1     M         0.831   0.836   0.889   1.048   1.048   1.096   0.855   0.864   0.938
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     A        -1.519  -1.517  -1.244  -1.577  -1.573  -1.176  -1.621  -1.630  -1.260
6     H        -0.607  -0.440  -0.425  -0.896  -0.642  -0.587  -0.906  -0.643  -0.655
7     F        -0.020   0.090  -0.375   0.089   0.211  -0.416  -0.011   0.131  -0.572
8     K        -2.006  -1.961  -1.789  -2.077  -1.972  -1.734  -1.868  -1.822  -1.524
9     E         0.831   0.836   0.889   0.829   0.836   0.918   0.855   0.864   0.938
10    Y         0.831   0.836   0.889   0.892   0.899   0.969   0.855   0.864   0.938
11    Q         0.831   0.836   0.889   1.022   1.027   1.074   0.855   0.864   0.938
12    V         0.831   0.836   0.889   0.658   0.678   0.779   0.855   0.864   0.938
13    I        -0.440  -0.378  -0.399  -0.476  -0.379  -0.497  -0.630  -0.543  -0.613
14    G         0.831   0.836   0.889   1.022   1.020   1.074   0.855   0.864   0.938
15    R         0.831   0.836   0.889   0.602   0.613   0.733   0.855   0.864   0.938
16    R        -2.006  -1.985  -1.795  -2.296  -2.239  -1.802  -1.868  -1.839  -1.529
17    L        -0.440  -0.378  -0.399  -0.569  -0.476  -0.566  -0.630  -0.543  -0.613
18    P         0.831   0.836   0.889   0.897   0.899   0.973   0.855   0.864   0.938
19    T         0.831   0.836   0.889   0.897   0.900   0.973   0.855   0.864   0.938
20    E        -0.020  -0.011  -0.382   0.132   0.143  -0.353  -0.011  -0.004  -0.584
21    S        -1.203  -1.197  -1.207  -1.077  -1.063  -1.129  -1.249  -1.235  -1.216
22    V        -2.154  -2.175  -1.798  -2.300  -2.287  -1.716  -1.992  -1.995  -1.531
23    P         0.831   0.836   0.889   0.897   0.899   0.973   0.855   0.864   0.938
24    E        -1.203  -1.279  -1.213  -1.225  -1.315  -1.262  -1.249  -1.331  -1.222
25    P        -0.020  -0.079  -0.387   0.195   0.122  -0.327  -0.011  -0.097  -0.593
26    K        -0.020  -0.182  -0.394  -0.196  -0.395  -0.694  -0.011  -0.244  -0.604
27    L         0.831   0.836   0.889   0.806   0.807   0.899   0.855   0.864   0.938
28    F        -0.664  -0.681  -0.460  -0.783  -0.831  -0.504  -1.002  -1.048  -0.715
29    R         0.831   0.836   0.889   0.602   0.613   0.733   0.855   0.864   0.938
30    M         0.831   0.836   0.889   1.052   1.065   1.099   0.855   0.864   0.938
31    R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
32    I        -0.366  -0.337  -0.396  -0.304  -0.278  -0.422  -0.514  -0.480  -0.607
33    F         0.831   0.836   0.889   0.907   0.896   0.981   0.855   0.864   0.938
34    A         0.831   0.836   0.889   0.793   0.775   0.888   0.855   0.864   0.938
35    S         0.043   0.169  -0.372   0.258   0.449  -0.355   0.073   0.231  -0.567
36    N         0.831   0.836   0.889   1.020   1.013   1.073   0.855   0.864   0.938
37    E        -1.766  -1.745  -1.779  -1.536  -1.515  -1.561  -1.590  -1.580  -1.514
38    V        -0.366  -0.337  -0.396  -0.548  -0.506  -0.589  -0.514  -0.480  -0.607
39    I         0.043   0.169  -0.372  -0.002   0.144  -0.533   0.073   0.231  -0.567
40    A         0.831   0.836   0.889   0.793   0.775   0.888   0.855   0.864   0.938
41    K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
42    S         0.831   0.836   0.889   0.867   0.856   0.948   0.855   0.864   0.938
43    R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
44    Y        -0.366  -0.510  -0.448  -0.293  -0.531  -0.484  -0.514  -0.757  -0.694
45    W         0.831   0.836   0.889   1.138   1.127   1.169   0.855   0.864   0.938
46    Y         0.831   0.836   0.889   0.891   0.904   0.968   0.855   0.864   0.938
