1     M         1.180   1.190   1.262   1.476   1.492   1.581   1.276   1.291   1.404
2     A        -1.051  -1.127  -1.047  -0.829  -0.972  -0.865  -1.037  -1.127  -1.005
3     V        -0.687  -0.658  -0.560  -1.069  -1.013  -0.884  -0.892  -0.853  -0.722
4     Q        -0.436  -0.358  -0.502  -0.283  -0.178  -0.386  -0.567  -0.469  -0.642
5     F         0.504   0.496   0.249   0.553   0.545   0.180   0.517   0.505   0.072
6     I         1.180   1.190   1.262   1.191   1.201   1.318   1.276   1.291   1.404
7     L         1.180   1.190   1.262   0.902   0.916   1.052   1.276   1.291   1.404
8     C        -0.763  -0.757  -0.597  -0.892  -0.886  -0.653  -1.001  -0.992  -0.771
9     F        -0.763  -0.727  -0.589  -1.197  -1.143  -0.915  -1.001  -0.957  -0.761
10    N         1.180   1.190   1.262   1.353   1.364   1.468   1.276   1.291   1.404
11    K        -0.008   0.012   0.105  -0.158  -0.126   0.008  -0.350  -0.320  -0.196
12    Q         0.504   0.424   0.241   0.738   0.637   0.369   0.517   0.394   0.058
13    G         1.180   1.190   1.262   1.362   1.376   1.476   1.276   1.291   1.404
14    V        -0.436  -0.429  -0.522  -0.461  -0.434  -0.627  -0.567  -0.542  -0.671
15    V        -1.074  -1.107  -1.051  -0.985  -1.023  -0.913  -1.109  -1.135  -1.013
16    R         1.180   1.190   1.262   1.277   1.293   1.398   1.276   1.291   1.404
17    L         1.180   1.190   1.262   0.902   0.916   1.052   1.276   1.291   1.404
18    V        -1.191  -1.218  -1.068  -1.404  -1.443  -1.219  -1.218  -1.236  -1.030
19    R        -0.008   0.012   0.105  -0.162  -0.133   0.005  -0.350  -0.320  -0.196
20    W         0.504   0.424   0.241   0.921   0.815   0.487   0.517   0.394   0.058
21    F        -0.064  -0.053   0.085  -0.363  -0.344  -0.112  -0.459  -0.443  -0.234
22    D        -0.028  -0.023   0.092  -0.307  -0.299  -0.114  -0.389  -0.385  -0.220
23    V        -0.763  -0.758  -0.593  -0.953  -0.946  -0.686  -1.001  -0.994  -0.766
24    H        -2.242  -2.212  -2.033  -1.873  -1.847  -1.632  -1.652  -1.625  -1.397
25    S        -1.309  -1.332  -1.415  -1.066  -1.119  -1.236  -1.109  -1.136  -1.167
26    S        -1.074  -1.089  -1.039  -0.913  -0.928  -0.848  -1.109  -1.118  -1.002
27    D        -1.309  -1.305  -1.401  -0.997  -0.994  -1.080  -1.109  -1.105  -1.155
28    P        -1.814  -1.762  -1.740  -1.413  -1.356  -1.306  -1.435  -1.389  -1.296
29    Q        -0.998  -0.995  -1.027  -1.021  -1.012  -1.050  -1.001  -0.988  -0.987
30    R        -0.436  -0.429  -0.522  -0.382  -0.355  -0.504  -0.567  -0.542  -0.671
31    S        -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    Q        -0.436  -0.476  -0.521  -0.399  -0.454  -0.576  -0.567  -0.608  -0.669
34    D        -1.620  -1.621  -1.454  -1.650  -1.649  -1.383  -1.435  -1.428  -1.202
35    A        -1.074  -1.002  -1.044  -1.361  -1.272  -1.230  -1.109  -1.042  -1.006
36    I        -0.998  -1.000  -1.033  -0.910  -0.922  -0.888  -1.001  -1.004  -0.993
37    A        -1.503  -1.505  -1.433  -1.224  -1.226  -1.115  -1.326  -1.321  -1.185
38    Q        -1.074  -1.107  -1.051  -1.134  -1.176  -1.073  -1.109  -1.135  -1.013
