1     M         1.301   1.396   1.444   1.553   1.675   1.759   1.387   1.521   1.606
2     N         0.602   0.399   0.356   0.729   0.477   0.383   0.607   0.260   0.157
3     A        -0.063  -0.399  -0.414   0.022  -0.422  -0.446  -0.062  -0.525  -0.555
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    P         1.301   1.396   1.444   1.416   1.547   1.630   1.387   1.521   1.606
13    D        -0.063  -0.399  -0.414   0.033  -0.438  -0.563  -0.062  -0.525  -0.555
14    R         1.301   1.396   1.444   1.410   1.551   1.625   1.387   1.521   1.606
15    F         0.602   0.490   0.373   0.765   0.670   0.459   0.607   0.414   0.189
16    E         1.301   1.396   1.444   1.181   1.318   1.407   1.387   1.521   1.606
17    L         1.301   1.396   1.444   0.969   1.089   1.207   1.387   1.521   1.606
18    F         0.602   0.490   0.373   0.741   0.629   0.398   0.607   0.414   0.189
19    L        -0.368  -0.307  -0.388  -0.721  -0.667  -0.759  -0.507  -0.395  -0.520
20    L         1.301   1.396   1.444   0.969   1.089   1.207   1.387   1.521   1.606
21    G        -0.948  -1.030  -0.952  -0.692  -0.811  -0.676  -0.953  -0.999  -0.897
22    E         0.035   0.237   0.264  -0.307   0.078   0.063  -0.360  -0.028  -0.014
23    G         1.301   1.396   1.444   1.448   1.591   1.660   1.387   1.521   1.606
24    E        -0.505  -0.487  -0.445  -0.781  -0.813  -0.743  -0.730  -0.656  -0.602
25    S        -1.148  -1.114  -0.985  -1.110  -1.086  -0.912  -1.176  -1.089  -0.933
26    K         1.301   1.396   1.444   1.269   1.405   1.491   1.387   1.521   1.606
27    L        -0.505  -0.531  -0.453  -0.881  -0.875  -0.711  -0.730  -0.723  -0.615
28    K        -0.368  -0.521  -0.458  -0.457  -0.752  -0.646  -0.507  -0.707  -0.621
29    I        -0.948  -1.096  -0.975  -0.831  -1.095  -0.898  -0.953  -1.067  -0.924
30    D        -1.590  -1.443  -1.374  -1.663  -1.485  -1.361  -1.399  -1.214  -1.103
31    P        -0.689  -0.889  -0.947  -0.429  -0.871  -0.921  -0.619  -0.860  -0.891
32    D         0.602   0.399   0.356   0.668   0.450   0.298   0.607   0.260   0.157
33    T         0.602   0.490   0.373   0.815   0.678   0.488   0.607   0.414   0.189
34    K        -0.063  -0.203  -0.382   0.081  -0.129  -0.371  -0.062  -0.276  -0.510
35    A        -1.469  -1.494  -1.397  -1.361  -1.325  -1.182  -1.287  -1.250  -1.122
36    P         0.258   0.226   0.235   0.343   0.248   0.249   0.050  -0.048  -0.070
37    N         0.602   0.794   0.412   0.729   0.999   0.473   0.607   0.879   0.258
38    A        -0.063  -0.203  -0.382   0.037  -0.146  -0.367  -0.062  -0.276  -0.510
39    V        -0.948  -0.836  -0.934  -0.956  -0.779  -0.909  -0.953  -0.798  -0.878
40    V        -1.469  -1.350  -1.363  -1.441  -1.280  -1.370  -1.287  -1.134  -1.095
41    I        -0.505  -0.575  -0.441  -0.550  -0.651  -0.448  -0.730  -0.773  -0.601
42    T         0.016   0.130   0.220  -0.220  -0.065   0.082  -0.396  -0.230  -0.097
43    F        -0.505  -0.531  -0.453  -0.649  -0.718  -0.632  -0.730  -0.723  -0.615
44    E         0.602   0.399   0.356   0.513   0.158   0.057   0.607   0.260   0.157
45    K         0.258   0.515   0.356   0.184   0.556   0.311   0.050   0.455   0.157
46    E         1.301   1.396   1.444   1.181   1.318   1.407   1.387   1.521   1.606
47    D         1.301   1.396   1.444   1.280   1.482   1.502   1.387   1.521   1.606
48    H         1.301   1.396   1.444   1.532   1.658   1.740   1.387   1.521   1.606
49    T         1.301   1.396   1.444   1.410   1.555   1.625   1.387   1.521   1.606
