1     M         0.952   1.003   1.026   1.183   1.222   1.261   0.996   1.063   1.096
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     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     T         0.004   0.083  -0.142  -0.176  -0.075  -0.322  -0.125   0.001  -0.397
8     P         0.952   1.003   1.026   1.024   1.080   1.119   0.996   1.063   1.096
9     R        -1.234  -0.975  -1.314  -1.020  -0.748  -1.191  -1.149  -0.823  -1.176
10    E        -0.849  -0.920  -0.870  -0.933  -1.079  -1.036  -0.966  -1.031  -0.967
11    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    K        -1.047  -1.015  -0.877  -1.549  -1.477  -1.279  -1.246  -1.154  -0.976
13    K         0.175  -0.074  -0.106  -0.222  -0.532  -0.631   0.138  -0.254  -0.334
14    R        -1.985  -1.939  -1.768  -2.101  -1.991  -1.721  -1.721  -1.595  -1.398
15    T        -0.859  -0.774  -0.856  -0.811  -0.889  -0.913  -1.006  -0.917  -0.952
16    T        -1.468  -1.323  -1.353  -1.013  -0.876  -0.865  -1.435  -1.247  -1.217
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    R        -0.557  -0.742  -0.835  -0.426  -0.715  -0.919  -0.577  -0.817  -0.922
25    K        -0.557  -0.796  -0.837  -0.881  -1.182  -1.270  -0.577  -0.880  -0.925
26    K         0.952   1.003   1.026   0.481   0.588   0.638   0.996   1.063   1.096
27    K         0.952   1.003   1.026   0.481   0.588   0.638   0.996   1.063   1.096
28    D         0.952   1.003   1.026   1.039   1.091   1.133   0.996   1.063   1.096
29    P         0.952   1.003   1.026   1.024   1.080   1.119   0.996   1.063   1.096
30    N        -0.182   0.044  -0.108  -0.084   0.253  -0.011  -0.434  -0.060  -0.338
31    A         0.175  -0.074  -0.106   0.063  -0.167  -0.254   0.138  -0.254  -0.334
32    P         0.952   1.003   1.026   1.024   1.080   1.119   0.996   1.063   1.096
33    K         0.952   1.003   1.026   0.481   0.588   0.638   0.996   1.063   1.096
34    R         0.952   1.003   1.026   0.922   0.949   1.029   0.996   1.063   1.096
35    A        -1.468  -1.494  -1.369  -1.392  -1.324  -1.181  -1.435  -1.389  -1.230
36    L         0.175  -0.074  -0.106   0.472   0.162   0.092   0.138  -0.254  -0.334
37    S         0.952   1.003   1.026   1.100   1.142   1.188   0.996   1.063   1.096
38    A         0.952   1.003   1.026   0.686   0.833   0.820   0.996   1.063   1.096
39    Y         0.175  -0.074  -0.106   0.479   0.152   0.084   0.138  -0.254  -0.334
40    M         0.952   1.003   1.026   1.183   1.222   1.261   0.996   1.063   1.096
41    F         0.952   1.003   1.026   1.138   1.184   1.221   0.996   1.063   1.096
42    F         0.952   1.003   1.026   1.138   1.184   1.221   0.996   1.063   1.096
43    A         0.175  -0.074  -0.106   0.062  -0.173  -0.258   0.138  -0.254  -0.334
44    N         0.175  -0.074  -0.106   0.428   0.139   0.060   0.138  -0.254  -0.334
45    E         0.175   0.246  -0.077   0.174   0.245  -0.146   0.138   0.246  -0.284
46    N         0.175   0.177  -0.077   0.429   0.456   0.104   0.138   0.144  -0.284
47    R         0.952   1.003   1.026   0.922   0.949   1.029   0.996   1.063   1.096
48    D        -0.182  -0.266  -0.180  -0.169  -0.403  -0.273  -0.434  -0.586  -0.464
49    I        -1.234  -1.389  -1.365  -0.866  -1.224  -1.307  -1.149  -1.287  -1.227
50    V        -0.557  -0.742  -0.835   0.001  -0.250  -0.394  -0.577  -0.817  -0.922
51    R         0.175  -0.074  -0.106   0.196  -0.256  -0.343   0.138  -0.254  -0.334
52    S        -1.234  -1.307  -1.354  -1.171  -1.208  -1.269  -1.149  -1.213  -1.216
53    E        -0.182  -0.252  -0.179  -0.301  -0.434  -0.285  -0.434  -0.562  -0.464
54    N         0.952   1.003   1.026   1.039   1.119   1.133   0.996   1.063   1.096
55    P         0.952   1.003   1.026   1.024   1.080   1.119   0.996   1.063   1.096
56    D        -0.182  -0.224  -0.174  -0.041  -0.141  -0.091  -0.434  -0.512  -0.455
57    I        -0.557  -0.796  -0.837  -0.101  -0.474  -0.596  -0.577  -0.880  -0.925
58    T        -0.951  -0.846  -0.853  -0.794  -0.644  -0.711  -1.149  -0.974  -0.949
59    F         0.952   1.003   1.026   1.138   1.184   1.221   0.996   1.063   1.096
