1     M         1.671   1.708   1.818   1.951   2.007   2.185   1.848   1.905   2.088
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     K         0.071  -0.090  -0.060  -0.117  -0.356  -0.317  -0.037  -0.287  -0.249
4     G        -0.781  -0.701  -0.671  -0.803  -0.674  -0.654  -0.874  -0.776  -0.712
5     S         0.393   0.427   0.548   0.037   0.079   0.284  -0.037   0.015   0.188
6     P        -1.297  -1.260  -1.131  -1.386  -1.314  -1.137  -1.168  -1.118  -0.954
7     I        -0.081   0.001  -0.094  -0.032   0.090  -0.052  -0.263  -0.139  -0.299
8     S        -0.786  -0.681  -0.691  -0.922  -0.754  -0.787  -0.866  -0.732  -0.730
9     Q        -1.297  -1.260  -1.131  -1.289  -1.242  -1.040  -1.168  -1.118  -0.954
10    F         1.671   1.708   1.818   1.859   1.916   2.094   1.848   1.905   2.088
11    S         0.748   0.796   0.683   0.841   0.907   0.699   0.642   0.718   0.461
12    K        -0.274  -0.238  -0.156  -0.656  -0.593  -0.490  -0.564  -0.512  -0.396
13    T         0.430   0.446   0.553   0.133   0.145   0.302   0.039   0.054   0.197
14    S        -1.297  -1.260  -1.131  -1.285  -1.226  -1.036  -1.168  -1.118  -0.954
15    I        -0.786  -0.779  -0.699  -0.819  -0.822  -0.730  -0.866  -0.851  -0.738
16    N        -0.786  -0.806  -0.708  -0.879  -0.908  -0.750  -0.866  -0.881  -0.749
17    A        -0.786  -0.727  -0.678  -0.731  -0.641  -0.588  -0.866  -0.791  -0.715
18    L         1.671   1.708   1.818   1.675   1.732   1.911   1.848   1.905   2.088
19    T         0.430   0.433   0.550   0.131   0.128   0.308   0.039   0.028   0.191
20    R         1.671   1.708   1.818   1.720   1.780   1.955   1.848   1.905   2.088
21    P         1.671   1.708   1.818   1.808   1.865   2.043   1.848   1.905   2.088
22    W         1.671   1.708   1.818   1.952   2.006   2.186   1.848   1.905   2.088
23    K        -0.274  -0.200  -0.169  -0.612  -0.476  -0.440  -0.564  -0.465  -0.412
24    K         0.430   0.433   0.550  -0.074  -0.067   0.112   0.039   0.028   0.191
25    Y         0.430   0.433   0.550   0.256   0.257   0.444   0.039   0.028   0.191
26    R         0.748   0.711   0.675   0.704   0.637   0.507   0.642   0.565   0.444
27    D         1.671   1.708   1.818   1.837   1.896   2.072   1.848   1.905   2.088
28    G         0.840   0.729   0.724   0.734   0.574   0.567   0.801   0.598   0.540
29    E        -1.049  -1.092  -1.062  -0.979  -1.064  -0.987  -0.921  -0.961  -0.890
30    L         0.568   0.510   0.581   0.474   0.368   0.477   0.309   0.181   0.255
31    F        -0.886  -1.010  -1.037  -0.527  -0.715  -0.754  -0.744  -0.869  -0.865
32    Y         0.634   0.558   0.612   0.629   0.494   0.563   0.434   0.276   0.318
33    G         0.976   0.887   0.804   0.879   0.761   0.643   1.023   0.874   0.693
34    L        -1.404  -1.274  -1.367  -1.147  -0.974  -1.065  -1.097  -0.959  -1.002
35    S        -0.566  -0.639  -0.630  -0.669  -0.819  -0.842  -0.626  -0.709  -0.669
36    K         0.203   0.056  -0.003   0.123  -0.043  -0.151   0.156  -0.068  -0.162
37    V        -1.553  -1.542  -1.447  -1.411  -1.399  -1.246  -1.229  -1.206  -1.068
38    G         1.671   1.708   1.818   1.503   1.550   1.740   1.848   1.905   2.088