39    I         0.171   0.136   0.121   0.055  -0.014  -0.083  -0.025  -0.092  -0.166
40    Y        -0.436  -0.429  -0.522  -0.260  -0.231  -0.453  -0.567  -0.542  -0.671
41    R        -0.140  -0.270  -0.466   0.077  -0.102  -0.418  -0.133  -0.310  -0.590
42    L         0.504   0.449   0.244   0.275   0.203  -0.098   0.517   0.434   0.063
43    I         0.171   0.209   0.176   0.055   0.117   0.029  -0.025   0.038  -0.062
44    S         0.171   0.209   0.176   0.212   0.273   0.198  -0.025   0.038  -0.062
45    S        -0.998  -0.998  -1.035  -0.818  -0.849  -0.830  -1.001  -1.019  -0.997
46    R         1.180   1.190   1.262   1.277   1.293   1.398   1.276   1.291   1.404
47    D         0.504   0.424   0.241   0.617   0.519   0.244   0.517   0.394   0.058
48    H        -1.074  -1.051  -1.056  -1.005  -0.972  -1.026  -1.109  -1.084  -1.018
49    K        -0.008  -0.010   0.092  -0.162  -0.176  -0.020  -0.350  -0.360  -0.221
50    H        -1.074  -1.144  -1.045  -0.992  -1.090  -0.950  -1.109  -1.167  -1.008
51    Q         1.180   1.190   1.262   1.322   1.334   1.439   1.276   1.291   1.404
52    S         0.504   0.424   0.241   0.687   0.587   0.310   0.517   0.394   0.058
53    N         1.180   1.190   1.262   1.353   1.364   1.468   1.276   1.291   1.404
54    F         1.180   1.190   1.262   1.163   1.178   1.293   1.276   1.291   1.404
55    V        -0.436  -0.522  -0.530  -0.605  -0.752  -0.819  -0.567  -0.679  -0.687
56    E         1.180   1.190   1.262   1.163   1.175   1.293   1.276   1.291   1.404
57    F        -0.747  -0.813  -0.977  -0.648  -0.736  -1.010  -0.676  -0.756  -0.928
58    S        -1.503  -1.506  -1.446  -1.379  -1.394  -1.295  -1.326  -1.326  -1.196
59    D        -1.503  -1.463  -1.445  -1.364  -1.309  -1.313  -1.326  -1.288  -1.195
60    S        -1.620  -1.602  -1.443  -1.447  -1.423  -1.189  -1.435  -1.415  -1.195
61    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    K         1.180   1.190   1.262   1.264   1.274   1.385   1.276   1.291   1.404
63    L         0.171   0.209   0.176  -0.230  -0.165  -0.220  -0.025   0.038  -0.062
64    I         0.171   0.209   0.135   0.034   0.102  -0.063  -0.025   0.038  -0.138
65    Y         1.180   1.190   1.262   1.259   1.275   1.381   1.276   1.291   1.404
66    R         0.171   0.162   0.149   0.173   0.155   0.098  -0.025  -0.045  -0.111
67    R         0.504   0.449   0.244   0.682   0.615   0.307   0.517   0.434   0.063
68    Y         1.180   1.190   1.262   1.259   1.275   1.381   1.276   1.291   1.404
69    A         1.180   1.190   1.262   1.371   1.388   1.485   1.276   1.291   1.404
70    G         1.180   1.190   1.262   1.362   1.376   1.476   1.276   1.291   1.404
71    L         1.180   1.190   1.262   0.902   0.916   1.052   1.276   1.291   1.404
72    Y         0.171   0.209   0.176   0.123   0.189   0.089  -0.025   0.038  -0.062
73    F         1.180   1.190   1.262   1.163   1.178   1.293   1.276   1.291   1.404
74    V        -1.074  -1.051  -1.056  -1.106  -1.061  -1.128  -1.109  -1.084  -1.018
75    M        -1.931  -1.891  -1.754  -1.656  -1.614  -1.401  -1.543  -1.509  -1.307
76    G        -0.998  -1.000  -1.033  -0.775  -0.781  -0.853  -1.001  -1.004  -0.993