47    F         0.831   0.836   0.889   0.907   0.896   0.981   0.855   0.864   0.938
48    L         0.831   0.836   0.889   0.809   0.846   0.902   0.855   0.864   0.938
49    Q        -1.766  -1.934  -1.791  -1.559  -1.829  -1.754  -1.590  -1.755  -1.525
50    K        -1.766  -1.934  -1.791  -1.715  -1.912  -1.587  -1.590  -1.755  -1.525
51    L        -0.366  -0.337  -0.396  -0.373  -0.310  -0.451  -0.514  -0.480  -0.607
52    H        -1.766  -1.934  -1.791  -1.469  -1.767  -1.713  -1.590  -1.755  -1.525
53    K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
54    V         0.831   0.836   0.889   0.642   0.657   0.766   0.855   0.864   0.938
55    K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
56    K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
57    A        -0.714  -0.814  -1.186  -0.495  -0.650  -1.161  -0.612  -0.741  -1.191
58    S        -1.350  -1.286  -1.222  -1.407  -1.295  -1.190  -1.492  -1.397  -1.235
59    G         0.831   0.836   0.889   1.024   1.043   1.076   0.855   0.864   0.938
60    E         0.831   0.836   0.889   0.842   0.889   0.928   0.855   0.864   0.938
61    I         0.043   0.194  -0.372   0.231   0.384  -0.442   0.073   0.262  -0.567
62    V         0.831   0.836   0.889   0.642   0.657   0.766   0.855   0.864   0.938
63    S        -1.286  -1.405  -1.233  -1.326  -1.519  -1.228  -1.395  -1.517  -1.248
64    I        -1.766  -1.745  -1.779  -1.532  -1.505  -1.558  -1.590  -1.580  -1.514
65    N         0.831   0.836   0.889   1.020   1.013   1.073   0.855   0.864   0.938
66    Q        -3.090  -3.003  -2.592  -2.936  -2.857  -2.299  -2.373  -2.291  -1.812
67    I         0.831   0.836   0.889   0.907   0.893   0.981   0.855   0.864   0.938
68    N        -2.114  -2.049  -2.208  -1.628  -1.614  -1.802  -1.688  -1.647  -1.679
69    E         0.831   0.836   0.889   0.842   0.889   0.928   0.855   0.864   0.938
70    A        -2.046  -2.073  -1.797  -2.141  -2.273  -1.807  -1.884  -1.915  -1.530
71    H        -1.286  -1.303  -1.223  -1.341  -1.367  -1.260  -1.395  -1.397  -1.236
72    P         0.831   0.836   0.889   0.907   0.966   0.981   0.855   0.864   0.938
73    T        -0.607  -0.635  -0.457  -0.733  -0.793  -0.554  -0.906  -0.969  -0.709
74    K         0.043   0.198  -0.371  -0.108   0.027  -0.614   0.073   0.267  -0.566
75    V        -0.366  -0.337  -0.396  -0.570  -0.530  -0.621  -0.514  -0.480  -0.607
76    K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
77    N        -1.418  -1.354  -1.220  -1.346  -1.268  -1.162  -1.492  -1.420  -1.232
78    F         0.831   0.836   0.889   0.907   0.896   0.981   0.855   0.864   0.938
79    G         0.831   0.836   0.889   1.024   1.043   1.076   0.855   0.864   0.938
80    V        -0.721  -0.686  -0.460  -1.099  -1.048  -0.653  -1.101  -1.056  -0.715
81    W         0.831   0.836   0.889   1.138   1.127   1.169   0.855   0.864   0.938
82    V        -1.286  -1.064  -1.198  -1.383  -1.016  -1.233  -1.395  -1.107  -1.206
83    R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
84    Y         0.831   0.836   0.889   0.891   0.904   0.968   0.855   0.864   0.938
85    D        -0.366  -0.321  -0.418  -0.162  -0.106  -0.356  -0.514  -0.454  -0.644
86    S         0.831   0.836   0.889   0.867   0.856   0.948   0.855   0.864   0.938
87    R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
88    S         0.831   0.836   0.889   0.867   0.856   0.948   0.855   0.864   0.938
89    G         0.831   0.836   0.889   1.024   1.043   1.076   0.855   0.864   0.938
90    T        -0.366  -0.321  -0.418  -0.293  -0.241  -0.432  -0.514  -0.454  -0.644