39    N        -0.886  -1.010  -1.037  -0.643  -0.828  -0.906  -0.744  -0.869  -0.865
40    K         0.634   0.558   0.612   0.338   0.210   0.269   0.434   0.276   0.318
41    R         0.976   0.925   0.802   1.045   0.974   0.759   1.023   0.937   0.689
42    V        -0.765  -0.641  -0.656  -0.863  -0.685  -0.695  -0.861  -0.718  -0.695
43    P         0.315   0.254   0.044   0.547   0.464   0.157   0.317   0.231  -0.091
44    L         0.976   0.887   0.804   1.061   0.951   0.860   1.023   0.874   0.693
45    T         1.671   1.708   1.818   1.630   1.680   1.866   1.848   1.905   2.088
46    T         0.315   0.345   0.065   0.345   0.385  -0.056   0.317   0.363  -0.059
47    K         1.671   1.708   1.818   1.476   1.546   1.712   1.848   1.905   2.088
48    Q         0.011  -0.066  -0.062   0.126   0.006  -0.011  -0.155  -0.251  -0.264
49    G         0.976   0.925   0.802   0.878   0.813   0.639   1.023   0.937   0.689
50    N         0.976   0.887   0.804   1.184   1.082   0.971   1.023   0.874   0.693
51    K         0.976   0.887   0.804   0.862   0.767   0.647   1.023   0.874   0.693
52    T        -1.553  -1.484  -1.441  -1.399  -1.337  -1.273  -1.229  -1.161  -1.063
53    M        -0.325  -0.295  -0.181  -0.353  -0.325  -0.150  -0.626  -0.579  -0.427
54    Y         1.671   1.708   1.818   1.734   1.793   1.969   1.848   1.905   2.088
55    K         1.671   1.708   1.818   1.476   1.546   1.712   1.848   1.905   2.088
56    G         1.671   1.708   1.818   1.508   1.561   1.744   1.848   1.905   2.088
57    T         0.315   0.280   0.060   0.424   0.377   0.090   0.317   0.268  -0.067
58    R         0.634   0.673   0.630   0.501   0.558   0.415   0.434   0.495   0.354
59    A        -0.246  -0.251  -0.168  -0.386  -0.428  -0.292  -0.508  -0.519  -0.409
60    S        -0.126  -0.122  -0.099  -0.422  -0.451  -0.397  -0.390  -0.385  -0.327
61    G         0.315   0.157   0.047   0.215  -0.020  -0.219   0.317   0.091  -0.087
62    I        -0.566  -0.590  -0.621  -0.319  -0.361  -0.408  -0.626  -0.665  -0.657
63    G         1.671   1.708   1.818   1.508   1.561   1.744   1.848   1.905   2.088
64    R        -1.085  -1.168  -1.077  -1.213  -1.338  -1.219  -0.979  -1.039  -0.908
65    H        -0.886  -0.946  -1.026  -0.570  -0.690  -0.866  -0.744  -0.800  -0.854
66    T         0.315   0.329   0.045   0.410   0.433   0.038   0.317   0.341  -0.089
67    K        -0.765  -0.685  -0.657  -0.992  -0.865  -0.819  -0.861  -0.770  -0.699
68    F        -1.525  -1.517  -1.417  -1.537  -1.483  -1.342  -1.215  -1.189  -1.047
69    G         1.671   1.708   1.818   1.508   1.561   1.744   1.848   1.905   2.088
70    G        -0.566  -0.600  -0.622  -0.750  -0.804  -0.810  -0.626  -0.653  -0.659
71    Y         0.634   0.604   0.615   0.629   0.575   0.569   0.434   0.365   0.325
72    V        -1.205  -1.216  -1.090  -1.275  -1.281  -1.085  -1.097  -1.083  -0.921
73    I         0.634   0.596   0.605   0.734   0.661   0.619   0.434   0.350   0.304
74    N        -0.309  -0.369  -0.520  -0.011  -0.096  -0.309  -0.272  -0.352  -0.524
75    W         0.315   0.280   0.060   0.712   0.669   0.315   0.317   0.268  -0.067
