1     M         1.178   1.191   1.307   1.537   1.554   1.695   1.222   1.246   1.434
2     S         1.178   1.191   1.307   1.299   1.318   1.480   1.222   1.246   1.434
3     T        -1.141  -1.112  -0.849  -1.221  -1.147  -0.777  -1.276  -1.246  -0.906
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     E         0.463   0.305   0.072   0.394   0.258  -0.056   0.519   0.302  -0.099
6     S        -1.635  -1.696  -1.408  -1.305  -1.428  -1.194  -1.510  -1.554  -1.197
7     A         0.463   0.305   0.072  -0.117  -0.290  -0.533   0.519   0.302  -0.099
8     L        -0.896  -0.936  -0.807  -0.543  -0.555  -0.420  -1.042  -1.052  -0.856
9     S         0.463   0.484   0.087   0.714   0.734   0.008   0.519   0.546  -0.074
10    Y         1.178   1.191   1.307   1.584   1.600   1.737   1.222   1.246   1.434
11    A         0.078   0.298   0.081  -0.510  -0.269  -0.443  -0.027   0.291  -0.085
12    A         1.178   1.191   1.307   0.407   0.422   0.673   1.222   1.246   1.434
13    L         1.178   1.191   1.307   1.138   1.177   1.334   1.222   1.246   1.434
14    I         1.178   1.191   1.307   1.373   1.392   1.546   1.222   1.246   1.434
15    L         1.178   1.191   1.307   1.138   1.177   1.334   1.222   1.246   1.434
16    A         1.178   1.191   1.307   0.407   0.422   0.673   1.222   1.246   1.434
17    D         1.178   1.191   1.307   1.244   1.256   1.430   1.222   1.246   1.434
18    S        -1.635  -1.558  -1.379  -2.134  -2.032  -1.672  -1.510  -1.416  -1.169
19    E        -1.141  -1.102  -0.845  -1.188  -1.144  -0.856  -1.276  -1.232  -0.901
20    I        -0.301  -0.294  -0.060  -0.023  -0.034   0.231  -0.652  -0.662  -0.331
21    E         1.178   1.191   1.307   0.896   0.945   1.115   1.222   1.246   1.434
22    I         0.463   0.461   0.087   0.895   0.894   0.442   0.519   0.516  -0.074
23    S        -0.301  -0.297  -0.060  -0.019  -0.045   0.201  -0.652  -0.667  -0.331
24    S         0.078   0.021  -0.029   0.176   0.048  -0.316  -0.027  -0.130  -0.275
25    E        -0.346  -0.302  -0.060  -0.572  -0.517  -0.216  -0.730  -0.676  -0.330
26    K         1.178   1.191   1.307   1.324   1.343   1.502   1.222   1.246   1.434
27    L         0.463   0.418   0.082   0.652   0.630   0.213   0.519   0.458  -0.082
28    L        -1.520  -1.720  -1.803  -0.843  -1.089  -1.306  -1.120  -1.329  -1.339
29    T        -1.710  -1.650  -1.384  -1.525  -1.522  -1.131  -1.589  -1.520  -1.175
30    L         0.078  -0.042  -0.035   0.241   0.099   0.053  -0.027  -0.231  -0.285
31    T        -0.227  -0.230  -0.718   0.516   0.512  -0.120  -0.105  -0.117  -0.739
32    N        -2.115  -2.087  -2.178  -1.238  -1.270  -1.629  -1.510  -1.492  -1.475
33    A         0.078   0.078  -0.010  -0.502  -0.513  -0.516  -0.027  -0.039  -0.242
34    A         0.463   0.589   0.095  -0.109   0.010  -0.476   0.519   0.679  -0.060
35    N        -0.889  -1.063  -1.334   0.100  -0.110  -0.538  -0.652  -0.857  -1.122
36    V        -0.585  -0.740  -0.793   0.067  -0.130  -0.307  -0.574  -0.767  -0.840
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    P        -1.216  -1.115  -0.846  -0.971  -0.819  -0.611  -1.354  -1.243  -0.903
