1     M         0.814   0.839   0.890   0.937   0.966   1.030   0.851   0.883   0.951
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     -        -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     S        -0.032   0.064  -0.405  -0.002   0.131  -0.536  -0.023   0.107  -0.603
9     D        -1.372  -1.480  -1.266  -1.643  -1.704  -1.350  -1.522  -1.585  -1.272
10    E        -0.032  -0.328  -0.430  -0.055  -0.432  -0.560  -0.023  -0.461  -0.644
11    E        -0.032   0.145  -0.401  -0.100   0.118  -0.652  -0.023   0.213  -0.596
12    H         0.814   0.839   0.890   0.956   0.977   1.047   0.851   0.883   0.951
13    T        -0.448  -0.371  -0.429  -0.516  -0.404  -0.541  -0.648  -0.528  -0.643
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    F         0.814   0.839   0.890   0.961   0.989   1.051   0.851   0.883   0.951
16    E        -0.448  -0.576  -0.479  -0.705  -0.950  -0.803  -0.648  -0.868  -0.727
17    N        -1.908  -1.978  -1.840  -1.804  -1.916  -1.688  -1.771  -1.811  -1.561
18    A        -1.519  -1.507  -1.272  -1.775  -1.785  -1.418  -1.647  -1.617  -1.279
19    D        -1.908  -1.691  -1.820  -1.994  -1.688  -1.818  -1.771  -1.523  -1.543
20    A         0.814   0.839   0.890   0.713   0.761   0.842   0.851   0.883   0.951
21    G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
22    A         0.814   0.839   0.890   0.713   0.761   0.842   0.851   0.883   0.951
23    S        -0.448  -0.229  -0.424  -0.523  -0.164  -0.543  -0.648  -0.309  -0.635
24    A        -1.206  -1.263  -1.262  -1.169  -1.299  -1.233  -1.272  -1.356  -1.269
25    T         0.814   0.839   0.890   0.797   0.836   0.913   0.851   0.883   0.951
26    Y        -0.671  -0.665  -0.481  -0.586  -0.597  -0.331  -1.022  -1.022  -0.731
27    P         0.814   0.839   0.890   0.952   0.981   1.043   0.851   0.883   0.951
28    M        -0.448  -0.318  -0.446  -0.351  -0.165  -0.427  -0.648  -0.445  -0.671
29    Q         0.814   0.839   0.890   1.060   1.080   1.134   0.851   0.883   0.951
30    C         0.814   0.839   0.890   1.088   1.107   1.157   0.851   0.883   0.951
31    S         0.814   0.839   0.890   0.802   0.862   0.917   0.851   0.883   0.951
32    A         0.814   0.839   0.890   0.713   0.761   0.842   0.851   0.883   0.951
33    L         0.814   0.839   0.890   0.777   0.823   0.896   0.851   0.883   0.951
34    R         0.814   0.839   0.890   1.004   1.025   1.086   0.851   0.883   0.951
35    K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
36    N        -0.032  -0.328  -0.430   0.269  -0.160  -0.414  -0.023  -0.461  -0.644
37    G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
38    F        -0.448  -0.274  -0.440  -0.295  -0.060  -0.347  -0.648  -0.377  -0.661
39    V         0.814   0.839   0.890   0.748   0.769   0.871   0.851   0.883   0.951
40    V         0.814   0.839   0.890   0.748   0.769   0.871   0.851   0.883   0.951
41    I         0.814   0.839   0.890   0.841   0.873   0.950   0.851   0.883   0.951
42    K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
43    G        -1.206  -1.134  -1.255  -1.184  -1.115  -1.223  -1.272  -1.220  -1.261
44    R         0.814   0.839   0.890   1.004   1.025   1.086   0.851   0.883   0.951
45    P         0.814   0.839   0.890   0.952   0.981   1.043   0.851   0.883   0.951
46    C         0.814   0.839   0.890   1.088   1.107   1.157   0.851   0.883   0.951
