1     M         0.629   0.639   0.697   0.892   0.892   0.921   0.654   0.668   0.741
2     G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
3     L        -1.228  -1.191  -1.670  -1.464  -1.398  -1.923  -1.147  -1.100  -1.627
4     F        -2.670  -2.768  -2.327  -2.624  -2.707  -2.041  -2.588  -2.616  -1.963
5     A        -3.348  -3.372  -2.818  -3.356  -3.408  -2.657  -2.948  -2.890  -2.147
6     S         0.629   0.639   0.697   0.756   0.788   0.822   0.654   0.668   0.741
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    K        -0.318  -0.207  -0.773  -0.119   0.017  -0.792  -0.307  -0.160  -0.989
11    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
12    F         0.629   0.639   0.697   0.808   0.817   0.860   0.654   0.668   0.741
13    S        -2.828  -2.695  -2.327  -2.754  -2.539  -2.064  -2.708  -2.537  -1.962
14    N        -2.252  -2.134  -1.705  -2.599  -2.416  -1.719  -2.468  -2.304  -1.666
15    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
16    F        -1.228  -1.380  -1.674  -0.895  -1.120  -1.784  -1.147  -1.336  -1.631
17    G        -0.318  -0.207  -0.773  -0.288  -0.157  -0.921  -0.307  -0.160  -0.989
18    N        -2.828  -2.684  -2.329  -2.795  -2.602  -2.022  -2.708  -2.526  -1.964
19    K        -0.809  -0.751  -0.801  -0.818  -0.736  -0.883  -1.027  -0.941  -1.035
20    E         0.629   0.639   0.697   0.559   0.574   0.679   0.654   0.668   0.741
21    M         0.629   0.639   0.697   0.892   0.892   0.921   0.654   0.668   0.741
22    R         0.629   0.639   0.697   0.661   0.663   0.753   0.654   0.668   0.741
23    I         0.629   0.639   0.697   0.579   0.597   0.693   0.654   0.668   0.741
24    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
25    M         0.629   0.639   0.697   0.892   0.892   0.921   0.654   0.668   0.741
26    V         0.629   0.639   0.697   0.646   0.646   0.742   0.654   0.668   0.741
27    G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
28    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
29    D         0.629   0.639   0.697   0.680   0.691   0.767   0.654   0.668   0.741
30    G        -0.809  -0.872  -0.808  -0.888  -1.005  -0.979  -1.027  -1.135  -1.046
31    A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
32    G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
33    K         0.629   0.639   0.697   0.685   0.701   0.770   0.654   0.668   0.741
34    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
35    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
36    V        -0.809  -0.872  -0.808  -0.925  -1.042  -0.964  -1.027  -1.135  -1.046
37    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
38    Y         0.629   0.639   0.697   0.869   0.868   0.904   0.654   0.668   0.741
39    K         0.629   0.639   0.697   0.685   0.701   0.770   0.654   0.668   0.741
40    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
41    K         0.629   0.639   0.697   0.685   0.701   0.770   0.654   0.668   0.741
42    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
43    G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
44    E         0.629   0.639   0.697   0.559   0.574   0.679   0.654   0.668   0.741
45    V        -1.099  -1.099  -0.820  -1.429  -1.456  -0.985  -1.507  -1.518  -1.067
46    I        -0.318  -0.475  -0.778  -0.180  -0.399  -0.898  -0.307  -0.526  -0.998
47    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
48    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
49    I         0.629   0.639   0.697   0.579   0.597   0.693   0.654   0.668   0.741
50    P         0.629   0.639   0.697   0.939   0.941   0.955   0.654   0.668   0.741
