1     M         1.344   1.375   1.426   1.579   1.627   1.696   1.443   1.485   1.557
2     H        -0.038   0.073  -0.245  -0.107   0.020  -0.318  -0.079   0.079  -0.372
3     N        -0.038   0.071  -0.251   0.028   0.168  -0.296  -0.079   0.076  -0.381
4     M        -1.689  -1.569  -1.550  -1.709  -1.535  -1.484  -1.324  -1.196  -1.131
5     F        -1.345  -1.248  -1.233  -1.105  -0.961  -0.946  -1.185  -1.076  -1.011
6     P        -1.689  -1.662  -1.560  -1.348  -1.320  -1.166  -1.324  -1.278  -1.139
7     A        -1.449  -1.382  -1.274  -1.683  -1.632  -1.410  -1.268  -1.185  -1.044
8     L        -0.460  -0.474  -0.397  -0.988  -1.005  -0.880  -0.675  -0.692  -0.584
9     T        -0.460  -0.467  -0.394  -0.422  -0.450  -0.346  -0.675  -0.683  -0.580
10    K        -0.460  -0.361  -0.369  -0.657  -0.448  -0.541  -0.675  -0.528  -0.545
11    T        -0.460  -0.350  -0.366  -0.399  -0.224  -0.263  -0.675  -0.512  -0.542
12    L         0.368   0.268   0.314   0.049  -0.126  -0.021   0.172  -0.019   0.028
13    S        -1.062  -1.000  -0.899  -1.571  -1.519  -1.303  -1.099  -1.014  -0.881
14    L        -0.487  -0.410  -0.382  -0.839  -0.760  -0.653  -0.726  -0.621  -0.567
15    Q        -0.487  -0.387  -0.386  -0.520  -0.424  -0.360  -0.726  -0.588  -0.571
16    G        -0.968  -0.927  -0.869  -0.830  -0.800  -0.687  -0.997  -0.942  -0.850
17    Y        -0.460  -0.451  -0.382  -0.338  -0.331  -0.249  -0.675  -0.659  -0.564
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    K        -0.963  -0.917  -0.861  -1.040  -0.927  -0.844  -1.005  -0.933  -0.843
22    I        -1.765  -1.704  -1.579  -1.838  -1.739  -1.558  -1.381  -1.305  -1.152
23    I        -0.812  -0.833  -0.840  -0.652  -0.671  -0.690  -0.816  -0.836  -0.818
24    N        -1.364  -1.271  -1.236  -1.338  -1.178  -1.169  -1.193  -1.081  -1.011
25    S        -1.216  -1.241  -1.226  -1.204  -1.203  -1.183  -1.047  -1.060  -1.002
26    Q        -0.872  -0.898  -0.856  -0.944  -1.062  -0.942  -0.909  -0.918  -0.839
27    T        -2.032  -1.964  -1.838  -1.785  -1.709  -1.507  -1.462  -1.384  -1.229
28    G        -1.345  -1.237  -1.233  -1.060  -0.892  -0.916  -1.185  -1.067  -1.011
29    S        -0.658  -0.733  -0.808  -0.549  -0.682  -0.788  -0.632  -0.722  -0.783
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    A        -1.689  -1.639  -1.558  -1.301  -1.193  -1.124  -1.324  -1.261  -1.137
34    A        -0.399  -0.478  -0.368  -0.472  -0.554  -0.394  -0.632  -0.699  -0.551
35    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    S        -0.460  -0.423  -0.385  -0.691  -0.629  -0.587  -0.675  -0.615  -0.567
37    C        -1.062  -1.030  -0.899  -1.066  -1.024  -0.823  -1.099  -1.045  -0.881
38    G        -0.460  -0.454  -0.402  -0.336  -0.330  -0.275  -0.675  -0.659  -0.590
39    R        -1.062  -1.030  -0.899  -1.349  -1.301  -1.092  -1.099  -1.045  -0.881
40    R        -1.062  -1.030  -0.899  -1.185  -1.140  -0.935  -1.099  -1.045  -0.881
41    W         0.475   0.500   0.357   0.624   0.672   0.440   0.358   0.393   0.110
42    F        -1.449  -1.413  -1.274  -1.207  -1.144  -0.957  -1.268  -1.211  -1.044
43    S        -0.487  -0.458  -0.396  -0.497  -0.441  -0.376  -0.726  -0.676  -0.585
44    S        -0.968  -0.958  -0.886  -1.078  -1.041  -0.917  -0.997  -0.969  -0.868
45    D        -0.968  -0.958  -0.886  -0.869  -0.858  -0.761  -0.997  -0.969  -0.868
46    K        -1.364  -1.348  -1.262  -1.263  -1.236  -1.157  -1.193  -1.154  -1.034
