1     M         0.692   0.695   0.731   0.830   0.837   0.864   0.713   0.721   0.766
2     S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
3     T         0.692   0.695   0.731   0.765   0.761   0.810   0.713   0.721   0.766
4     P        -1.487  -1.625  -1.570  -1.501  -1.723  -1.591  -1.484  -1.676  -1.533
5     A         0.692   0.695   0.731   0.665   0.662   0.727   0.713   0.721   0.766
6     R        -0.220  -0.140  -0.674  -0.024   0.054  -0.663  -0.191  -0.092  -0.878
7     R         0.692   0.695   0.731   0.715   0.712   0.769   0.713   0.721   0.766
8     R         0.692   0.695   0.731   0.715   0.712   0.769   0.713   0.721   0.766
9     L         0.692   0.695   0.731   0.644   0.650   0.711   0.713   0.721   0.766
10    M         0.692   0.695   0.731   0.830   0.837   0.864   0.713   0.721   0.766
11    R         0.692   0.695   0.731   0.715   0.712   0.769   0.713   0.721   0.766
12    D         0.692   0.695   0.731   0.442   0.481   0.544   0.713   0.721   0.766
13    F         0.692   0.695   0.731   0.830   0.834   0.864   0.713   0.721   0.766
14    K         0.692   0.695   0.731   0.800   0.808   0.839   0.713   0.721   0.766
15    R         0.692   0.695   0.731   0.715   0.712   0.769   0.713   0.721   0.766
16    M         0.692   0.695   0.731   0.830   0.837   0.864   0.713   0.721   0.766
17    K        -0.909  -0.778  -0.705  -0.872  -0.673  -0.610  -1.226  -1.027  -0.929
18    E        -1.666  -1.619  -1.562  -1.571  -1.472  -1.405  -1.743  -1.668  -1.523
19    D         0.692   0.695   0.731   0.442   0.481   0.544   0.713   0.721   0.766
20    A        -1.824  -1.621  -1.568  -2.071  -1.760  -1.687  -1.872  -1.634  -1.530
21    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
22    P        -2.504  -2.511  -2.186  -2.593  -2.595  -2.059  -2.260  -2.262  -1.834
23    G         0.692   0.695   0.731   0.919   0.918   0.936   0.713   0.721   0.766
24    V         0.692   0.695   0.731   0.659   0.653   0.723   0.713   0.721   0.766
25    S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
26    A         0.692   0.695   0.731   0.665   0.662   0.727   0.713   0.721   0.766
27    S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
28    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
29    L        -0.909  -0.942  -0.730  -1.144  -1.238  -0.877  -1.226  -1.301  -0.969
30    P        -1.088  -1.307  -1.556  -0.984  -1.286  -1.672  -0.967  -1.245  -1.516
31    D         0.692   0.695   0.731   0.442   0.481   0.544   0.713   0.721   0.766
32    N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
33    V         0.692   0.695   0.731   0.659   0.653   0.723   0.713   0.721   0.766
34    M        -0.220  -0.338  -0.685   0.069  -0.084  -0.672  -0.191  -0.359  -0.896
35    V        -3.501  -3.356  -3.040  -3.099  -2.947  -2.509  -2.647  -2.544  -2.124
36    W         0.692   0.695   0.731   0.963   0.962   0.972   0.713   0.721   0.766
37    N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
38    A         0.692   0.695   0.731   0.665   0.662   0.727   0.713   0.721   0.766
39    M        -0.909  -0.778  -0.705  -1.039  -0.852  -0.736  -1.226  -1.027  -0.929
40    I         0.692   0.695   0.731   0.835   0.844   0.868   0.713   0.721   0.766
41    I         0.692   0.695   0.731   0.835   0.844   0.868   0.713   0.721   0.766
42    G         0.692   0.695   0.731   0.919   0.918   0.936   0.713   0.721   0.766