77    V         0.171   0.192   0.162   0.034   0.073  -0.010  -0.025   0.009  -0.087
78    D         1.180   1.190   1.262   1.214   1.233   1.339   1.276   1.291   1.404
79    L        -1.309  -1.367  -1.414  -1.413  -1.513  -1.482  -1.109  -1.172  -1.167
80    L        -2.242  -2.222  -2.038  -2.089  -2.034  -1.779  -1.652  -1.634  -1.401
81    D         1.180   1.190   1.262   1.214   1.233   1.339   1.276   1.291   1.404
82    D        -1.191  -1.142  -1.073  -1.242  -1.179  -1.073  -1.218  -1.171  -1.034
83    E         0.504   0.424   0.241   0.546   0.438   0.150   0.517   0.394   0.058
84    P        -0.140  -0.035  -0.441  -0.257  -0.128  -0.603  -0.133   0.008  -0.556
85    I        -1.503  -1.496  -1.444  -1.465  -1.457  -1.374  -1.326  -1.317  -1.194
86    Y        -0.140  -0.200  -0.456   0.040  -0.046  -0.457  -0.133  -0.217  -0.577
87    L         1.180   1.190   1.262   0.902   0.916   1.052   1.276   1.291   1.404
88    C        -0.436  -0.384  -0.529  -0.451  -0.398  -0.545  -0.567  -0.511  -0.681
89    H        -1.620  -1.655  -1.463  -1.365  -1.398  -1.117  -1.435  -1.452  -1.210
90    I         0.171   0.192   0.162  -0.027   0.006  -0.112  -0.025   0.009  -0.087
91    H         1.180   1.190   1.262   1.442   1.459   1.549   1.276   1.291   1.404
92    L        -0.064  -0.053   0.085  -0.630  -0.612  -0.361  -0.459  -0.443  -0.233
93    F         0.504   0.527   0.252   0.502   0.536   0.061   0.517   0.551   0.077
94    V         1.180   1.190   1.262   1.158   1.179   1.289   1.276   1.291   1.404
95    E         1.180   1.190   1.262   1.163   1.175   1.293   1.276   1.291   1.404
96    V         0.171   0.134   0.127   0.034  -0.030  -0.079  -0.025  -0.094  -0.153
97    L         1.180   1.190   1.262   0.902   0.916   1.052   1.276   1.291   1.404
98    D         1.180   1.190   1.262   1.214   1.233   1.339   1.276   1.291   1.404
99    A        -1.191  -1.160  -1.052  -1.184  -1.127  -0.934  -1.218  -1.177  -1.012
100   F         0.171   0.192   0.162   0.061   0.096   0.025  -0.025   0.009  -0.087
101   F         1.180   1.190   1.262   1.163   1.178   1.293   1.276   1.291   1.404
102   G         0.171   0.192   0.162   0.239   0.274   0.171  -0.025   0.009  -0.087
103   N         0.504   0.521   0.252   0.746   0.766   0.359   0.517   0.542   0.077
104   V         1.180   1.190   1.262   1.158   1.179   1.289   1.276   1.291   1.404
105   C         1.180   1.190   1.262   1.490   1.504   1.593   1.276   1.291   1.404
106   E         1.180   1.190   1.262   1.163   1.175   1.293   1.276   1.291   1.404
107   L         0.504   0.521   0.252   0.275   0.299  -0.084   0.517   0.542   0.077
108   D         1.180   1.190   1.262   1.214   1.233   1.339   1.276   1.291   1.404
109   I        -0.008   0.012   0.105  -0.533  -0.505  -0.325  -0.350  -0.320  -0.196
110   V        -0.436  -0.513  -0.529  -0.605  -0.739  -0.817  -0.567  -0.672  -0.684
111   F         1.180   1.190   1.262   1.163   1.178   1.293   1.276   1.291   1.404
112   N         1.180   1.190   1.262   1.353   1.364   1.468   1.276   1.291   1.404
113   F         1.180   1.190   1.262   1.163   1.178   1.293   1.276   1.291   1.404