50    L         1.301   1.396   1.444   0.969   1.089   1.207   1.387   1.521   1.606
51    G         0.258   0.293   0.257   0.288   0.316   0.174   0.050   0.074  -0.028
52    N         1.301   1.396   1.444   1.324   1.487   1.543   1.387   1.521   1.606
53    L         0.602   0.490   0.373   0.387   0.241   0.131   0.607   0.414   0.189
54    I         0.016   0.198   0.252  -0.470  -0.261  -0.136  -0.396  -0.101  -0.038
55    R         0.258   0.143   0.220   0.252  -0.042   0.044   0.050  -0.204  -0.099
56    A        -0.689  -0.931  -0.958  -0.619  -1.023  -1.046  -0.619  -0.900  -0.904
57    E        -0.505  -0.510  -0.437  -0.542  -0.495  -0.376  -0.730  -0.680  -0.588
58    L         1.301   1.396   1.444   0.969   1.089   1.207   1.387   1.521   1.606
59    L         0.602   0.399   0.356   0.343   0.026  -0.015   0.607   0.260   0.157
60    N        -1.912  -1.819  -1.725  -1.722  -1.556  -1.430  -1.510  -1.369  -1.240
61    D         0.602   0.399   0.356   0.646   0.403   0.238   0.607   0.260   0.157
62    R        -1.790  -1.527  -1.662  -1.642  -1.314  -1.463  -1.399  -1.146  -1.194
63    K        -0.948  -0.836  -0.934  -0.785  -0.603  -0.744  -0.953  -0.798  -0.878
64    V         1.301   1.396   1.444   1.384   1.504   1.599   1.387   1.521   1.606
65    L         0.602   0.732   0.401   0.358   0.517   0.098   0.607   0.792   0.239
66    F         0.602   0.399   0.356   0.768   0.538   0.440   0.607   0.260   0.157
67    A         1.301   1.396   1.444   1.197   1.365   1.423   1.387   1.521   1.606
68    A         0.258   0.143   0.220   0.127  -0.054   0.056   0.050  -0.204  -0.099
69    Y         1.301   1.396   1.444   1.532   1.677   1.740   1.387   1.521   1.606
70    K         1.301   1.396   1.444   1.269   1.405   1.491   1.387   1.521   1.606
71    V         0.602   0.399   0.356   0.774   0.465   0.396   0.607   0.260   0.157
72    E        -0.063  -0.399  -0.414  -0.049  -0.566  -0.597  -0.062  -0.525  -0.555
73    H         1.301   1.396   1.444   1.532   1.658   1.740   1.387   1.521   1.606
74    P         1.301   1.396   1.444   1.416   1.547   1.630   1.387   1.521   1.606
75    F        -0.368  -0.336  -0.380  -0.698  -0.652  -0.694  -0.507  -0.442  -0.507
76    F        -0.063  -0.399  -0.414   0.137  -0.338  -0.420  -0.062  -0.525  -0.555
77    A        -0.063  -0.399  -0.414   0.026  -0.415  -0.437  -0.062  -0.525  -0.555
78    R        -0.948  -0.836  -0.934  -0.918  -0.793  -0.959  -0.953  -0.798  -0.878
79    F         0.602   0.399   0.356   0.686   0.369   0.215   0.607   0.260   0.157
80    K        -1.027  -1.123  -0.990  -1.046  -1.168  -0.973  -1.064  -1.097  -0.939
81    L        -0.063  -0.151  -0.368  -0.207  -0.382  -0.573  -0.062  -0.215  -0.491
82    R         1.301   1.396   1.444   1.410   1.551   1.625   1.387   1.521   1.606
83    I         0.602   0.490   0.373   0.760   0.608   0.418   0.607   0.414   0.189
84    Q         1.301   1.396   1.444   1.479   1.585   1.690   1.387   1.521   1.606
85    T         1.301   1.396   1.444   1.410   1.555   1.625   1.387   1.521   1.606
86    T        -1.027  -0.947  -0.960  -1.116  -1.021  -0.984  -1.064  -0.953  -0.908
87    E        -0.505  -0.544  -0.455  -0.747  -0.730  -0.621  -0.730  -0.728  -0.615
88    G        -0.505  -0.510  -0.437  -0.557  -0.483  -0.421  -0.730  -0.680  -0.588
89    Y        -0.063  -0.399  -0.414   0.357  -0.127  -0.174  -0.062  -0.525  -0.555
90    D        -0.505  -0.510  -0.437  -0.517  -0.452  -0.386  -0.730  -0.680  -0.588