43    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
44    A        -0.220  -0.136  -0.675  -0.108  -0.020  -0.806  -0.191  -0.087  -0.880
45    D        -0.220  -0.338  -0.685  -0.321  -0.437  -0.951  -0.191  -0.359  -0.896
46    T         0.692   0.695   0.731   0.765   0.761   0.810   0.713   0.721   0.766
47    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
48    Y        -0.909  -0.778  -0.705  -0.860  -0.663  -0.593  -1.226  -1.027  -0.929
49    E         0.692   0.695   0.731   0.639   0.659   0.706   0.713   0.721   0.766
50    D         0.692   0.695   0.731   0.442   0.481   0.544   0.713   0.721   0.766
51    G         0.692   0.695   0.731   0.919   0.918   0.936   0.713   0.721   0.766
52    T         0.692   0.695   0.731   0.765   0.761   0.810   0.713   0.721   0.766
53    F         0.692   0.695   0.731   0.830   0.834   0.864   0.713   0.721   0.766
54    R        -0.220  -0.345  -0.686  -0.024  -0.188  -0.682  -0.191  -0.369  -0.898
55    L        -0.220  -0.338  -0.685  -0.090  -0.234  -0.716  -0.191  -0.359  -0.896
56    L        -1.666  -1.596  -1.568  -1.730  -1.679  -1.512  -1.743  -1.689  -1.531
57    L        -0.220  -0.289  -0.681  -0.090  -0.174  -0.710  -0.191  -0.290  -0.890
58    E        -2.504  -2.509  -2.184  -2.377  -2.386  -1.873  -2.260  -2.264  -1.832
59    F         0.692   0.695   0.731   0.830   0.834   0.864   0.713   0.721   0.766
60    D        -0.220  -0.289  -0.681  -0.321  -0.374  -0.945  -0.191  -0.290  -0.890
61    E         0.692   0.695   0.731   0.639   0.659   0.706   0.713   0.721   0.766
62    E        -1.487  -1.255  -1.552  -1.277  -0.948  -1.517  -1.484  -1.206  -1.511
63    Y         0.692   0.695   0.731   0.889   0.891   0.912   0.713   0.721   0.766
64    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
65    N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
66    K         0.692   0.695   0.731   0.800   0.808   0.839   0.713   0.721   0.766
67    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
68    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
69    H        -2.924  -2.961  -2.655  -2.457  -2.599  -2.204  -2.389  -2.420  -2.008
70    V         0.692   0.695   0.731   0.659   0.653   0.723   0.713   0.721   0.766
71    K         0.692   0.695   0.731   0.800   0.808   0.839   0.713   0.721   0.766
72    F         0.692   0.695   0.731   0.830   0.834   0.864   0.713   0.721   0.766
73    L        -1.927  -1.903  -1.580  -1.999  -1.988  -1.510  -2.001  -1.981  -1.544
74    S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
75    E        -1.088  -1.307  -1.556  -0.818  -1.093  -1.430  -0.967  -1.245  -1.516
76    M         0.692   0.695   0.731   0.830   0.837   0.864   0.713   0.721   0.766
77    F         0.692   0.695   0.731   0.830   0.834   0.864   0.713   0.721   0.766
78    H         0.692   0.695   0.731   0.982   0.983   0.988   0.713   0.721   0.766
79    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
80    N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
81    V         0.692   0.695   0.731   0.659   0.653   0.723   0.713   0.721   0.766
82    Y         0.692   0.695   0.731   0.889   0.891   0.912   0.713   0.721   0.766
83    A        -0.220  -0.338  -0.685  -0.108  -0.272  -0.825  -0.191  -0.359  -0.896
84    N        -1.666  -1.682  -1.572  -1.763  -1.796  -1.570  -1.743  -1.758  -1.535
85    G         0.692   0.695   0.731   0.919   0.918   0.936   0.713   0.721   0.766