47    K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
48    I         0.814   0.839   0.890   0.841   0.873   0.950   0.851   0.883   0.951
49    V        -0.032   0.008  -0.409   0.038   0.077  -0.500  -0.023   0.032  -0.609
50    D         0.814   0.839   0.890   0.648   0.696   0.788   0.851   0.883   0.951
51    M         0.814   0.839   0.890   0.937   0.966   1.030   0.851   0.883   0.951
52    S         0.814   0.839   0.890   0.802   0.862   0.917   0.851   0.883   0.951
53    T         0.814   0.839   0.890   0.797   0.836   0.913   0.851   0.883   0.951
54    S         0.814   0.839   0.890   0.802   0.862   0.917   0.851   0.883   0.951
55    K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
56    T         0.814   0.839   0.890   0.797   0.836   0.913   0.851   0.883   0.951
57    G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
58    K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
59    H         0.814   0.839   0.890   0.956   0.977   1.047   0.851   0.883   0.951
60    G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
61    H         0.814   0.839   0.890   0.956   0.977   1.047   0.851   0.883   0.951
62    A         0.814   0.839   0.890   0.713   0.761   0.842   0.851   0.883   0.951
63    K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
64    V         0.814   0.839   0.890   0.748   0.769   0.871   0.851   0.883   0.951
65    H         0.814   0.839   0.890   0.956   0.977   1.047   0.851   0.883   0.951
66    L        -0.448  -0.371  -0.429  -0.505  -0.385  -0.512  -0.648  -0.528  -0.643
67    V         0.814   0.839   0.890   0.748   0.769   0.871   0.851   0.883   0.951
68    T        -0.032   0.064  -0.405  -0.003   0.128  -0.538  -0.023   0.107  -0.603
69    L        -1.372  -1.277  -1.259  -1.450  -1.302  -1.263  -1.522  -1.378  -1.265
70    D         0.814   0.839   0.890   0.648   0.696   0.788   0.851   0.883   0.951
71    I         0.814   0.839   0.890   0.841   0.873   0.950   0.851   0.883   0.951
72    F         0.814   0.839   0.890   0.961   0.989   1.051   0.851   0.883   0.951
73    T        -0.448  -0.371  -0.429  -0.434  -0.324  -0.425  -0.648  -0.528  -0.643
74    G        -0.448  -0.310  -0.451  -0.529  -0.331  -0.525  -0.648  -0.433  -0.679
75    K        -0.448  -0.371  -0.429  -0.537  -0.436  -0.501  -0.648  -0.528  -0.643
76    K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
77    L        -0.448  -0.371  -0.429  -0.419  -0.307  -0.391  -0.648  -0.528  -0.643
78    E         0.814   0.839   0.890   0.638   0.676   0.779   0.851   0.883   0.951
79    D         0.814   0.839   0.890   0.648   0.696   0.788   0.851   0.883   0.951
80    L        -0.448  -0.371  -0.429  -0.474  -0.355  -0.468  -0.648  -0.528  -0.643
81    S        -0.032  -0.328  -0.430   0.128  -0.213  -0.381  -0.023  -0.461  -0.644
82    P         0.814   0.839   0.890   0.952   0.981   1.043   0.851   0.883   0.951
83    S         0.814   0.839   0.890   0.802   0.862   0.917   0.851   0.883   0.951
84    T         0.814   0.839   0.890   0.797   0.836   0.913   0.851   0.883   0.951
85    H         0.814   0.839   0.890   0.956   0.977   1.047   0.851   0.883   0.951
86    N         0.814   0.839   0.890   0.999   1.025   1.082   0.851   0.883   0.951
87    L        -0.032   0.064  -0.405   0.218   0.332  -0.377  -0.023   0.107  -0.603