91    H         0.831   0.836   0.889   0.996   0.995   1.053   0.855   0.864   0.938
92    N         0.831   0.836   0.889   1.020   1.013   1.073   0.855   0.864   0.938
93    M         0.831   0.836   0.889   1.052   1.065   1.099   0.855   0.864   0.938
94    Y         0.831   0.836   0.889   0.891   0.904   0.968   0.855   0.864   0.938
95    K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
96    E         0.831   0.836   0.889   0.842   0.889   0.928   0.855   0.864   0.938
97    I        -1.566  -1.428  -1.216  -1.615  -1.404  -1.122  -1.688  -1.516  -1.227
98    R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
99    D         0.043  -0.141  -0.390   0.391   0.148  -0.299   0.073  -0.186  -0.596
100   V        -1.087  -1.215  -1.208  -1.165  -1.320  -1.313  -1.101  -1.249  -1.217
101   S        -0.721  -0.691  -0.460  -0.926  -0.898  -0.530  -1.101  -1.064  -0.715
102   R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
103   V        -0.366  -0.510  -0.448  -0.541  -0.764  -0.655  -0.514  -0.757  -0.694
104   A        -1.286  -1.320  -1.224  -1.166  -1.203  -1.074  -1.395  -1.421  -1.238
105   A         0.831   0.836   0.889   0.793   0.775   0.888   0.855   0.864   0.938
106   V         0.831   0.836   0.889   0.642   0.657   0.766   0.855   0.864   0.938
107   E         0.831   0.836   0.889   0.842   0.889   0.928   0.855   0.864   0.938
108   T        -1.914  -1.846  -1.789  -1.798  -1.751  -1.569  -1.786  -1.731  -1.524
109   L        -0.721  -0.679  -0.459  -0.871  -0.777  -0.471  -1.101  -1.043  -0.713
110   Y         0.831   0.836   0.889   0.891   0.904   0.968   0.855   0.864   0.938
111   Q        -1.087  -1.215  -1.208  -0.821  -0.986  -1.091  -1.101  -1.249  -1.217
112   D         0.831   0.836   0.889   1.044   1.031   1.092   0.855   0.864   0.938
113   M        -0.366  -0.321  -0.418  -0.163  -0.085  -0.365  -0.514  -0.454  -0.644
114   A         0.831   0.836   0.889   0.793   0.775   0.888   0.855   0.864   0.938
115   A         0.831   0.836   0.889   0.793   0.775   0.888   0.855   0.864   0.938
116   R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
117   H         0.831   0.836   0.889   0.996   0.995   1.053   0.855   0.864   0.938
118   R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
119   A         0.043  -0.046  -0.385   0.143   0.010  -0.462   0.073  -0.051  -0.590
120   R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
121   F         0.831   0.836   0.889   0.907   0.896   0.981   0.855   0.864   0.938
122   R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
123   S         0.043   0.026  -0.380   0.237   0.200  -0.337   0.073   0.046  -0.581
124   I         0.831   0.836   0.889   0.907   0.893   0.981   0.855   0.864   0.938
125   H        -0.366  -0.337  -0.396  -0.271  -0.235  -0.441  -0.514  -0.480  -0.607
126   I         0.043  -0.046  -0.385   0.231   0.097  -0.470   0.073  -0.051  -0.590
127   L         0.831   0.836   0.889   0.809   0.846   0.902   0.855   0.864   0.938
128   K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
129   V         0.831   0.836   0.889   0.642   0.657   0.766   0.855   0.864   0.938
130   A        -0.366  -0.187  -0.391  -0.570  -0.309  -0.613  -0.514  -0.252  -0.599
131   E         0.831   0.836   0.889   0.842   0.889   0.928   0.855   0.864   0.938
132   I        -1.418  -1.251  -1.201  -1.533  -1.263  -1.254  -1.492  -1.293  -1.208
133   E         0.831   0.836   0.889   0.842   0.889   0.928   0.855   0.864   0.938
134   K         0.043  -0.046  -0.385  -0.111  -0.253  -0.647   0.073  -0.051  -0.590
135   T        -1.087  -1.136  -1.204  -1.029  -1.104  -1.277  -1.101  -1.157  -1.212