86    E         0.692   0.695   0.731   0.639   0.659   0.706   0.713   0.721   0.766
87    I        -0.909  -0.778  -0.705  -1.050  -0.851  -0.744  -1.226  -1.027  -0.929
88    C         0.692   0.695   0.731   1.040   1.038   1.036   0.713   0.721   0.766
89    L         0.692   0.695   0.731   0.644   0.650   0.711   0.713   0.721   0.766
90    D         0.692   0.695   0.731   0.442   0.481   0.544   0.713   0.721   0.766
91    I         0.692   0.695   0.731   0.835   0.844   0.868   0.713   0.721   0.766
92    L         0.692   0.695   0.731   0.644   0.650   0.711   0.713   0.721   0.766
93    Q         0.692   0.695   0.731   0.870   0.861   0.896   0.713   0.721   0.766
94    N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
95    R         0.692   0.695   0.731   0.715   0.712   0.769   0.713   0.721   0.766
96    W         0.692   0.695   0.731   0.963   0.962   0.972   0.713   0.721   0.766
97    T        -0.909  -0.778  -0.705  -1.155  -0.959  -0.831  -1.226  -1.027  -0.929
98    P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
99    T         0.692   0.695   0.731   0.765   0.761   0.810   0.713   0.721   0.766
100   Y         0.692   0.695   0.731   0.889   0.891   0.912   0.713   0.721   0.766
101   D         0.692   0.695   0.731   0.442   0.481   0.544   0.713   0.721   0.766
102   V         0.692   0.695   0.731   0.659   0.653   0.723   0.713   0.721   0.766
103   A        -0.669  -0.568  -0.700  -0.742  -0.603  -0.855  -0.838  -0.695  -0.921
104   S        -0.909  -0.942  -0.730  -1.210  -1.293  -0.920  -1.226  -1.301  -0.969
105   I        -0.220  -0.289  -0.681   0.076  -0.012  -0.653  -0.191  -0.290  -0.890
106   L         0.692   0.695   0.731   0.644   0.650   0.711   0.713   0.721   0.766
107   T         0.692   0.695   0.731   0.765   0.761   0.810   0.713   0.721   0.766
108   S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
109   I        -0.669  -0.687  -0.716  -0.547  -0.593  -0.725  -0.838  -0.880  -0.947
110   Q         0.692   0.695   0.731   0.870   0.861   0.896   0.713   0.721   0.766
111   S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
112   L         0.692   0.695   0.731   0.644   0.650   0.711   0.713   0.721   0.766
113   F        -0.909  -0.778  -0.705  -1.052  -0.856  -0.746  -1.226  -1.027  -0.929
114   N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
115   D         0.692   0.695   0.731   0.442   0.481   0.544   0.713   0.721   0.766
116   P         0.692   0.695   0.731   0.541   0.555   0.626   0.713   0.721   0.766
117   N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
118   P        -2.504  -2.514  -2.186  -2.445  -2.458  -1.962  -2.260  -2.265  -1.834
119   A        -1.666  -1.682  -1.572  -1.752  -1.782  -1.516  -1.743  -1.758  -1.535
120   S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
121   P        -0.220  -0.289  -0.681  -0.210  -0.290  -0.837  -0.191  -0.290  -0.890
122   A         0.692   0.695   0.731   0.665   0.662   0.727   0.713   0.721   0.766
123   N         0.692   0.695   0.731   0.690   0.693   0.748   0.713   0.721   0.766
124   V        -0.220  -0.345  -0.686  -0.099  -0.274  -0.785  -0.191  -0.369  -0.898
125   E         0.692   0.695   0.731   0.639   0.659   0.706   0.713   0.721   0.766
126   A         0.692   0.695   0.731   0.665   0.662   0.727   0.713   0.721   0.766
127   A        -0.669  -0.760  -0.721  -0.742  -0.924  -0.898  -0.838  -0.997  -0.954
