1     M         1.205   1.219   1.300   1.304   1.329   1.440   1.289   1.307   1.422
2     T        -1.389  -1.387  -1.319  -1.310  -1.301  -1.217  -1.249  -1.232  -1.091
3     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    P        -1.589  -1.548  -1.358  -1.632  -1.582  -1.310  -1.418  -1.369  -1.123
17    Q        -1.107  -1.079  -0.967  -1.256  -1.222  -1.017  -1.147  -1.111  -0.940
18    E         0.336   0.331   0.248   0.077   0.073  -0.039   0.206   0.191   0.008
19    P        -1.107  -1.079  -0.967  -0.945  -0.922  -0.782  -1.147  -1.111  -0.940
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    E        -1.107  -1.112  -0.980  -1.357  -1.347  -1.111  -1.147  -1.147  -0.953
26    E        -0.445  -0.353  -0.438  -0.768  -0.636  -0.737  -0.606  -0.476  -0.595
27    E        -0.445  -0.529  -0.480  -0.733  -0.850  -0.735  -0.606  -0.725  -0.652
28    E        -1.829  -1.737  -1.639  -1.775  -1.597  -1.547  -1.473  -1.388  -1.215
29    Q        -0.538  -0.588  -0.478  -0.838  -0.881  -0.723  -0.782  -0.823  -0.654
30    D        -0.177  -0.194  -0.408  -0.201  -0.256  -0.604  -0.230  -0.260  -0.553
31    V        -0.177  -0.166  -0.406   0.018   0.019  -0.364  -0.230  -0.224  -0.550
32    D        -0.952  -0.971  -0.954  -1.026  -1.072  -1.085  -0.967  -0.993  -0.927
33    M         0.423   0.487   0.257   0.614   0.699   0.349   0.349   0.447   0.023
34    T        -1.504  -1.474  -1.348  -1.544  -1.497  -1.374  -1.342  -1.308  -1.115
35    G        -1.504  -1.414  -1.331  -1.377  -1.259  -1.132  -1.342  -1.246  -1.100
36    D        -0.952  -0.845  -0.929  -0.906  -0.739  -0.911  -0.967  -0.836  -0.899
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.107  -0.984  -0.960  -1.374  -1.214  -1.134  -1.147  -1.000  -0.933
43    -        -0.445  -0.347  -0.446  -0.667  -0.546  -0.632  -0.606  -0.470  -0.606
44    -        -0.301  -0.361  -0.441  -0.201  -0.286  -0.505  -0.403  -0.494  -0.599
45    -        -1.504  -1.403  -1.334  -1.638  -1.507  -1.366  -1.342  -1.239  -1.102
46    -        -0.952  -0.943  -0.938  -1.143  -1.137  -1.099  -0.967  -0.953  -0.910
47    -        -1.504  -1.521  -1.353  -1.344  -1.385  -1.165  -1.342  -1.347  -1.118
48    E         0.020   0.024   0.157  -0.512  -0.498  -0.261  -0.368  -0.369  -0.164
49    E        -0.702  -0.673  -0.514  -1.089  -1.070  -0.808  -0.967  -0.925  -0.698
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    Q        -0.901  -1.025  -0.947  -0.746  -0.951  -0.859  -0.931  -1.058  -0.922
52    E        -0.658  -0.858  -0.918  -0.667  -0.910  -0.930  -0.614  -0.851  -0.888
53    E        -0.901  -0.927  -0.926  -1.026  -1.049  -1.001  -0.931  -0.937  -0.898
54    E         1.205   1.219   1.300   0.877   0.897   1.040   1.289   1.307   1.422
55    P        -1.803  -1.728  -1.635  -1.387  -1.303  -1.159  -1.460  -1.393  -1.213
56    D        -1.201  -1.326  -1.313  -1.096  -1.318  -1.318  -1.037  -1.163  -1.084
57    R        -2.405  -2.335  -2.135  -2.035  -1.944  -1.687  -1.671  -1.611  -1.362
58    E        -1.088  -1.036  -0.966  -1.305  -1.232  -1.085  -1.143  -1.090  -0.942
59    K         1.205   1.219   1.300   1.191   1.220   1.333   1.289   1.307   1.422
60    I        -0.658  -0.745  -0.914  -0.402  -0.522  -0.722  -0.614  -0.724  -0.883
61    K        -0.658  -0.858  -0.918  -0.399  -0.661  -0.782  -0.614  -0.851  -0.888
62    L         0.057   0.058   0.160  -0.163  -0.177  -0.023  -0.297  -0.304  -0.158
63    L         1.205   1.219   1.300   1.132   1.145   1.279   1.289   1.307   1.422
64    T         0.229   0.316   0.218   0.284   0.415   0.216   0.020   0.166  -0.048
65    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    A         0.057   0.129   0.182  -0.100   0.037   0.075  -0.297  -0.169  -0.116
67    T        -0.974  -1.030  -0.942  -0.926  -0.967  -0.839  -1.037  -1.073  -0.918
68    S         0.551   0.444   0.276   0.629   0.513   0.232   0.549   0.379   0.060