136   A        -1.286  -1.064  -1.198  -1.320  -0.949  -1.121  -1.395  -1.107  -1.206
137   D         0.831   0.836   0.889   1.044   1.031   1.092   0.855   0.864   0.938
138   V         0.043  -0.141  -0.390  -0.002  -0.222  -0.561   0.073  -0.186  -0.596
139   K        -0.366  -0.337  -0.396  -0.726  -0.715  -0.780  -0.514  -0.480  -0.607
140   R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
141   Q        -1.087  -1.215  -1.208  -0.744  -0.882  -0.985  -1.101  -1.249  -1.217
142   Y         0.831   0.836   0.889   0.891   0.904   0.968   0.855   0.864   0.938
143   V         0.043  -0.141  -0.390  -0.015  -0.232  -0.604   0.073  -0.186  -0.596
144   K         0.831   0.836   0.889   0.539   0.512   0.682   0.855   0.864   0.938
145   Q         0.831   0.836   0.889   1.020   1.049   1.073   0.855   0.864   0.938
146   F        -1.350  -1.286  -1.222  -1.422  -1.300  -1.186  -1.492  -1.397  -1.235
147   L         0.043  -0.141  -0.390   0.132  -0.079  -0.552   0.073  -0.186  -0.596
148   T        -1.766  -1.689  -1.772  -1.475  -1.409  -1.541  -1.590  -1.522  -1.507
149   K        -0.607  -0.607  -0.452  -1.011  -1.015  -0.717  -0.906  -0.920  -0.702
150   D        -1.087  -1.215  -1.208  -0.785  -1.010  -1.122  -1.101  -1.249  -1.217
151   L         0.831   0.836   0.889   0.809   0.846   0.902   0.855   0.864   0.938
152   K         0.043  -0.141  -0.390  -0.111  -0.375  -0.653   0.073  -0.186  -0.596
153   F         0.831   0.836   0.889   0.907   0.896   0.981   0.855   0.864   0.938
154   P         0.831   0.836   0.889   0.907   0.966   0.981   0.855   0.864   0.938
155   L         0.831   0.836   0.889   0.809   0.846   0.902   0.855   0.864   0.938
156   P         0.831   0.836   0.889   0.907   0.966   0.981   0.855   0.864   0.938
157   H         0.831   0.836   0.889   0.996   0.995   1.053   0.855   0.864   0.938
158   R         0.831   0.836   0.889   0.608   0.638   0.738   0.855   0.864   0.938
159   V        -1.087  -1.076  -1.197  -1.243  -1.215  -1.375  -1.101  -1.089  -1.203
160   Q        -1.087  -1.215  -1.208  -0.785  -0.922  -1.035  -1.101  -1.249  -1.217
161   K        -0.366  -0.337  -0.396  -0.602  -0.592  -0.591  -0.514  -0.480  -0.607
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   S        -1.087  -1.215  -1.208  -0.870  -1.038  -1.031  -1.101  -1.249  -1.217
168   T        -1.286  -1.210  -1.204  -1.616  -1.516  -1.455  -1.395  -1.261  -1.212
169   K         0.043  -0.046  -0.385  -0.091  -0.226  -0.579   0.073  -0.051  -0.590
170   T        -2.263  -2.167  -1.802  -2.420  -2.269  -1.736  -2.079  -1.988  -1.535
171   F         0.043   0.026  -0.380   0.261   0.224  -0.360   0.073   0.046  -0.581
172   S        -1.418  -1.405  -1.234  -1.425  -1.439  -1.177  -1.492  -1.487  -1.248
173   Y        -2.131  -2.088  -1.791  -2.119  -2.045  -1.628  -1.982  -1.919  -1.525
174   K        -1.766  -1.685  -1.776  -1.765  -1.694  -1.657  -1.590  -1.511  -1.511
175   R        -0.714  -0.652  -1.183  -0.729  -0.637  -1.412  -0.612  -0.545  -1.187
176   P         0.831   0.836   0.889   0.907   0.966   0.981   0.855   0.864   0.938
177   S        -1.087  -1.109  -1.204  -0.949  -0.987  -1.168  -1.101  -1.109  -1.212
178   T         0.831   0.836   0.889   0.891   0.892   0.968   0.855   0.864   0.938
179   F         0.831   0.836   0.889   0.907   0.896   0.981   0.855   0.864   0.938
180   Y         0.043  -0.141  -0.390   0.233   0.001  -0.429   0.073  -0.186  -0.596
* 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/P0CX24
Output conservation file - output/P0CX24
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