91    P         1.301   1.396   1.444   1.416   1.547   1.630   1.387   1.521   1.606
92    K        -0.505  -0.387  -0.447  -0.586  -0.442  -0.456  -0.730  -0.576  -0.608
93    D        -0.505  -0.448  -0.426  -0.740  -0.590  -0.561  -0.730  -0.598  -0.574
94    A         0.602   0.490   0.373   0.590   0.469   0.267   0.607   0.414   0.189
95    L         0.602   0.490   0.373   0.358   0.195   0.054   0.607   0.414   0.189
96    K        -1.590  -1.270  -1.365  -1.472  -1.035  -1.136  -1.399  -1.044  -1.097
97    N        -0.063  -0.399  -0.414   0.114  -0.344  -0.432  -0.062  -0.525  -0.555
98    A         1.301   1.396   1.444   1.197   1.365   1.423   1.387   1.521   1.606
99    C         0.602   0.490   0.373   0.965   0.803   0.558   0.607   0.414   0.189
100   N        -0.705  -0.581  -0.497  -0.838  -0.703  -0.570  -0.953  -0.775  -0.669
101   S        -0.948  -0.916  -0.955  -0.722  -0.692  -0.780  -0.953  -0.882  -0.900
102   I         0.074   0.330   0.313  -0.417  -0.048  -0.042  -0.285   0.140   0.078
103   I         0.602   0.399   0.356   0.760   0.467   0.388   0.607   0.260   0.157
104   N        -1.790  -1.730  -1.721  -1.504  -1.499  -1.423  -1.399  -1.311  -1.237
105   K        -1.469  -1.494  -1.397  -1.364  -1.331  -1.165  -1.287  -1.250  -1.122
106   L         0.602   0.399   0.356   0.384   0.116   0.098   0.607   0.260   0.157
107   G        -1.469  -1.322  -1.361  -1.361  -1.138  -1.255  -1.287  -1.095  -1.092
108   A        -1.590  -1.443  -1.367  -1.599  -1.375  -1.277  -1.399  -1.202  -1.097
109   L         0.074   0.177   0.234  -0.417  -0.292  -0.157  -0.285  -0.140  -0.071
110   K        -0.368  -0.442  -0.434  -0.335  -0.449  -0.418  -0.507  -0.583  -0.588
111   T        -1.469  -1.487  -1.366  -1.242  -1.309  -1.145  -1.287  -1.244  -1.097
112   N        -0.948  -0.886  -0.958  -0.950  -0.913  -1.010  -0.953  -0.865  -0.906
113   F         1.301   1.396   1.444   1.351   1.527   1.569   1.387   1.521   1.606
114   E        -1.469  -1.320  -1.370  -1.388  -1.151  -1.186  -1.287  -1.118  -1.100
115   T        -1.148  -1.114  -0.985  -1.157  -1.109  -0.946  -1.176  -1.089  -0.933
116   E         1.301   1.396   1.444   1.181   1.318   1.407   1.387   1.521   1.606
117   W         0.602   0.399   0.356   0.946   0.592   0.451   0.607   0.260   0.157
118   N        -1.027  -0.965  -0.958  -1.173  -1.082  -1.072  -1.064  -0.944  -0.905
119   L         1.301   1.396   1.444   0.969   1.089   1.207   1.387   1.521   1.606
120   Q        -0.705  -0.599  -0.486  -0.805  -0.698  -0.504  -0.953  -0.801  -0.655
121   T        -1.790  -1.730  -1.721  -1.346  -1.290  -1.261  -1.399  -1.311  -1.237
122   L        -0.063  -0.399  -0.414  -0.211  -0.666  -0.637  -0.062  -0.525  -0.555
123   A        -0.948  -0.859  -0.941  -1.145  -0.944  -1.100  -0.953  -0.810  -0.886
124   A        -1.469  -1.448  -1.387  -1.449  -1.384  -1.325  -1.287  -1.215  -1.113
125   D        -1.590  -1.440  -1.374  -1.619  -1.393  -1.279  -1.399  -1.213  -1.103
126   D        -1.067  -0.833  -0.962  -1.049  -0.705  -0.873  -1.087  -0.817  -0.909
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.169  -1.128  -1.006  -1.132  -1.118  -0.934  -1.180  -1.102  -0.954
140   A        -1.592  -1.503  -1.404  -1.623  -1.443  -1.327  -1.386  -1.257  -1.127
141   F        -1.164  -0.972  -0.966  -0.976  -0.687  -0.671  -1.188  -0.942  -0.912
* 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/P38902
Output conservation file - output/P38902
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