51    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
52    I         0.629   0.639   0.697   0.579   0.597   0.693   0.654   0.668   0.741
53    G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
54    F         0.629   0.639   0.697   0.808   0.817   0.860   0.654   0.668   0.741
55    N         0.629   0.639   0.697   0.670   0.682   0.760   0.654   0.668   0.741
56    V         0.629   0.639   0.697   0.646   0.646   0.742   0.654   0.668   0.741
57    E         0.629   0.639   0.697   0.559   0.574   0.679   0.654   0.668   0.741
58    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
59    V         0.629   0.639   0.697   0.646   0.646   0.742   0.654   0.668   0.741
60    Q        -1.228  -1.125  -1.668  -1.043  -0.939  -1.636  -1.147  -1.049  -1.624
61    Y         0.629   0.639   0.697   0.869   0.868   0.904   0.654   0.668   0.741
62    K        -0.318  -0.220  -0.774  -0.131  -0.012  -0.832  -0.307  -0.177  -0.991
63    N         0.629   0.639   0.697   0.670   0.682   0.760   0.654   0.668   0.741
64    I        -0.318  -0.465  -0.781  -0.239  -0.424  -0.916  -0.307  -0.511  -1.002
65    S        -1.228  -1.359  -1.677  -0.864  -1.027  -1.591  -1.147  -1.310  -1.635
66    F         0.629   0.639   0.697   0.808   0.817   0.860   0.654   0.668   0.741
67    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
68    V         0.629   0.639   0.697   0.646   0.646   0.742   0.654   0.668   0.741
69    W         0.629   0.639   0.697   0.934   0.931   0.952   0.654   0.668   0.741
70    D         0.629   0.639   0.697   0.680   0.691   0.767   0.654   0.668   0.741
71    V        -0.318  -0.465  -0.781  -0.180  -0.384  -0.903  -0.307  -0.511  -1.002
72    G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
73    G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
74    Q         0.629   0.639   0.697   0.794   0.813   0.850   0.654   0.668   0.741
75    D         0.629   0.639   0.697   0.680   0.691   0.767   0.654   0.668   0.741
76    R        -0.809  -0.961  -0.817  -0.818  -1.092  -0.913  -1.027  -1.282  -1.061
77    I         0.629   0.639   0.697   0.579   0.597   0.693   0.654   0.668   0.741
78    R         0.629   0.639   0.697   0.661   0.663   0.753   0.654   0.668   0.741
79    S        -0.318  -0.475  -0.778   0.133  -0.072  -0.645  -0.307  -0.526  -0.998
80    L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
81    W         0.629   0.639   0.697   0.934   0.931   0.952   0.654   0.668   0.741
82    R         0.629   0.639   0.697   0.661   0.663   0.753   0.654   0.668   0.741
83    H        -1.236  -1.169  -0.820  -1.215  -1.121  -0.624  -1.747  -1.640  -1.066
84    Y         0.629   0.639   0.697   0.869   0.868   0.904   0.654   0.668   0.741
85    Y        -0.809  -0.961  -0.817  -0.640  -0.902  -0.742  -1.027  -1.282  -1.061
86    R        -0.809  -0.872  -0.808  -0.711  -0.828  -0.832  -1.027  -1.135  -1.046
87    N         0.629   0.639   0.697   0.670   0.682   0.760   0.654   0.668   0.741
88    T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
89    E        -0.809  -0.872  -0.808  -0.739  -0.858  -0.878  -1.027  -1.135  -1.046
90    G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
91    V        -0.809  -0.961  -0.817  -0.925  -1.197  -0.980  -1.027  -1.282  -1.061
92    I         0.629   0.639   0.697   0.579   0.597   0.693   0.654   0.668   0.741
93    F        -0.318  -0.465  -0.781   0.017  -0.166  -0.682  -0.307  -0.511  -1.002
94    V         0.629   0.639   0.697   0.646   0.646   0.742   0.654   0.668   0.741
95    V         0.629   0.639   0.697   0.646   0.646   0.742   0.654   0.668   0.741
96    D         0.629   0.639   0.697   0.680   0.691   0.767   0.654   0.668   0.741