39    V         1.178   1.191   1.307   1.446   1.457   1.612   1.222   1.246   1.434
40    E         1.178   1.191   1.307   0.896   0.945   1.115   1.222   1.246   1.434
41    N        -1.940  -2.006  -1.835  -0.971  -1.047  -0.896  -1.589  -1.634  -1.366
42    I         0.463   0.305   0.072   0.895   0.738   0.421   0.519   0.302  -0.099
43    W         1.178   1.191   1.307   1.589   1.606   1.741   1.222   1.246   1.434
44    A         0.463   0.412   0.084  -0.070  -0.119  -0.355   0.519   0.449  -0.080
45    D        -0.796  -0.664  -0.758  -0.362  -0.200  -0.355  -0.886  -0.684  -0.792
46    I        -0.585  -0.724  -0.791  -0.045  -0.204  -0.414  -0.574  -0.745  -0.837
47    F         0.463   0.412   0.084   0.992   0.945   0.555   0.519   0.449  -0.080
48    A         1.178   1.191   1.307   0.407   0.422   0.673   1.222   1.246   1.434
49    K         1.178   1.191   1.307   1.324   1.343   1.502   1.222   1.246   1.434
50    A         1.178   1.191   1.307   0.407   0.422   0.673   1.222   1.246   1.434
51    L         1.178   1.191   1.307   1.138   1.177   1.334   1.222   1.246   1.434
52    D        -0.911  -0.951  -0.837  -1.168  -1.309  -1.306  -0.964  -1.034  -0.892
53    G         0.463   0.461   0.087   0.702   0.715   0.248   0.519   0.516  -0.074
54    Q        -0.165  -0.132  -0.031   0.190   0.220   0.315  -0.418  -0.380  -0.278
55    N        -0.165  -0.159  -0.044   0.093   0.085   0.212  -0.418  -0.427  -0.301
56    L        -0.227  -0.281  -0.724   0.184   0.146  -0.379  -0.105  -0.178  -0.746
57    K         1.178   1.191   1.307   1.324   1.343   1.502   1.222   1.246   1.434
58    D        -0.896  -0.858  -0.798  -0.912  -0.849  -0.730  -1.042  -1.007  -0.850
59    L        -0.227  -0.336  -0.731   0.185   0.084  -0.384  -0.105  -0.253  -0.756
60    L         0.078   0.078  -0.010   0.262   0.274   0.127  -0.027  -0.039  -0.242
61    V        -1.710  -1.643  -1.387  -1.105  -0.990  -0.759  -1.589  -1.514  -1.177
62    N         0.463   0.461   0.087   1.044   1.044   0.532   0.519   0.516  -0.074
63    F        -0.896  -0.893  -0.809  -0.377  -0.373  -0.283  -1.042  -1.031  -0.862
64    S        -1.390  -1.396  -1.373  -0.915  -0.906  -0.938  -1.276  -1.274  -1.164
65    A        -0.301  -0.192  -0.025  -0.933  -0.840  -0.539  -0.652  -0.484  -0.268
66    G        -0.323  -0.280  -0.058  -0.836  -0.774  -0.540  -0.690  -0.637  -0.327
67    A        -1.201  -1.139  -0.852  -1.160  -1.083  -0.840  -1.340  -1.276  -0.910
68    A        -0.227  -0.387  -0.737  -0.608  -0.787  -1.117  -0.105  -0.312  -0.763
69    A        -0.301  -0.287  -0.060  -1.008  -0.967  -0.579  -0.652  -0.650  -0.331
70    P        -0.911  -0.934  -0.839  -1.238  -1.255  -0.950  -0.964  -1.010  -0.894
71    A         0.463   0.484   0.087  -0.074  -0.058  -0.366   0.519   0.546  -0.074
72    G        -1.505  -1.553  -1.393  -1.021  -1.197  -1.205  -1.354  -1.410  -1.183
73    V        -1.635  -1.474  -1.377  -1.692  -1.612  -1.294  -1.510  -1.363  -1.169
74    A         0.463   0.516   0.093  -0.109  -0.059  -0.478   0.519   0.587  -0.063