47    D        -0.411  -0.386  -0.380  -0.377  -0.330  -0.337  -0.628  -0.588  -0.565
48    D        -1.364  -1.348  -1.262  -1.308  -1.294  -1.189  -1.193  -1.154  -1.034
49    H        -1.364  -1.338  -1.256  -1.131  -1.097  -0.948  -1.193  -1.145  -1.029
50    D        -0.812  -0.795  -0.854  -0.747  -0.721  -0.814  -0.816  -0.782  -0.834
51    D         0.562   0.618   0.389   0.614   0.696   0.346   0.501   0.587   0.170
52    V        -0.305  -0.271  -0.367  -0.098  -0.046  -0.232  -0.455  -0.400  -0.543
53    V        -0.411  -0.366  -0.380  -0.482  -0.418  -0.408  -0.628  -0.560  -0.563
54    T        -1.364  -1.314  -1.251  -1.308  -1.215  -1.182  -1.193  -1.121  -1.025
55    R        -0.872  -0.838  -0.852  -1.043  -1.032  -1.004  -0.909  -0.865  -0.836
56    I        -1.216  -1.233  -1.234  -1.009  -1.011  -1.038  -1.047  -1.053  -1.010
57    K        -0.038  -0.141  -0.285  -0.112  -0.264  -0.501  -0.079  -0.233  -0.429
58    I        -0.038  -0.134  -0.283   0.083  -0.104  -0.332  -0.079  -0.224  -0.425
59    A        -1.689  -1.640  -1.560  -1.485  -1.473  -1.276  -1.324  -1.261  -1.138
60    P         0.632   0.460   0.407   0.821   0.562   0.448   0.613   0.325   0.202
61    I         0.632   0.460   0.407   0.776   0.561   0.461   0.613   0.325   0.202
62    K        -1.216  -1.233  -1.234  -1.115  -1.126  -1.074  -1.047  -1.053  -1.010
63    R         1.344   1.375   1.426   1.315   1.347   1.445   1.443   1.485   1.557
64    T        -0.658  -0.733  -0.808  -0.387  -0.519  -0.623  -0.632  -0.722  -0.783
65    N        -0.314  -0.398  -0.351  -0.143  -0.244  -0.215  -0.494  -0.581  -0.525
66    E         1.344   1.375   1.426   1.300   1.353   1.431   1.443   1.485   1.557
67    P        -0.872  -0.850  -0.851  -0.877  -0.837  -0.829  -0.909  -0.876  -0.834
68    L        -0.872  -0.934  -0.857  -1.046  -1.152  -1.024  -0.909  -0.951  -0.840
69    D         0.306   0.362   0.303   0.167   0.262   0.116   0.060   0.152   0.007
70    K        -0.872  -0.929  -0.861  -0.902  -0.953  -0.835  -0.909  -0.946  -0.844
71    K         0.632   0.460   0.407   0.583   0.377   0.296   0.613   0.325   0.202
72    R         0.632   0.460   0.407   0.612   0.309   0.205   0.613   0.325   0.202
73    A         1.344   1.375   1.426   1.472   1.524   1.594   1.443   1.485   1.557
74    R         1.344   1.375   1.426   1.315   1.347   1.445   1.443   1.485   1.557
75    L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
76    I        -0.872  -0.908  -0.857  -1.053  -1.141  -1.046  -0.909  -0.930  -0.840
77    Y         1.344   1.375   1.426   1.477   1.541   1.599   1.443   1.485   1.557
78    Q         1.344   1.375   1.426   1.537   1.585   1.656   1.443   1.485   1.557
79    S         1.344   1.375   1.426   1.344   1.404   1.472   1.443   1.485   1.557
80    R         1.344   1.375   1.426   1.315   1.347   1.445   1.443   1.485   1.557
81    K         1.344   1.375   1.426   1.202   1.268   1.337   1.443   1.485   1.557
82    R         1.344   1.375   1.426   1.315   1.347   1.445   1.443   1.485   1.557
83    G         1.344   1.375   1.426   1.570   1.622   1.687   1.443   1.485   1.557
84    I         1.344   1.375   1.426   1.401   1.465   1.527   1.443   1.485   1.557
85    L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
86    E         1.344   1.375   1.426   1.300   1.353   1.431   1.443   1.485   1.557
87    T         0.306   0.394   0.344   0.292   0.448   0.320   0.060   0.211   0.085