69    E        -0.358  -0.498  -0.464  -0.608  -0.803  -0.704  -0.509  -0.699  -0.635
70    D         1.205   1.219   1.300   1.074   1.090   1.224   1.289   1.307   1.422
71    G        -0.177  -0.334  -0.436   0.012  -0.209  -0.414  -0.230  -0.449  -0.592
72    T         1.205   1.219   1.300   1.150   1.175   1.296   1.289   1.307   1.422
73    S        -0.486  -0.440  -0.458  -0.541  -0.497  -0.453  -0.720  -0.674  -0.631
74    A        -0.072  -0.198  -0.389   0.081  -0.078  -0.313  -0.086  -0.259  -0.526
75    S         0.551   0.488   0.290   0.629   0.571   0.256   0.549   0.449   0.085
76    F         1.205   1.219   1.300   1.317   1.330   1.452   1.289   1.307   1.422
77    Q        -0.072  -0.135  -0.405   0.143   0.035  -0.384  -0.086  -0.179  -0.549
78    I         0.229   0.142   0.168   0.202   0.066   0.104   0.020  -0.145  -0.144
79    V        -1.803  -1.772  -1.636  -1.599  -1.570  -1.386  -1.460  -1.422  -1.213
80    E        -0.901  -0.895  -0.922  -1.007  -1.009  -1.043  -0.931  -0.921  -0.896
81    E         1.205   1.219   1.300   0.877   0.897   1.040   1.289   1.307   1.422
82    D         0.551   0.444   0.276   0.552   0.423   0.199   0.549   0.379   0.060
83    H         1.205   1.219   1.300   1.360   1.374   1.493   1.289   1.307   1.422
84    T         1.205   1.219   1.300   1.150   1.175   1.296   1.289   1.307   1.422
85    L         0.551   0.487   0.284   0.583   0.498   0.202   0.549   0.447   0.073
86    G         1.205   1.219   1.300   1.217   1.249   1.358   1.289   1.307   1.422
87    N         1.205   1.219   1.300   1.274   1.297   1.412   1.289   1.307   1.422
88    A        -0.072  -0.095  -0.391   0.032  -0.000  -0.425  -0.086  -0.120  -0.529
89    L         1.205   1.219   1.300   1.132   1.145   1.279   1.289   1.307   1.422
90    R         0.551   0.487   0.284   0.795   0.709   0.415   0.549   0.447   0.073
91    Y         1.205   1.219   1.300   1.343   1.367   1.476   1.289   1.307   1.422
92    V        -0.486  -0.454  -0.461  -0.518  -0.486  -0.436  -0.720  -0.687  -0.635
93    I         1.205   1.219   1.300   1.141   1.161   1.287   1.289   1.307   1.422
94    M         1.205   1.219   1.300   1.304   1.329   1.440   1.289   1.307   1.422
95    K         1.205   1.219   1.300   1.191   1.220   1.333   1.289   1.307   1.422
96    N         1.205   1.219   1.300   1.274   1.297   1.412   1.289   1.307   1.422
97    P         1.205   1.219   1.300   1.283   1.299   1.420   1.289   1.307   1.422
98    D         0.229   0.217   0.182  -0.135  -0.160  -0.222   0.020  -0.008  -0.116
99    V         1.205   1.219   1.300   1.230   1.243   1.371   1.289   1.307   1.422
100   E         1.205   1.219   1.300   0.877   0.897   1.040   1.289   1.307   1.422
101   F         1.205   1.219   1.300   1.317   1.330   1.452   1.289   1.307   1.422
102   C         1.205   1.219   1.300   1.382   1.397   1.512   1.289   1.307   1.422
103   G         0.551   0.444   0.276   0.664   0.539   0.255   0.549   0.379   0.060
104   Y         1.205   1.219   1.300   1.343   1.367   1.476   1.289   1.307   1.422
105   S         0.551   0.444   0.276   0.624   0.504   0.220   0.549   0.379   0.060
106   I         1.205   1.219   1.300   1.141   1.161   1.287   1.289   1.307   1.422
107   P         1.205   1.219   1.300   1.283   1.299   1.420   1.289   1.307   1.422
108   H         1.205   1.219   1.300   1.360   1.374   1.493   1.289   1.307   1.422
109   P         1.205   1.219   1.300   1.283   1.299   1.420   1.289   1.307   1.422
110   S         1.205   1.219   1.300   1.177   1.214   1.321   1.289   1.307   1.422
111   E         1.205   1.219   1.300   0.877   0.897   1.040   1.289   1.307   1.422
112   N        -0.486  -0.440  -0.460  -0.563  -0.534  -0.577  -0.720  -0.674  -0.632
113   L        -0.358  -0.238  -0.423  -0.295  -0.111  -0.383  -0.509  -0.333  -0.577
114   L         0.229   0.142   0.173   0.189   0.052   0.097   0.020  -0.144  -0.133
115   N         0.551   0.601   0.292   0.755   0.817   0.422   0.549   0.621   0.088