76    K        -1.845  -1.790  -1.726  -1.711  -1.622  -1.565  -1.333  -1.275  -1.158
77    K         0.634   0.634   0.620   0.338   0.345   0.284   0.434   0.423   0.335
78    V         1.671   1.708   1.818   1.719   1.777   1.954   1.848   1.905   2.088
79    R         1.671   1.708   1.818   1.708   1.762   1.944   1.848   1.905   2.088
80    T         1.671   1.708   1.818   1.630   1.680   1.866   1.848   1.905   2.088
81    Y         0.451   0.476   0.563   0.309   0.345   0.473   0.081   0.114   0.218
82    V         0.976   1.089   0.828   1.076   1.231   0.861   1.023   1.197   0.737
83    T        -0.566  -0.621  -0.593  -0.527  -0.565  -0.528  -0.626  -0.663  -0.619
84    P         1.671   1.708   1.818   1.775   1.828   2.010   1.848   1.905   2.088
85    D        -1.205  -1.215  -1.090  -1.221  -1.188  -1.004  -1.097  -1.082  -0.921
86    M        -0.181  -0.085  -0.110  -0.368  -0.276  -0.231  -0.460  -0.332  -0.338
87    V        -0.457  -0.205  -0.539  -0.377  -0.018  -0.509  -0.460  -0.132  -0.548
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    N        -0.886  -0.991  -1.018  -0.670  -0.846  -0.916  -0.744  -0.850  -0.846
90    F        -0.765  -0.706  -0.673  -0.695  -0.623  -0.509  -0.861  -0.802  -0.717
91    E         0.011   0.058  -0.016   0.089   0.182   0.017  -0.155  -0.060  -0.186
92    L         1.671   1.708   1.818   1.656   1.706   1.892   1.848   1.905   2.088
93    K         0.315   0.157   0.047   0.197  -0.019  -0.221   0.317   0.091  -0.087
94    P         0.976   0.995   0.802   1.167   1.198   0.944   1.023   1.052   0.688
95    Y        -0.126  -0.068  -0.096  -0.255  -0.183  -0.178  -0.390  -0.330  -0.324
96    V         0.976   1.089   0.828   1.080   1.234   0.868   1.023   1.197   0.737
97    N         0.976   1.077   0.826   1.104   1.241   0.908   1.023   1.179   0.734
98    A        -1.085  -1.090  -1.050  -0.947  -0.984  -0.913  -0.979  -0.962  -0.881
99    N        -0.566  -0.653  -0.619  -0.605  -0.759  -0.751  -0.626  -0.720  -0.655
100   V        -0.765  -0.754  -0.676  -0.842  -0.803  -0.697  -0.861  -0.840  -0.719
101   P        -0.309  -0.436  -0.540  -0.045  -0.232  -0.390  -0.272  -0.430  -0.549
102   P        -1.085  -1.092  -1.051  -0.963  -0.955  -0.914  -0.979  -0.961  -0.882
103   L        -1.085  -1.168  -1.077  -1.030  -1.154  -0.995  -0.979  -1.039  -0.908
104   K        -0.309  -0.364  -0.548  -0.304  -0.354  -0.599  -0.272  -0.336  -0.558
105   H        -1.085  -1.157  -1.083  -0.863  -1.003  -0.893  -0.979  -1.031  -0.913
106   E        -1.404  -1.344  -1.370  -1.175  -1.114  -1.160  -1.097  -1.030  -1.004
107   F         0.315   0.220   0.045   0.581   0.448   0.168   0.317   0.180  -0.090
108   K        -1.525  -1.451  -1.425  -1.652  -1.484  -1.478  -1.215  -1.133  -1.052
109   G         0.976   0.887   0.804   0.894   0.783   0.677   1.023   0.874   0.693
110   F        -0.566  -0.652  -0.615  -0.525  -0.657  -0.612  -0.626  -0.704  -0.648
111   S        -1.085  -1.087  -1.043  -1.134  -1.128  -1.063  -0.979  -0.969  -0.879
112   G        -1.187  -1.196  -1.101  -1.373  -1.342  -1.246  -1.075  -1.067  -0.929
113   G         0.315   0.329   0.045   0.311   0.336  -0.029   0.317   0.341  -0.089
