1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    M         0.370   0.389   0.400   1.223   1.124   0.951   0.361   0.393   0.409
42    A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
43    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
44    T         0.370   0.389   0.400   0.506   0.510   0.505   0.361   0.393   0.409
45    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
46    Q        -0.878  -1.845  -2.052  -0.281  -1.493  -1.965  -0.640  -1.888  -2.218
47    T         0.370   0.389   0.400   0.506   0.510   0.505   0.361   0.393   0.409
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
51    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
52    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
53    S        -0.878  -1.845  -2.052  -0.329  -1.449  -1.869  -0.640  -1.888  -2.218
54    T         0.370   0.389   0.400   0.506   0.510   0.505   0.361   0.393   0.409
55    G         0.370   0.389   0.400   0.642   0.609   0.589   0.361   0.393   0.409
56    G         0.370   0.389   0.400   0.642   0.609   0.589   0.361   0.393   0.409
57    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
58    A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
59    P         0.370   0.389   0.400   0.866   0.826   0.729   0.361   0.393   0.409
60    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
61    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
62    Q         0.370   0.389   0.400   0.537   0.544   0.524   0.361   0.393   0.409
63    L        -0.878  -1.845  -2.052  -0.711  -1.840  -2.071  -0.640  -1.888  -2.218
64    A        -0.878  -1.845  -2.052  -1.022  -2.120  -2.248  -0.640  -1.888  -2.218
65    S         0.370   0.389   0.400   0.469   0.543   0.482   0.361   0.393   0.409
66    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
67    A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
68    A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
69    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
70    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
71    S        -2.207  -1.920  -2.051  -1.942  -1.768  -2.285  -2.242  -1.993  -2.217
72    A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
73    P        -0.878  -1.845  -2.052   0.006  -1.370  -2.087  -0.640  -1.888  -2.218
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    S        -4.533  -4.960  -4.515  -3.536  -4.506  -3.962  -3.777  -4.244  -3.545
78    T        -1.642  -2.261  -2.058  -1.069  -2.141  -1.991  -1.508  -2.486  -2.227
79    G         0.370   0.389   0.400   0.642   0.609   0.589   0.361   0.393   0.409
80    G         0.370   0.389   0.400   0.642   0.609   0.589   0.361   0.393   0.409
81    V         0.370   0.389   0.400   0.770   0.719   0.669   0.361   0.393   0.409
82    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
83    K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
84    P         0.370   0.389   0.400   0.866   0.826   0.729   0.361   0.393   0.409
85    H         0.370   0.389   0.400   1.158   1.058   0.910   0.361   0.393   0.409
86    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
87    Y         0.370   0.389   0.400   1.135   1.033   0.896   0.361   0.393   0.409
88    K        -2.207  -1.920  -2.051  -2.562  -2.340  -2.644  -2.242  -1.993  -2.217
89    P         0.370   0.389   0.400   0.866   0.826   0.729   0.361   0.393   0.409
90    G         0.370   0.389   0.400   0.642   0.609   0.589   0.361   0.393   0.409
91    T         0.370   0.389   0.400   0.506   0.510   0.505   0.361   0.393   0.409
92    V         0.370   0.389   0.400   0.770   0.719   0.669   0.361   0.393   0.409
93    A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
94    L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
95    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
96    E         0.370   0.389   0.400   0.684   0.659   0.616   0.361   0.393   0.409
97    I         0.370   0.389   0.400   0.715   0.675   0.635   0.361   0.393   0.409
98    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
99    R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
100   F        -2.947  -2.689  -2.056  -2.190  -2.266  -1.511  -3.310  -3.147  -2.224
101   Q         0.370   0.389   0.400   0.537   0.544   0.524   0.361   0.393   0.409
102   K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
103   S         0.370   0.389   0.400   0.469   0.543   0.482   0.361   0.393   0.409
104   T         0.370   0.389   0.400   0.506   0.510   0.505   0.361   0.393   0.409
105   E         0.370   0.389   0.400   0.684   0.659   0.616   0.361   0.393   0.409
106   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
107   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
108   I         0.370   0.389   0.400   0.715   0.675   0.635   0.361   0.393   0.409
109   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
110   K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
111   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
112   P         0.370   0.389   0.400   0.866   0.826   0.729   0.361   0.393   0.409
113   F         0.370   0.389   0.400   0.909   0.869   0.755   0.361   0.393   0.409
114   Q         0.370   0.389   0.400   0.537   0.544   0.524   0.361   0.393   0.409
115   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
