321
83    R        -0.641  -0.653  -0.637  -0.536  -0.590  -0.571  -0.661  -0.677  -0.628
84    G         2.046   2.056   2.212   1.886   1.914   2.131   2.258   2.273   2.541
85    A        -0.224  -0.229  -0.122  -0.383  -0.360  -0.254  -0.489  -0.498  -0.361
86    E         0.371   0.373   0.157   0.442   0.428   0.156   0.369   0.370   0.050
87    G         2.046   2.056   2.212   1.886   1.914   2.131   2.258   2.273   2.541
88    E        -1.214  -1.214  -1.163  -1.163  -1.162  -1.067  -1.004  -0.997  -0.909
89    L         0.371   0.373   0.157   0.595   0.596   0.316   0.369   0.370   0.050
90    G        -0.641  -0.711  -0.676  -0.770  -0.855  -0.814  -0.661  -0.727  -0.666
91    A         0.035  -0.040  -0.006  -0.097  -0.198  -0.163  -0.146  -0.238  -0.208
92    A         2.046   2.056   2.212   2.082   2.127   2.331   2.258   2.273   2.541
93    S         1.183   1.231   1.043   1.248   1.307   1.060   1.228   1.301   0.957
94    K         1.183   1.149   1.027   1.091   1.040   0.902   1.228   1.170   0.928
95    A        -0.224  -0.212  -0.116  -0.300  -0.256  -0.147  -0.489  -0.475  -0.353
96    Q        -0.641  -0.649  -0.664  -0.462  -0.513  -0.504  -0.661  -0.673  -0.656
97    V         1.183   1.267   1.050   1.281   1.375   1.093   1.228   1.358   0.970
98    E         1.183   1.221   1.040   1.154   1.184   0.957   1.228   1.286   0.951
99    N         1.183   1.221   1.040   1.303   1.375   1.104   1.228   1.286   0.951
100   E         0.371   0.290   0.143   0.442   0.307   0.134   0.369   0.248   0.028
101   F         2.046   2.056   2.212   2.112   2.133   2.362   2.258   2.273   2.541
102   G         1.183   1.231   1.043   1.083   1.162   0.857   1.228   1.301   0.957
103   K        -0.141  -0.175  -0.093  -0.402  -0.486  -0.331  -0.371  -0.426  -0.321
104   G        -0.798  -0.820  -0.704  -1.116  -1.133  -0.977  -0.833  -0.843  -0.700
105   K         0.787   0.833   0.849   0.464   0.527   0.524   0.541   0.620   0.586
106   K        -0.798  -0.757  -0.703  -1.007  -0.923  -0.855  -0.833  -0.788  -0.698
107   I         0.035   0.103   0.022  -0.014   0.075  -0.041  -0.146  -0.064  -0.166
108   E         0.707   0.736   0.803   0.419   0.463   0.537   0.388   0.437   0.494
109   E         0.035   0.017  -0.009  -0.074  -0.143  -0.129  -0.146  -0.195  -0.213
110   V        -0.381  -0.351  -0.507  -0.218  -0.185  -0.411  -0.317  -0.281  -0.460
111   I         0.371   0.300   0.157   0.538   0.417   0.214   0.369   0.261   0.050
112   D        -0.641  -0.654  -0.644  -0.860  -0.878  -0.872  -0.661  -0.666  -0.632
113   L        -1.214  -1.239  -1.182  -1.150  -1.221  -1.110  -1.004  -1.017  -0.925
114   I         1.183   1.149   1.027   1.288   1.231   1.063   1.228   1.170   0.928
115   L         2.046   2.056   2.212   2.052   2.054   2.301   2.258   2.273   2.541
116   R        -0.641  -0.658  -0.633  -0.815  -0.868  -0.775  -0.661  -0.680  -0.623
117   N        -0.798  -0.820  -0.702  -1.078  -1.104  -0.946  -0.833  -0.843  -0.698
118   G         2.046   2.056   2.212   1.886   1.914   2.131   2.258   2.273   2.541
119   K        -1.057  -1.008  -1.100  -1.056  -0.987  -1.115  -0.833  -0.779  -0.844
120   P        -0.082  -0.125  -0.072   0.006  -0.061  -0.009  -0.313  -0.362  -0.296
121   N        -0.751  -0.761  -0.707  -0.834  -0.833  -0.735  -0.780  -0.785  -0.700
122   S        -0.082  -0.122  -0.046  -0.378  -0.435  -0.358  -0.313  -0.356  -0.261
123   T        -1.237  -1.236  -1.163  -1.243  -1.212  -1.122  -1.014  -1.009  -0.905
124   T         2.046   2.056   2.212   2.104   2.114   2.354   2.258   2.273   2.541
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   S        -1.214  -1.243  -1.160  -1.042  -1.051  -0.940  -1.004  -1.021  -0.906
127   -         0.047   0.101   0.054   0.031   0.122   0.024  -0.098  -0.023  -0.105
128   -        -0.173  -0.156  -0.081  -0.261  -0.193  -0.107  -0.434  -0.406  -0.309
129   -        -0.173  -0.195  -0.078  -0.168  -0.193  -0.018  -0.434  -0.456  -0.306
130   -        -0.757  -0.661  -0.677  -0.758  -0.581  -0.684  -0.771  -0.658  -0.664
131   -        -0.757  -0.800  -0.714  -0.771  -0.836  -0.690  -0.771  -0.818  -0.705
132   S        -1.631  -1.588  -1.562  -1.235  -1.141  -1.096  -1.176  -1.136  -1.066
133   L        -1.631  -1.615  -1.585  -1.450  -1.447  -1.382  -1.176  -1.158  -1.084
134   K         0.371   0.451   0.183   0.358   0.454   0.118   0.369   0.481   0.089
135   T        -0.067  -0.125  -0.043  -0.103  -0.139  -0.020  -0.317  -0.375  -0.263
136   K        -0.641  -0.595  -0.640  -0.783  -0.737  -0.813  -0.661  -0.615  -0.630
137   G        -0.568  -0.587  -0.621  -0.617  -0.666  -0.757  -0.546  -0.571  -0.598
138   G        -1.237  -1.252  -1.193  -1.214  -1.214  -1.170  -1.014  -1.023  -0.933
139   N         0.707   0.772   0.822   0.492   0.640   0.637   0.388   0.507   0.533
140   A        -0.757  -0.770  -0.714  -0.654  -0.688  -0.592  -0.771  -0.785  -0.705
141   G         0.221   0.135   0.054   0.155   0.030  -0.102   0.155   0.028  -0.104
142   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   K        -1.237  -1.154  -1.156  -1.204  -1.059  -1.106  -1.014  -0.927  -0.898
144   A        -1.237  -1.242  -1.165  -1.033  -1.047  -0.924  -1.014  -1.014  -0.907
145   Y        -1.237  -1.238  -1.169  -0.945  -0.956  -0.832  -1.014  -1.011  -0.910
146   N        -0.751  -0.763  -0.677  -0.565  -0.566  -0.460  -0.780  -0.786  -0.670
* 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/P38804
Output conservation file - output/P38804
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