97    S         0.629   0.639   0.697   0.756   0.788   0.822   0.654   0.668   0.741
98    N         0.629   0.639   0.697   0.670   0.682   0.760   0.654   0.668   0.741
99    D         0.629   0.639   0.697   0.680   0.691   0.767   0.654   0.668   0.741
100   R         0.629   0.639   0.697   0.661   0.663   0.753   0.654   0.668   0.741
101   S        -2.094  -2.115  -2.315  -1.743  -1.785  -2.141  -1.867  -1.889  -1.952
102   R         0.629   0.639   0.697   0.661   0.663   0.753   0.654   0.668   0.741
103   I        -0.318  -0.310  -0.777  -0.239  -0.225  -0.909  -0.307  -0.296  -0.995
104   G        -3.925  -3.906  -3.221  -3.671  -3.654  -2.690  -3.188  -3.103  -2.270
105   E        -0.318  -0.465  -0.781  -0.254  -0.438  -0.914  -0.307  -0.511  -1.002
106   A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
107   R        -0.318  -0.220  -0.774  -0.107  -0.007  -0.690  -0.307  -0.177  -0.991
108   E         0.629   0.639   0.697   0.559   0.574   0.679   0.654   0.668   0.741
109   V        -0.809  -0.872  -0.808  -0.944  -1.063  -0.976  -1.027  -1.135  -1.046
110   M        -0.318  -0.475  -0.778  -0.622  -0.785  -1.061  -0.307  -0.526  -0.998
111   Q         0.629   0.639   0.697   0.794   0.813   0.850   0.654   0.668   0.741
112   R        -1.915  -1.679  -1.678  -1.968  -1.576  -1.567  -2.108  -1.745  -1.636
113   M        -0.318  -0.465  -0.781   0.017  -0.204  -0.916  -0.307  -0.511  -1.002
114   L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
115   N         0.629   0.639   0.697   0.670   0.682   0.760   0.654   0.668   0.741
116   E        -0.318  -0.465  -0.781  -0.254  -0.438  -0.914  -0.307  -0.511  -1.002
117   D         0.629   0.639   0.697   0.680   0.691   0.767   0.654   0.668   0.741
118   E         0.629   0.639   0.697   0.559   0.574   0.679   0.654   0.668   0.741
119   L        -0.318  -0.283  -0.774  -0.665  -0.595  -1.197  -0.307  -0.260  -0.991
120   R        -0.318  -0.333  -0.773  -0.152  -0.180  -0.835  -0.307  -0.327  -0.989
121   N        -0.809  -0.872  -0.808  -0.820  -0.939  -0.894  -1.027  -1.135  -1.046
122   A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
123   A        -2.491  -2.492  -2.322  -2.825  -2.823  -2.342  -2.348  -2.331  -1.958
124   W        -0.318  -0.475  -0.778  -0.616  -0.777  -1.041  -0.307  -0.526  -0.998
125   L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
126   V         0.629   0.639   0.697   0.646   0.646   0.742   0.654   0.668   0.741
127   F        -0.809  -0.652  -0.795  -0.830  -0.574  -1.012  -1.027  -0.788  -1.025
128   A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
129   N         0.629   0.639   0.697   0.670   0.682   0.760   0.654   0.668   0.741
130   K         0.629   0.639   0.697   0.685   0.701   0.770   0.654   0.668   0.741
131   Q         0.629   0.639   0.697   0.794   0.813   0.850   0.654   0.668   0.741
132   D         0.629   0.639   0.697   0.680   0.691   0.767   0.654   0.668   0.741
133   L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
134   P         0.629   0.639   0.697   0.939   0.941   0.955   0.654   0.668   0.741
135   E        -0.809  -0.872  -0.808  -0.860  -0.984  -0.951  -1.027  -1.135  -1.046
136   A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
137   M         0.629   0.639   0.697   0.892   0.892   0.921   0.654   0.668   0.741
138   S        -2.094  -2.315  -2.322  -1.685  -1.997  -2.008  -1.867  -2.105  -1.958
139   A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
140   A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
141   E         0.629   0.639   0.697   0.559   0.574   0.679   0.654   0.668   0.741