128   T        -2.346  -2.424  -2.182  -2.113  -2.212  -1.828  -2.130  -2.185  -1.830
129   L         0.692   0.695   0.731   0.644   0.650   0.711   0.713   0.721   0.766
130   F        -1.666  -1.661  -1.567  -1.399  -1.359  -1.226  -1.743  -1.711  -1.529
131   K        -1.088  -1.095  -1.543  -0.667  -0.704  -1.335  -0.967  -0.996  -1.501
132   D        -0.220  -0.345  -0.686  -0.321  -0.446  -0.953  -0.191  -0.369  -0.898
133   H        -0.669  -0.763  -0.722  -0.397  -0.581  -0.628  -0.838  -1.003  -0.957
134   K        -0.986  -0.945  -0.729  -1.134  -1.090  -0.750  -1.355  -1.306  -0.968
135   S        -1.487  -1.646  -1.571  -1.422  -1.652  -1.470  -1.484  -1.692  -1.534
136   Q        -1.487  -1.490  -1.566  -1.241  -1.322  -1.468  -1.484  -1.533  -1.528
137   Y         0.692   0.695   0.731   0.889   0.891   0.912   0.713   0.721   0.766
138   V        -2.243  -2.288  -2.170  -1.959  -2.028  -1.831  -2.001  -2.037  -1.821
139   K        -0.220  -0.345  -0.686   0.049  -0.111  -0.662  -0.191  -0.369  -0.898
140   R         0.692   0.695   0.731   0.715   0.712   0.769   0.713   0.721   0.766
141   V         0.692   0.695   0.731   0.659   0.653   0.723   0.713   0.721   0.766
142   K        -0.909  -0.778  -0.705  -1.006  -0.811  -0.714  -1.226  -1.027  -0.929
143   E        -1.088  -1.307  -1.556  -0.883  -1.168  -1.602  -0.967  -1.245  -1.516
144   T         0.692   0.695   0.731   0.765   0.761   0.810   0.713   0.721   0.766
145   V         0.692   0.695   0.731   0.659   0.653   0.723   0.713   0.721   0.766
146   E         0.692   0.695   0.731   0.639   0.659   0.706   0.713   0.721   0.766
147   K        -2.243  -2.333  -2.179  -2.014  -2.164  -2.044  -2.001  -2.081  -1.828
148   S         0.692   0.695   0.731   0.567   0.573   0.647   0.713   0.721   0.766
149   W         0.692   0.695   0.731   0.963   0.962   0.972   0.713   0.721   0.766
150   E        -1.487  -1.496  -1.561  -1.417  -1.411  -1.518  -1.484  -1.487  -1.522
151   D        -0.519  -0.593  -0.715  -0.884  -0.993  -1.133  -0.610  -0.734  -0.945
152   D        -0.519  -0.403  -0.712  -0.851  -0.691  -1.060  -0.610  -0.451  -0.940
153   M        -0.937  -0.945  -0.730  -1.238  -1.327  -0.983  -1.272  -1.306  -0.969
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   D        -0.937  -0.832  -0.720  -1.461  -1.244  -1.103  -1.272  -1.115  -0.953
161   D         0.692   0.695   0.731   0.283   0.300   0.414   0.713   0.721   0.766
162   M        -0.937  -0.945  -0.730  -1.069  -1.125  -0.802  -1.272  -1.306  -0.969
163   D        -0.519  -0.429  -0.712  -0.853  -0.725  -1.064  -0.610  -0.488  -0.941
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   D        -0.519  -0.612  -0.715  -0.853  -0.982  -1.067  -0.610  -0.763  -0.946
166   D        -1.608  -1.398  -1.570  -1.787  -1.461  -1.841  -1.603  -1.357  -1.532
167   D         0.692   0.695   0.731   0.283   0.300   0.414   0.713   0.721   0.766
168   D        -0.519  -0.385  -0.711  -0.652  -0.450  -1.079  -0.610  -0.426  -0.939
169   D         0.692   0.695   0.731   0.283   0.300   0.414   0.713   0.721   0.766
170   D        -1.608  -1.589  -1.572  -1.907  -1.880  -1.759  -1.603  -1.598  -1.534
171   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   D        -1.666  -1.675  -1.560  -1.970  -1.939  -1.749  -1.743  -1.731  -1.522
* 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/P06104
Output conservation file - output/P06104
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