116   I        -0.658  -0.755  -0.912  -0.436  -0.568  -0.786  -0.614  -0.734  -0.881
117   R         1.205   1.219   1.300   1.330   1.339   1.464   1.289   1.307   1.422
118   I         1.205   1.219   1.300   1.141   1.161   1.287   1.289   1.307   1.422
119   Q         1.205   1.219   1.300   1.248   1.266   1.387   1.289   1.307   1.422
120   T         1.205   1.219   1.300   1.150   1.175   1.296   1.289   1.307   1.422
121   Y         0.551   0.488   0.290   0.790   0.715   0.390   0.549   0.449   0.085
122   G        -0.072  -0.236  -0.413   0.105  -0.115  -0.443  -0.086  -0.312  -0.559
123   E        -1.689  -1.738  -1.632  -1.419  -1.493  -1.440  -1.354  -1.389  -1.210
124   T         0.057   0.047   0.158  -0.151  -0.176  -0.015  -0.297  -0.325  -0.163
125   T         0.229   0.344   0.230   0.165   0.345   0.138   0.020   0.214  -0.027
126   A         1.205   1.219   1.300   1.119   1.131   1.266   1.289   1.307   1.422
127   V         0.551   0.487   0.284   0.680   0.595   0.288   0.549   0.447   0.073
128   D         0.057   0.090   0.174  -0.426  -0.376  -0.235  -0.297  -0.242  -0.131
129   A         0.551   0.488   0.290   0.582   0.501   0.235   0.549   0.449   0.085
130   L         1.205   1.219   1.300   1.132   1.145   1.279   1.289   1.307   1.422
131   Q        -0.674  -0.673  -0.513  -0.565  -0.574  -0.346  -0.931  -0.924  -0.697
132   K         0.229   0.344   0.230   0.226   0.403   0.205   0.020   0.214  -0.027
133   G         1.205   1.219   1.300   1.217   1.249   1.358   1.289   1.307   1.422
134   L         1.205   1.219   1.300   1.132   1.145   1.279   1.289   1.307   1.422
135   K        -0.658  -0.641  -0.902  -0.482  -0.463  -0.794  -0.614  -0.599  -0.870
136   D         0.229   0.344   0.230   0.131   0.291   0.127   0.020   0.214  -0.027
137   L         0.551   0.444   0.276   0.583   0.442   0.189   0.549   0.379   0.060
138   M        -1.088  -1.058  -0.959  -1.026  -0.960  -0.828  -1.143  -1.087  -0.933
139   D        -0.358  -0.323  -0.437  -0.509  -0.420  -0.635  -0.509  -0.439  -0.595
140   L        -0.072  -0.096  -0.399   0.062   0.019  -0.389  -0.086  -0.122  -0.540
141   C         1.205   1.219   1.300   1.382   1.397   1.512   1.289   1.307   1.422
142   D        -0.072   0.099  -0.379   0.007   0.211  -0.411  -0.086   0.143  -0.512
143   V        -0.486  -0.430  -0.459  -0.569  -0.512  -0.501  -0.720  -0.663  -0.632
144   V         0.229   0.344   0.230   0.230   0.398   0.190   0.020   0.214  -0.027
145   E        -0.901  -1.019  -0.945  -1.080  -1.215  -1.083  -0.931  -1.051  -0.920
146   S        -0.901  -0.879  -0.915  -1.004  -0.981  -1.026  -0.931  -0.907  -0.889
147   K         0.551   0.601   0.292   0.668   0.737   0.338   0.549   0.621   0.088
148   F         1.205   1.219   1.300   1.317   1.330   1.452   1.289   1.307   1.422
149   T        -1.201  -1.106  -1.291  -0.984  -0.864  -1.156  -1.037  -0.940  -1.065
150   E        -0.600  -0.542  -0.495  -0.946  -0.870  -0.766  -0.826  -0.745  -0.672
151   K        -1.088  -1.044  -0.951  -1.023  -0.960  -0.815  -1.143  -1.074  -0.926
152   I        -0.901  -1.020  -0.946  -0.806  -0.965  -0.844  -0.931  -1.052  -0.921
153   K        -1.689  -1.659  -1.619  -1.390  -1.340  -1.329  -1.354  -1.320  -1.199
154   S        -1.502  -1.458  -1.335  -1.546  -1.469  -1.313  -1.354  -1.297  -1.105
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.589  -1.537  -1.358  -1.446  -1.378  -1.136  -1.418  -1.361  -1.123
161   -        -0.445  -0.519  -0.470  -0.538  -0.699  -0.669  -0.606  -0.712  -0.639
162   -        -1.107  -1.076  -0.964  -1.084  -1.065  -0.912  -1.147  -1.108  -0.938
163   -        -1.107  -1.145  -0.983  -1.352  -1.390  -1.144  -1.147  -1.180  -0.957
164   M        -1.485  -1.531  -1.348  -1.213  -1.295  -1.049  -1.335  -1.355  -1.115
* 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/P28000
Output conservation file - output/P28000
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