88    D         1.344   1.375   1.426   1.354   1.404   1.481   1.443   1.485   1.557
89    L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
90    L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
91    L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
92    S         1.344   1.375   1.426   1.344   1.404   1.472   1.443   1.485   1.557
93    G        -0.314  -0.398  -0.351  -0.322  -0.443  -0.352  -0.494  -0.581  -0.525
94    F         0.632   0.659   0.420   0.957   1.004   0.629   0.613   0.652   0.226
95    A         1.344   1.375   1.426   1.472   1.524   1.594   1.443   1.485   1.557
96    A        -0.399  -0.324  -0.357  -0.601  -0.499  -0.529  -0.632  -0.530  -0.537
97    K        -0.658  -0.737  -0.820  -0.810  -0.947  -1.127  -0.632  -0.726  -0.797
98    Y        -0.038  -0.134  -0.283   0.264   0.133  -0.066  -0.079  -0.224  -0.425
99    L         0.632   0.460   0.407   0.430   0.177   0.115   0.613   0.325   0.202
100   K        -0.658  -0.690  -0.798  -0.743  -0.797  -0.973  -0.632  -0.674  -0.771
101   K        -1.689  -1.559  -1.544  -1.691  -1.494  -1.459  -1.324  -1.187  -1.126
102   M        -0.038  -0.138  -0.282   0.339   0.184  -0.027  -0.079  -0.230  -0.425
103   N        -0.658  -0.710  -0.801  -0.416  -0.497  -0.657  -0.632  -0.696  -0.775
104   E        -2.032  -1.964  -1.838  -1.660  -1.551  -1.388  -1.462  -1.384  -1.229
105   E         0.632   0.460   0.407   0.640   0.395   0.291   0.613   0.325   0.202
106   E        -0.038  -0.141  -0.285  -0.021  -0.229  -0.430  -0.079  -0.233  -0.429
107   L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
108   E        -0.399  -0.478  -0.368  -0.629  -0.748  -0.565  -0.632  -0.699  -0.551
109   E         1.344   1.375   1.426   1.300   1.353   1.431   1.443   1.485   1.557
110   Y         1.344   1.375   1.426   1.477   1.541   1.599   1.443   1.485   1.557
111   D         1.344   1.375   1.426   1.354   1.404   1.481   1.443   1.485   1.557
112   S        -0.872  -0.814  -0.846  -0.946  -0.837  -0.856  -0.909  -0.842  -0.830
113   L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
114   L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
115   N         0.159   0.220   0.278  -0.035   0.073   0.154  -0.217  -0.111  -0.041
116   E         1.344   1.375   1.426   1.300   1.353   1.431   1.443   1.485   1.557
117   L        -0.399  -0.324  -0.357  -0.647  -0.510  -0.513  -0.632  -0.530  -0.537
118   D         1.344   1.375   1.426   1.354   1.404   1.481   1.443   1.485   1.557
119   W         1.344   1.375   1.426   1.597   1.648   1.713   1.443   1.485   1.557
120   D         1.344   1.375   1.426   1.354   1.404   1.481   1.443   1.485   1.557
121   I         1.344   1.375   1.426   1.401   1.465   1.527   1.443   1.485   1.557
122   Y        -0.038  -0.188  -0.303   0.167  -0.092  -0.287  -0.079  -0.293  -0.454
123   Y         1.344   1.375   1.426   1.477   1.541   1.599   1.443   1.485   1.557
124   W         1.344   1.375   1.426   1.597   1.648   1.713   1.443   1.485   1.557
125   A        -0.038  -0.134  -0.283   0.266   0.143  -0.058  -0.079  -0.224  -0.425
126   T         0.632   0.460   0.407   0.807   0.558   0.442   0.613   0.325   0.202
127   K        -0.658  -0.739  -0.820  -0.697  -0.789  -0.932  -0.632  -0.728  -0.797
128   N         0.632   0.460   0.407   0.786   0.541   0.414   0.613   0.325   0.202
129   F        -0.658  -0.753  -0.820  -0.411  -0.582  -0.687  -0.632  -0.743  -0.797