75    G        -1.635  -1.608  -1.392  -1.713  -1.639  -1.247  -1.510  -1.482  -1.183
76    G        -0.585  -0.635  -0.786  -0.434  -0.567  -0.967  -0.574  -0.664  -0.832
77    V        -0.585  -0.522  -0.765  -0.996  -0.943  -1.071  -0.574  -0.508  -0.803
78    A        -0.301  -0.202  -0.039  -1.008  -0.906  -0.614  -0.652  -0.500  -0.293
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    G        -0.165  -0.137  -0.047  -0.855  -0.828  -0.613  -0.418  -0.389  -0.306
83    G         0.078   0.079  -0.019  -0.542  -0.551  -0.604  -0.027  -0.038  -0.257
84    E        -1.390  -1.408  -1.368  -1.782  -1.750  -1.626  -1.276  -1.308  -1.161
85    A        -1.940  -1.819  -1.795  -1.971  -1.892  -1.618  -1.589  -1.497  -1.337
86    G        -1.635  -1.551  -1.385  -1.871  -1.802  -1.683  -1.510  -1.421  -1.176
87    E        -0.585  -0.744  -0.792  -0.758  -0.969  -1.264  -0.574  -0.772  -0.838
88    A         1.178   1.191   1.307   0.407   0.422   0.673   1.222   1.246   1.434
89    E        -1.216  -1.235  -1.351  -1.421  -1.442  -1.447  -1.042  -1.076  -1.142
90    A        -0.165  -0.111  -0.042  -1.006  -0.934  -0.826  -0.418  -0.345  -0.299
91    E         0.463   0.305   0.072   0.301   0.119  -0.404   0.519   0.302  -0.099
92    K         0.463   0.510   0.090   0.404   0.480   0.001   0.519   0.579  -0.069
93    E        -1.488  -1.457  -1.372  -1.143  -1.196  -1.234  -1.340  -1.328  -1.163
94    E        -0.896  -0.970  -0.814  -0.927  -1.069  -1.053  -1.042  -1.103  -0.868
95    E         0.463   0.418   0.082   0.419   0.408   0.042   0.519   0.458  -0.082
96    E         1.178   1.191   1.307   0.896   0.945   1.115   1.222   1.246   1.434
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    A        -0.301  -0.258  -0.053  -1.059  -0.984  -0.765  -0.652  -0.598  -0.318
100   K        -0.165   0.041   0.043  -0.086   0.244   0.114  -0.418  -0.097  -0.149
101   E         0.463   0.305   0.072   0.394   0.258  -0.056   0.519   0.302  -0.099
102   E         1.178   1.191   1.307   0.896   0.945   1.115   1.222   1.246   1.434
103   S         1.178   1.191   1.307   1.299   1.318   1.480   1.222   1.246   1.434
104   D         1.178   1.191   1.307   1.244   1.256   1.430   1.222   1.246   1.434
105   D        -0.301  -0.192  -0.025  -0.440  -0.244  -0.103  -0.652  -0.484  -0.268
106   D         1.178   1.191   1.307   1.244   1.256   1.430   1.222   1.246   1.434
107   M         1.178   1.191   1.307   1.537   1.554   1.695   1.222   1.246   1.434
108   G         1.178   1.191   1.307   1.194   1.226   1.384   1.222   1.246   1.434
109   F         0.463   0.412   0.084   0.986   0.939   0.538   0.519   0.449  -0.080
110   G         1.178   1.191   1.307   1.194   1.226   1.384   1.222   1.246   1.434
111   L         1.178   1.191   1.307   1.138   1.177   1.334   1.222   1.246   1.434
112   F         1.178   1.191   1.307   1.456   1.474   1.621   1.222   1.246   1.434
113   D         1.178   1.191   1.307   1.244   1.256   1.430   1.222   1.246   1.434
* 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/P05318
Output conservation file - output/P05318
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