114   P        -1.049  -0.908  -1.040  -0.779  -0.577  -0.755  -0.921  -0.759  -0.869
115   L        -0.644  -0.511  -0.606  -0.915  -0.752  -0.815  -0.744  -0.605  -0.647
116   D         0.011  -0.037  -0.072   0.110   0.046  -0.037  -0.155  -0.213  -0.274
117   P         0.315   0.322   0.071   0.515   0.499   0.141   0.317   0.318  -0.050
118   R        -1.205  -1.100  -1.089  -1.227  -1.046  -1.037  -1.097  -0.994  -0.921
119   L         0.315   0.157   0.047   0.390   0.159  -0.026   0.317   0.091  -0.087
120   Q        -0.566  -0.486  -0.598  -0.480  -0.371  -0.523  -0.626  -0.529  -0.627
121   L        -1.085  -0.999  -1.030  -0.909  -0.802  -0.807  -0.979  -0.887  -0.865
122   L        -1.085  -1.073  -1.053  -1.033  -1.000  -0.983  -0.979  -0.954  -0.887
123   K        -0.091  -0.199  -0.122  -0.406  -0.556  -0.434  -0.306  -0.444  -0.348
124   I        -1.187  -1.225  -1.094  -1.030  -1.040  -0.854  -1.075  -1.089  -0.923
125   K         0.203   0.202   0.005   0.033   0.039  -0.274   0.156   0.158  -0.150
126   E         0.071   0.136  -0.044   0.154   0.257  -0.086  -0.037   0.058  -0.225
127   Y         0.497   0.506   0.570   0.393   0.404   0.486   0.173   0.173   0.232
128   I         0.497   0.544   0.574   0.385   0.452   0.492   0.173   0.248   0.241
129   V        -0.781  -0.675  -0.681  -1.067  -0.922  -0.918  -0.874  -0.756  -0.722
130   N        -1.634  -1.582  -1.465  -1.622  -1.524  -1.372  -1.293  -1.234  -1.081
131   G         1.671   1.708   1.818   1.524   1.580   1.760   1.848   1.905   2.088
132   R        -1.207  -1.221  -1.114  -1.230  -1.237  -1.101  -1.084  -1.085  -0.939
133   V        -0.355  -0.313  -0.192  -0.515  -0.474  -0.271  -0.665  -0.605  -0.443
134   Q        -0.194  -0.264  -0.156  -0.212  -0.312  -0.155  -0.456  -0.541  -0.396
135   S         0.203   0.202   0.005   0.343   0.354   0.045   0.156   0.158  -0.150
136   E         0.915   0.935   0.762   1.123   1.163   0.905   0.925   0.955   0.614
137   G        -1.297  -1.261  -1.131  -1.374  -1.312  -1.125  -1.168  -1.119  -0.954
138   A        -0.091  -0.199  -0.122  -0.024  -0.220  -0.128  -0.306  -0.444  -0.348
139   T        -0.684  -0.563  -0.627  -0.807  -0.605  -0.715  -0.768  -0.605  -0.659
140   D        -0.194  -0.129  -0.144  -0.205  -0.122  -0.139  -0.456  -0.376  -0.379
141   T        -1.207  -1.223  -1.118  -1.342  -1.373  -1.236  -1.084  -1.086  -0.943
142   S        -1.207  -1.173  -1.095  -1.238  -1.245  -1.093  -1.084  -1.041  -0.922
143   C        -1.207  -1.221  -1.114  -1.030  -1.092  -0.951  -1.084  -1.085  -0.939
144   Y         0.840   0.729   0.724   0.963   0.822   0.808   0.801   0.598   0.540
145   K        -0.684  -0.594  -0.628  -0.725  -0.619  -0.681  -0.768  -0.679  -0.666
146   E        -0.457  -0.590  -0.595  -0.163  -0.363  -0.357  -0.460  -0.628  -0.616
147   R         0.203   0.056  -0.003   0.359   0.149   0.073   0.156  -0.068  -0.162
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   G        -1.404  -1.485  -1.425  -1.339  -1.438  -1.309  -1.097  -1.154  -1.051
* 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/P36526
Output conservation file - output/P36526
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