114   Y         1.180   1.190   1.262   1.259   1.275   1.381   1.276   1.291   1.404
115   K         1.180   1.190   1.262   1.264   1.274   1.385   1.276   1.291   1.404
116   V        -0.998  -1.001  -1.027  -1.126  -1.115  -1.100  -1.001  -1.001  -0.985
117   Y         0.504   0.424   0.241   0.652   0.550   0.258   0.517   0.394   0.058
118   M        -1.503  -1.491  -1.445  -1.315  -1.312  -1.299  -1.326  -1.306  -1.195
119   I         0.171   0.162   0.149   0.055   0.034  -0.023  -0.025  -0.045  -0.111
120   M        -0.008   0.012   0.105  -0.367  -0.341  -0.149  -0.350  -0.320  -0.196
121   D         1.180   1.190   1.262   1.214   1.233   1.339   1.276   1.291   1.404
122   E         1.180   1.190   1.262   1.163   1.175   1.293   1.276   1.291   1.404
123   M        -0.763  -0.739  -0.588  -0.894  -0.861  -0.637  -1.001  -0.971  -0.760
124   F        -0.140  -0.206  -0.455  -0.060  -0.154  -0.543  -0.133  -0.225  -0.576
125   I         0.171   0.180   0.150  -0.218  -0.206  -0.250  -0.025  -0.012  -0.110
126   G        -0.008  -0.002   0.097  -0.027  -0.022   0.117  -0.350  -0.345  -0.211
127   G         1.180   1.190   1.262   1.362   1.376   1.476   1.276   1.291   1.404
128   E         1.180   1.190   1.262   1.163   1.175   1.293   1.276   1.291   1.404
129   I        -0.747  -0.713  -0.960  -0.718  -0.673  -1.138  -0.676  -0.634  -0.909
130   Q        -0.436  -0.476  -0.521  -0.371  -0.417  -0.511  -0.567  -0.608  -0.669
131   E         0.504   0.449   0.244   0.586   0.520   0.254   0.517   0.434   0.063
132   I        -1.503  -1.499  -1.427  -1.402  -1.382  -1.372  -1.326  -1.315  -1.181
133   S        -0.140  -0.200  -0.456   0.029  -0.052  -0.512  -0.133  -0.217  -0.577
134   K         1.180   1.190   1.262   1.264   1.274   1.385   1.276   1.291   1.404
135   D        -0.569  -0.485  -0.524  -0.683  -0.557  -0.570  -0.784  -0.679  -0.680
136   M        -1.931  -1.930  -1.773  -1.809  -1.823  -1.534  -1.543  -1.538  -1.320
137   L        -0.763  -0.746  -0.596  -1.307  -1.275  -1.007  -1.001  -0.980  -0.770
138   L         0.504   0.547   0.254   0.275   0.333  -0.079   0.517   0.581   0.081
139   E        -0.747  -0.688  -0.968  -0.547  -0.477  -0.817  -0.676  -0.605  -0.918
140   R         1.180   1.190   1.262   1.277   1.293   1.398   1.276   1.291   1.404
141   L         0.171   0.099   0.114  -0.218  -0.348  -0.310  -0.025  -0.157  -0.179
142   S        -1.074  -1.088  -1.050  -1.104  -1.122  -0.998  -1.109  -1.116  -1.012
143   I        -1.931  -1.893  -1.758  -1.731  -1.681  -1.475  -1.543  -1.511  -1.310
144   L         0.504   0.496   0.249   0.280   0.270  -0.077   0.517   0.505   0.072
145   D         0.504   0.424   0.241   0.590   0.485   0.176   0.517   0.394   0.058
146   R        -0.569  -0.548  -0.551  -0.635  -0.607  -0.562  -0.784  -0.756  -0.714
147   L         0.504   0.496   0.249   0.308   0.300  -0.008   0.517   0.505   0.072
148   D        -1.074  -1.107  -1.038  -1.178  -1.213  -1.065  -1.109  -1.133  -1.000
* 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/Q00381
Output conservation file - output/Q00381
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