88    E        -0.671  -0.666  -0.482  -1.112  -1.127  -0.809  -1.022  -1.023  -0.732
89    V         0.814   0.839   0.890   0.748   0.769   0.871   0.851   0.883   0.951
90    P         0.814   0.839   0.890   0.952   0.981   1.043   0.851   0.883   0.951
91    F        -1.372  -1.216  -1.258  -1.304  -1.080  -1.116  -1.522  -1.308  -1.264
92    V         0.814   0.839   0.890   0.748   0.769   0.871   0.851   0.883   0.951
93    K        -0.837  -0.521  -1.207  -0.751  -0.366  -1.306  -0.772  -0.381  -1.201
94    R         0.814   0.839   0.890   1.004   1.025   1.086   0.851   0.883   0.951
95    S        -3.074  -2.798  -2.644  -2.848  -2.506  -2.222  -2.396  -2.137  -1.847
96    E        -0.032  -0.328  -0.430  -0.100  -0.515  -0.707  -0.023  -0.461  -0.644
97    Y        -0.741  -0.637  -0.473  -0.690  -0.526  -0.310  -1.147  -0.973  -0.717
98    Q         0.814   0.839   0.890   1.060   1.080   1.134   0.851   0.883   0.951
99    L        -0.032  -0.328  -0.430   0.085  -0.286  -0.457  -0.023  -0.461  -0.644
100   L        -1.908  -2.012  -1.842  -1.836  -1.992  -1.750  -1.771  -1.839  -1.564
101   D        -1.206  -1.376  -1.261  -1.172  -1.349  -1.141  -1.272  -1.448  -1.266
102   I         0.814   0.839   0.890   0.841   0.873   0.950   0.851   0.883   0.951
103   D         0.814   0.839   0.890   0.648   0.696   0.788   0.851   0.883   0.951
104   D        -0.032  -0.328  -0.430  -0.091  -0.501  -0.704  -0.023  -0.461  -0.644
105   G        -0.032  -0.328  -0.430  -0.040  -0.452  -0.661  -0.023  -0.461  -0.644
106   Y        -0.741  -0.661  -0.481  -0.690  -0.591  -0.334  -1.147  -1.014  -0.729
107   L         0.814   0.839   0.890   0.777   0.823   0.896   0.851   0.883   0.951
108   S        -1.206  -1.376  -1.261  -1.097  -1.338  -1.206  -1.272  -1.448  -1.266
109   L         0.814   0.839   0.890   0.777   0.823   0.896   0.851   0.883   0.951
110   M        -0.837  -1.081  -1.246  -0.453  -0.814  -1.077  -0.772  -1.090  -1.248
111   T        -0.032  -0.328  -0.430   0.060  -0.357  -0.587  -0.023  -0.461  -0.644
112   M        -2.685  -2.573  -2.291  -2.513  -2.373  -1.952  -2.271  -2.123  -1.739
113   D        -0.032  -0.328  -0.430  -0.038  -0.398  -0.532  -0.023  -0.461  -0.644
114   G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
115   E        -2.150  -1.960  -1.833  -2.384  -2.074  -1.885  -2.021  -1.785  -1.555
116   T        -0.032  -0.328  -0.430   0.058  -0.362  -0.592  -0.023  -0.461  -0.644
117   K         0.814   0.839   0.890   0.688   0.719   0.821   0.851   0.883   0.951
118   D        -0.032  -0.328  -0.430  -0.037  -0.397  -0.530  -0.023  -0.461  -0.644
119   D         0.814   0.839   0.890   0.648   0.696   0.788   0.851   0.883   0.951
120   V         0.814   0.839   0.890   0.748   0.769   0.871   0.851   0.883   0.951
121   K        -1.372  -1.258  -1.257  -1.401  -1.254  -1.172  -1.522  -1.349  -1.263
122   A        -2.150  -2.096  -1.843  -2.227  -2.087  -1.752  -2.021  -1.908  -1.564
123   P         0.814   0.839   0.890   0.952   0.981   1.043   0.851   0.883   0.951
124   E         0.814   0.839   0.890   0.638   0.676   0.779   0.851   0.883   0.951
125   G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
126   E         0.814   0.839   0.890   0.638   0.676   0.779   0.851   0.883   0.951
127   L        -0.032   0.008  -0.409   0.068   0.130  -0.477  -0.023   0.032  -0.609