116   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
117   V         0.370   0.389   0.400   0.770   0.719   0.669   0.361   0.393   0.409
118   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
119   E         0.370   0.389   0.400   0.684   0.659   0.616   0.361   0.393   0.409
120   I         0.370   0.389   0.400   0.715   0.675   0.635   0.361   0.393   0.409
121   A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
122   Q         0.370   0.389   0.400   0.537   0.544   0.524   0.361   0.393   0.409
123   D         0.370   0.389   0.400   0.974   0.910   0.796   0.361   0.393   0.409
124   F         0.370   0.389   0.400   0.909   0.869   0.755   0.361   0.393   0.409
125   K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
126   T        -1.642  -1.665  -2.056  -1.069  -1.286  -1.987  -1.508  -1.644  -2.224
127   D         0.370   0.389   0.400   0.974   0.910   0.796   0.361   0.393   0.409
128   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
129   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
130   F         0.370   0.389   0.400   0.909   0.869   0.755   0.361   0.393   0.409
131   Q         0.370   0.389   0.400   0.537   0.544   0.524   0.361   0.393   0.409
132   S         0.370   0.389   0.400   0.469   0.543   0.482   0.361   0.393   0.409
133   S         0.370   0.389   0.400   0.469   0.543   0.482   0.361   0.393   0.409
134   A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
135   I         0.370   0.389   0.400   0.715   0.675   0.635   0.361   0.393   0.409
136   G         0.370   0.389   0.400   0.642   0.609   0.589   0.361   0.393   0.409
137   A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
138   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
139   Q         0.370   0.389   0.400   0.537   0.544   0.524   0.361   0.393   0.409
140   E         0.370   0.389   0.400   0.684   0.659   0.616   0.361   0.393   0.409
141   S        -3.163  -2.584  -2.058  -3.595  -3.016  -2.314  -3.643  -2.981  -2.227
142   V         0.370   0.389   0.400   0.770   0.719   0.669   0.361   0.393   0.409
143   E         0.370   0.389   0.400   0.684   0.659   0.616   0.361   0.393   0.409
144   A        -0.878  -0.976  -2.049  -1.035  -1.115  -2.325  -0.640  -0.791  -2.213
145   Y         0.370   0.389   0.400   1.135   1.033   0.896   0.361   0.393   0.409
146   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
147   V         0.370   0.389   0.400   0.770   0.719   0.669   0.361   0.393   0.409
148   S        -2.207  -1.685  -2.051  -1.750  -1.266  -1.923  -2.242  -1.671  -2.217
149   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
150   F         0.370   0.389   0.400   0.909   0.869   0.755   0.361   0.393   0.409
151   E         0.370   0.389   0.400   0.684   0.659   0.616   0.361   0.393   0.409
152   D         0.370   0.389   0.400   0.974   0.910   0.796   0.361   0.393   0.409
153   T         0.370   0.389   0.400   0.506   0.510   0.505   0.361   0.393   0.409
154   N         0.370   0.389   0.400   1.252   1.156   0.969   0.361   0.393   0.409
155   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
156   A        -3.163  -2.059  -2.049  -2.846  -1.374  -1.858  -3.643  -2.191  -2.213
157   A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
158   I         0.370   0.389   0.400   0.715   0.675   0.635   0.361   0.393   0.409
159   H         0.370   0.389   0.400   1.158   1.058   0.910   0.361   0.393   0.409
160   A        -2.207  -1.920  -2.051  -2.426  -2.221  -2.248  -2.242  -1.993  -2.217
161   K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
162   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
163   V         0.370   0.389   0.400   0.770   0.719   0.669   0.361   0.393   0.409
164   T         0.370   0.389   0.400   0.506   0.510   0.505   0.361   0.393   0.409
165   I         0.370   0.389   0.400   0.715   0.675   0.635   0.361   0.393   0.409
166   Q         0.370   0.389   0.400   0.537   0.544   0.524   0.361   0.393   0.409
167   K        -3.384  -3.180  -3.491  -3.066  -3.016  -3.230  -3.043  -2.897  -3.101
168   K         0.370   0.389   0.400  -0.116  -0.015   0.118   0.361   0.393   0.409
169   D         0.370   0.389   0.400   0.974   0.910   0.796   0.361   0.393   0.409
170   I        -3.163  -2.584  -2.058  -2.627  -2.225  -1.565  -3.643  -2.981  -2.227
171   K        -4.248  -4.012  -3.492  -4.137  -3.681  -3.065  -4.244  -3.786  -3.102
172   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
173   A         0.370   0.389   0.400  -0.214  -0.109   0.057   0.361   0.393   0.409
174   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
175   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
176   L         0.370   0.389   0.400   0.090   0.157   0.247   0.361   0.393   0.409
177   R         0.370   0.389   0.400  -0.346  -0.151  -0.025   0.361   0.393   0.409
178   G         0.370   0.389   0.400   0.642   0.609   0.589   0.361   0.393   0.409
179   E         0.370   0.389   0.400   0.684   0.659   0.616   0.361   0.393   0.409
180   R         0.370   0.389   0.400  -0.351  -0.219  -0.028   0.361   0.393   0.409
181   S        -0.938  -1.444  -2.054  -0.343  -0.926  -1.663  -0.702  -1.355  -2.221
* 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/P61830
Output conservation file - output/P61830
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