130   K        -1.216  -1.233  -1.226  -1.303  -1.331  -1.316  -1.047  -1.053  -1.003
131   T        -0.411  -0.363  -0.369  -0.435  -0.364  -0.348  -0.628  -0.556  -0.548
132   S        -0.411  -0.420  -0.377  -0.523  -0.531  -0.509  -0.628  -0.625  -0.560
133   P         1.344   1.375   1.426   1.481   1.529   1.602   1.443   1.485   1.557
134   L        -0.658  -0.733  -0.808  -0.681  -0.799  -0.796  -0.632  -0.722  -0.783
135   P         1.344   1.375   1.426   1.486   1.538   1.608   1.443   1.485   1.557
136   D         0.159   0.172   0.264  -0.131  -0.123   0.027  -0.217  -0.202  -0.068
137   K         0.159   0.210   0.270  -0.249  -0.159  -0.064  -0.217  -0.128  -0.056
138   W         1.344   1.375   1.426   1.597   1.648   1.713   1.443   1.485   1.557
139   A         0.306   0.352   0.300   0.089   0.178   0.081   0.060   0.134   0.002
140   N        -0.658  -0.739  -0.828  -0.520  -0.656  -0.867  -0.632  -0.728  -0.805
141   S         1.344   1.375   1.426   1.344   1.404   1.472   1.443   1.485   1.557
142   K        -1.216  -1.230  -1.223  -1.194  -1.179  -1.168  -1.047  -1.051  -1.000
143   L        -0.314  -0.328  -0.361  -0.335  -0.352  -0.441  -0.494  -0.528  -0.541
144   L        -0.038  -0.188  -0.303  -0.124  -0.327  -0.416  -0.079  -0.293  -0.454
145   K         0.632   0.659   0.420   0.534   0.594   0.208   0.613   0.652   0.226
146   Q        -1.002  -0.936  -0.875  -1.264  -1.160  -1.093  -1.047  -0.962  -0.859
147   L         0.632   0.716   0.433   0.430   0.532   0.157   0.613   0.739   0.249
148   Q        -0.038  -0.188  -0.303   0.220  -0.025  -0.249  -0.079  -0.293  -0.454
149   E        -0.314  -0.297  -0.353  -0.530  -0.539  -0.616  -0.494  -0.488  -0.531
150   F        -1.216  -1.233  -1.234  -0.972  -1.015  -1.098  -1.047  -1.053  -1.010
151   S        -0.399  -0.478  -0.374  -0.422  -0.477  -0.322  -0.632  -0.700  -0.559
152   E        -0.658  -0.698  -0.808  -0.654  -0.742  -0.924  -0.632  -0.683  -0.783
153   N         0.632   0.460   0.407   0.793   0.555   0.430   0.613   0.325   0.202
154   K        -0.038  -0.141  -0.294  -0.065  -0.190  -0.423  -0.079  -0.233  -0.441
155   E        -0.038  -0.141  -0.285  -0.013  -0.189  -0.415  -0.079  -0.233  -0.429
156   K        -0.314  -0.414  -0.361  -0.545  -0.666  -0.593  -0.494  -0.605  -0.539
157   E        -0.658  -0.692  -0.806  -0.542  -0.566  -0.741  -0.632  -0.676  -0.781
158   I        -0.038  -0.188  -0.303   0.157  -0.046  -0.222  -0.079  -0.293  -0.454
159   L         0.632   0.716   0.433   0.462   0.558   0.225   0.613   0.739   0.249
160   S         0.306   0.382   0.326   0.146   0.260   0.154   0.060   0.189   0.052
161   M         1.344   1.375   1.426   1.579   1.627   1.696   1.443   1.485   1.557
162   P         1.344   1.375   1.426   1.486   1.538   1.608   1.443   1.485   1.557
163   D         0.159   0.174   0.266  -0.131  -0.117   0.034  -0.217  -0.198  -0.064
164   L         1.344   1.375   1.426   1.081   1.115   1.222   1.443   1.485   1.557
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   S         0.368   0.407   0.328   0.257   0.320   0.161   0.172   0.233   0.056
171   K         0.141   0.176   0.264  -0.227  -0.149  -0.018  -0.252  -0.195  -0.067
172   Y         0.368   0.332   0.314   0.432   0.367   0.308   0.172   0.098   0.028
173   Q        -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/Q08230
Output conservation file - output/Q08230
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