128   G        -0.032  -0.328  -0.430  -0.030  -0.433  -0.631  -0.023  -0.461  -0.644
129   D        -1.206  -1.376  -1.261  -1.253  -1.504  -1.327  -1.272  -1.448  -1.266
130   S        -2.539  -2.458  -2.289  -2.448  -2.330  -2.005  -2.146  -2.040  -1.738
131   M        -0.837  -0.602  -1.211  -0.562  -0.280  -1.119  -0.772  -0.479  -1.205
132   Q        -0.671  -0.666  -0.482  -0.737  -0.820  -0.550  -1.022  -1.023  -0.732
133   A        -2.685  -2.616  -2.293  -2.796  -2.704  -2.221  -2.271  -2.146  -1.741
134   A        -2.150  -2.147  -1.848  -2.411  -2.374  -1.928  -2.021  -1.958  -1.568
135   F        -0.032  -0.328  -0.430   0.223  -0.212  -0.469  -0.023  -0.461  -0.644
136   D        -0.448  -0.567  -0.478  -0.698  -0.923  -0.800  -0.648  -0.852  -0.725
137   E         0.814   0.839   0.890   0.638   0.676   0.779   0.851   0.883   0.951
138   G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
139   K        -0.032   0.024  -0.399   0.003   0.067  -0.457  -0.023   0.053  -0.592
140   D         0.814   0.839   0.890   0.648   0.696   0.788   0.851   0.883   0.951
141   L        -0.032  -0.328  -0.430   0.085  -0.286  -0.457  -0.023  -0.461  -0.644
142   M        -1.908  -1.867  -1.831  -1.671  -1.620  -1.576  -1.771  -1.704  -1.554
143   V        -0.448  -0.371  -0.429  -0.534  -0.436  -0.534  -0.648  -0.528  -0.643
144   T        -0.032  -0.328  -0.430   0.067  -0.344  -0.564  -0.023  -0.461  -0.644
145   I        -0.741  -0.627  -0.469  -1.031  -0.863  -0.601  -1.147  -0.955  -0.710
146   I        -1.372  -1.481  -1.267  -1.413  -1.511  -1.183  -1.522  -1.586  -1.274
147   S        -0.837  -0.947  -1.237  -0.635  -0.801  -1.272  -0.772  -0.946  -1.236
148   A         0.814   0.839   0.890   0.713   0.761   0.842   0.851   0.883   0.951
149   M         0.814   0.839   0.890   0.937   0.966   1.030   0.851   0.883   0.951
150   G         0.814   0.839   0.890   0.698   0.740   0.830   0.851   0.883   0.951
151   E         0.814   0.839   0.890   0.638   0.676   0.779   0.851   0.883   0.951
152   E         0.814   0.839   0.890   0.638   0.676   0.779   0.851   0.883   0.951
153   A        -0.837  -0.739  -1.226  -0.703  -0.567  -1.262  -0.772  -0.642  -1.224
154   A        -0.032   0.008  -0.409  -0.010   0.053  -0.566  -0.023   0.032  -0.609
155   I        -0.448  -0.371  -0.429  -0.464  -0.352  -0.495  -0.648  -0.528  -0.643
156   S        -1.206  -1.376  -1.261  -1.226  -1.475  -1.385  -1.272  -1.448  -1.266
157   F        -2.150  -2.160  -1.846  -1.775  -1.843  -1.418  -2.021  -1.970  -1.567
158   K        -0.448  -0.371  -0.429  -0.537  -0.436  -0.501  -0.648  -0.528  -0.643
159   E        -0.448  -0.371  -0.429  -0.705  -0.584  -0.706  -0.648  -0.528  -0.643
160   A         0.814   0.839   0.890   0.713   0.761   0.842   0.851   0.883   0.951
161   P        -0.032  -0.328  -0.430   0.236  -0.168  -0.403  -0.023  -0.461  -0.644
162   R        -1.456  -1.517  -1.278  -1.491  -1.547  -1.168  -1.591  -1.625  -1.286
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   S        -0.973  -1.167  -1.249  -0.839  -1.159  -1.348  -0.943  -1.194  -1.252
165   D        -2.663  -2.434  -2.278  -2.713  -2.383  -2.143  -2.248  -2.005  -1.730
* 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/P19211
Output conservation file - output/P19211
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