60    G         0.952   1.003   1.026   1.085   1.143   1.174   0.996   1.063   1.096
61    Q         0.952   1.003   1.026   1.198   1.246   1.275   0.996   1.063   1.096
62    V         0.175  -0.074  -0.106   0.575   0.246   0.144   0.138  -0.254  -0.334
63    G         0.952   1.003   1.026   1.085   1.143   1.174   0.996   1.063   1.096
64    K        -0.557  -0.644  -0.815  -0.785  -0.863  -1.034  -0.577  -0.709  -0.897
65    K        -1.468  -1.266  -1.352  -1.268  -0.924  -1.235  -1.435  -1.172  -1.215
66    L         0.952   1.003   1.026   1.085   1.155   1.174   0.996   1.063   1.096
67    G         0.952   1.003   1.026   1.085   1.143   1.174   0.996   1.063   1.096
68    E         0.175  -0.074  -0.106   0.081  -0.352  -0.441   0.138  -0.254  -0.334
69    K        -0.182  -0.266  -0.180  -0.668  -0.771  -0.587  -0.434  -0.586  -0.464
70    W         0.952   1.003   1.026   1.250   1.302   1.321   0.996   1.063   1.096
71    K         0.952   1.003   1.026   0.481   0.588   0.638   0.996   1.063   1.096
72    A        -0.557  -0.742  -0.835  -0.599  -0.824  -0.948  -0.577  -0.817  -0.922
73    L         0.952   1.003   1.026   1.085   1.155   1.174   0.996   1.063   1.096
74    T        -0.859  -0.708  -0.828  -0.574  -0.346  -0.547  -1.006  -0.754  -0.915
75    P        -1.610  -1.410  -1.369  -1.384  -1.121  -1.083  -1.578  -1.325  -1.232
76    E        -1.843  -1.838  -1.764  -1.819  -1.801  -1.777  -1.578  -1.520  -1.395
77    E        -0.859  -0.702  -0.820  -0.817  -0.605  -0.703  -1.006  -0.747  -0.903
78    K        -0.182  -0.266  -0.180  -0.668  -0.771  -0.587  -0.434  -0.586  -0.464
79    Q        -2.360  -2.150  -2.085  -1.927  -1.719  -1.513  -1.864  -1.629  -1.503
80    P         0.952   1.003   1.026   1.024   1.080   1.119   0.996   1.063   1.096
81    Y         0.952   1.003   1.026   1.100   1.159   1.188   0.996   1.063   1.096
82    E         0.952   1.003   1.026   0.810   0.855   0.929   0.996   1.063   1.096
83    A        -1.093  -0.968  -0.874  -1.370  -1.161  -1.031  -1.292  -1.103  -0.973
84    K         0.952   1.003   1.026   0.481   0.588   0.638   0.996   1.063   1.096
85    A         0.952   1.003   1.026   0.686   0.833   0.820   0.996   1.063   1.096
86    Q        -2.360  -2.213  -2.089  -2.048  -1.910  -1.668  -1.864  -1.671  -1.506
87    A        -0.557  -0.636  -0.818  -0.515  -0.538  -0.755  -0.577  -0.700  -0.900
88    D         0.952   1.003   1.026   1.039   1.091   1.133   0.996   1.063   1.096
89    K         0.952   1.003   1.026   0.481   0.588   0.638   0.996   1.063   1.096
90    K         0.175  -0.074  -0.106  -0.199  -0.524  -0.569   0.138  -0.254  -0.334
91    R         0.952   1.003   1.026   0.922   0.949   1.029   0.996   1.063   1.096
92    Y         0.952   1.003   1.026   1.100   1.159   1.188   0.996   1.063   1.096
93    E         0.952   1.003   1.026   0.810   0.855   0.929   0.996   1.063   1.096
94    S        -1.610  -1.548  -1.377  -1.671  -1.549  -1.306  -1.578  -1.439  -1.238
95    E         0.952   1.003   1.026   0.810   0.855   0.929   0.996   1.063   1.096
96    K         0.175  -0.074  -0.106  -0.178  -0.486  -0.513   0.138  -0.254  -0.334
97    E        -1.468  -1.497  -1.372  -1.703  -1.753  -1.537  -1.435  -1.392  -1.234
98    L        -1.093  -0.937  -0.872  -1.310  -1.079  -0.998  -1.292  -1.057  -0.970
99    Y         0.952   1.003   1.026   1.100   1.159   1.188   0.996   1.063   1.096
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   N        -1.468  -1.437  -1.368  -1.567  -1.444  -1.264  -1.435  -1.353  -1.231
102   A        -1.468  -1.494  -1.369  -1.740  -1.554  -1.452  -1.435  -1.389  -1.230
103   T        -0.965  -1.002  -0.872  -0.913  -1.098  -0.893  -1.145  -1.136  -0.970
104   L        -1.568  -1.330  -1.364  -1.645  -1.221  -1.360  -1.535  -1.237  -1.227
105   A         0.952   1.003   1.026   0.712   0.810   0.843   0.996   1.063   1.096
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -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/P11632
Output conservation file - output/P11632
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