142   I         0.629   0.639   0.697   0.579   0.597   0.693   0.654   0.668   0.741
143   T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
144   E        -0.809  -0.736  -0.803  -0.935  -0.829  -0.952  -1.027  -0.918  -1.038
145   K         0.629   0.639   0.697   0.685   0.701   0.770   0.654   0.668   0.741
146   L        -0.318  -0.333  -0.773  -0.622  -0.612  -1.055  -0.307  -0.327  -0.989
147   G        -0.318  -0.207  -0.773  -0.290  -0.159  -0.927  -0.307  -0.160  -0.989
148   L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
149   H        -0.809  -0.879  -0.812  -0.448  -0.589  -0.657  -1.027  -1.146  -1.053
150   S         0.629   0.639   0.697   0.756   0.788   0.822   0.654   0.668   0.741
151   I        -1.236  -1.165  -0.821  -2.007  -1.891  -1.244  -1.747  -1.634  -1.067
152   R         0.629   0.639   0.697   0.661   0.663   0.753   0.654   0.668   0.741
153   N        -1.675  -1.664  -1.686  -1.427  -1.469  -1.462  -1.747  -1.761  -1.646
154   R         0.629   0.639   0.697   0.661   0.663   0.753   0.654   0.668   0.741
155   P        -1.228  -1.132  -1.672  -0.656  -0.550  -1.410  -1.147  -1.029  -1.628
156   W         0.629   0.639   0.697   0.934   0.931   0.952   0.654   0.668   0.741
157   F        -0.809  -0.896  -0.812  -0.598  -0.765  -0.730  -1.027  -1.176  -1.054
158   I         0.629   0.639   0.697   0.579   0.597   0.693   0.654   0.668   0.741
159   Q         0.629   0.639   0.697   0.794   0.813   0.850   0.654   0.668   0.741
160   A        -0.318  -0.207  -0.773  -0.153  -0.010  -0.812  -0.307  -0.160  -0.989
161   T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
162   C         0.629   0.639   0.697   1.063   1.055   1.046   0.654   0.668   0.741
163   A         0.629   0.639   0.697   0.651   0.674   0.746   0.654   0.668   0.741
164   T         0.629   0.639   0.697   0.554   0.585   0.675   0.654   0.668   0.741
165   S        -1.236  -1.126  -0.817  -1.609  -1.383  -0.926  -1.747  -1.566  -1.061
166   G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
167   E        -0.809  -0.872  -0.808  -0.851  -0.976  -0.946  -1.027  -1.135  -1.046
168   G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
169   L        -0.318  -0.465  -0.781  -0.665  -0.828  -1.207  -0.307  -0.511  -1.002
170   Y        -0.318  -0.310  -0.777   0.070   0.068  -0.663  -0.307  -0.296  -0.995
171   E         0.629   0.639   0.697   0.559   0.574   0.679   0.654   0.668   0.741
172   G         0.629   0.639   0.697   0.525   0.537   0.654   0.654   0.668   0.741
173   L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
174   E        -0.318  -0.310  -0.777  -0.254  -0.242  -0.907  -0.307  -0.296  -0.995
175   W         0.629   0.639   0.697   0.934   0.931   0.952   0.654   0.668   0.741
176   L         0.629   0.639   0.697   0.164   0.203   0.391   0.654   0.668   0.741
177   S        -0.318  -0.465  -0.781  -0.062  -0.234  -0.806  -0.307  -0.511  -1.002
178   N        -1.099  -1.087  -0.818  -1.440  -1.424  -0.983  -1.507  -1.497  -1.063
179   S        -3.246  -3.199  -2.815  -3.046  -2.990  -2.480  -2.828  -2.749  -2.145
180   L        -0.318  -0.333  -0.773  -0.656  -0.650  -1.165  -0.307  -0.327  -0.989
181   K        -0.318  -0.333  -0.773  -0.148  -0.165  -0.885  -0.307  -0.327  -0.989
182   N        -0.809  -0.802  -0.807  -0.825  -0.825  -0.891  -1.027  -1.023  -1.044
183   S        -3.428  -3.351  -2.818  -3.242  -3.149  -2.445  -2.993  -2.873  -2.147
184   T        -2.839  -2.591  -2.326  -2.823  -2.551  -2.078  -2.720  -2.473  -1.962
185   -        -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/P11076
Output conservation file - output/P11076
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
