1     M         1.084   1.091   1.101   1.668   1.669   1.667   1.122   1.128   1.139
2     K         1.084   1.091   1.101   1.505   1.509   1.510   1.122   1.128   1.139
3     F         1.084   1.091   1.101   1.657   1.657   1.656   1.122   1.128   1.139
4     S        -0.518  -0.424  -0.545  -1.324  -1.142  -1.357  -0.607  -0.464  -0.639
5     T        -0.518  -0.578  -0.578  -0.281  -0.437  -0.491  -0.607  -0.692  -0.688
6     I        -1.681  -1.648  -1.602  -2.015  -1.842  -1.862  -1.471  -1.423  -1.351
7     F        -1.681  -1.648  -1.602  -0.974  -0.911  -0.864  -1.471  -1.423  -1.351
8     G        -1.681  -1.648  -1.602  -0.739  -0.710  -0.639  -1.471  -1.423  -1.351
9     A        -1.681  -1.648  -1.602  -0.995  -0.987  -0.884  -1.471  -1.423  -1.351
10    T        -1.681  -1.648  -1.602  -2.432  -2.352  -2.261  -1.471  -1.423  -1.351
11    T        -0.518  -0.578  -0.578  -0.743  -0.879  -0.904  -0.607  -0.692  -0.688
12    V        -0.518  -0.490  -0.560  -0.578  -0.530  -0.706  -0.607  -0.561  -0.661
13    M        -1.681  -1.648  -1.602  -1.160  -1.059  -1.042  -1.471  -1.423  -1.351
14    T        -1.681  -1.648  -1.602  -2.432  -2.402  -2.261  -1.471  -1.423  -1.351
15    A        -0.518  -0.578  -0.578  -0.391  -0.499  -0.510  -0.607  -0.692  -0.688
16    V         1.084   1.091   1.101   1.190   1.198   1.209   1.122   1.128   1.139
17    S        -0.661  -0.647  -0.604  -1.165  -1.139  -1.047  -0.823  -0.797  -0.728
18    A         1.084   1.091   1.101   1.035   1.050   1.060   1.122   1.128   1.139
19    A        -0.518  -0.490  -0.560  -0.275  -0.233  -0.286  -0.607  -0.561  -0.661
20    A         1.084   1.091   1.101   1.035   1.050   1.060   1.122   1.128   1.139
21    V        -0.518  -0.490  -0.560  -0.391  -0.345  -0.475  -0.607  -0.561  -0.661
22    S        -0.518  -0.490  -0.560  -1.324  -1.268  -1.387  -0.607  -0.561  -0.661
23    S        -1.681  -1.648  -1.602  -1.925  -1.973  -1.775  -1.471  -1.423  -1.351
24    V        -0.518  -0.424  -0.545  -0.641  -0.446  -0.742  -0.607  -0.464  -0.639
25    M        -0.518  -0.578  -0.578  -0.737  -0.753  -0.671  -0.607  -0.692  -0.688
26    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
27    T        -1.681  -1.648  -1.602  -1.520  -1.529  -1.387  -1.471  -1.423  -1.351
28    K         1.084   1.091   1.101   1.505   1.509   1.510   1.122   1.128   1.139
29    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
30    I         1.084   1.091   1.101   1.493   1.500   1.499   1.122   1.128   1.139
31    T        -0.518  -0.490  -0.560  -0.862  -0.825  -0.868  -0.607  -0.561  -0.661
32    A         1.084   1.091   1.101   1.035   1.050   1.060   1.122   1.128   1.139
33    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
34    N         1.084   1.091   1.101   1.505   1.513   1.510   1.122   1.128   1.139
35    G         1.084   1.091   1.101   1.469   1.470   1.476   1.122   1.128   1.139
36    N        -1.681  -1.648  -1.602  -0.838  -0.790  -0.734  -1.471  -1.423  -1.351
37    N        -0.518  -0.578  -0.578   0.281   0.185   0.158  -0.607  -0.692  -0.688
38    V         1.084   1.091   1.101   1.200   1.206   1.218   1.122   1.128   1.139
39    Y         1.084   1.091   1.101   1.575   1.579   1.578   1.122   1.128   1.139
40    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
41    K         1.084   1.091   1.101   1.505   1.509   1.510   1.122   1.128   1.139
42    V         1.084   1.091   1.101   1.200   1.206   1.218   1.122   1.128   1.139
43    V         1.084   1.091   1.101   1.200   1.206   1.218   1.122   1.128   1.139
44    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
45    D         1.084   1.091   1.101   1.505   1.515   1.510   1.122   1.128   1.139
46    T        -0.518  -0.490  -0.560  -1.247  -1.193  -1.342  -0.607  -0.561  -0.661
47    A         1.084   1.091   1.101   1.035   1.050   1.060   1.122   1.128   1.139
48    D        -0.518  -0.490  -0.560  -0.107  -0.055  -0.220  -0.607  -0.561  -0.661
49    P         1.084   1.091   1.101   1.645   1.647   1.644   1.122   1.128   1.139
50    I        -0.518  -0.490  -0.560  -0.047  -0.004  -0.144  -0.607  -0.561  -0.661
51    I        -0.518  -0.490  -0.560   0.118   0.155   0.055  -0.607  -0.561  -0.661
52    S        -0.518  -0.578  -0.578  -1.247  -1.389  -1.387  -0.607  -0.692  -0.688
53    Y        -1.681  -1.648  -1.602  -0.981  -0.895  -0.871  -1.471  -1.423  -1.351
54    S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
55    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
56    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
57    R        -0.518  -0.490  -0.560   0.154   0.195   0.035  -0.607  -0.561  -0.661
58    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
59    V        -0.518  -0.578  -0.578  -0.862  -0.934  -0.883  -0.607  -0.692  -0.688
60    V        -0.518  -0.578  -0.578  -0.862  -0.934  -0.883  -0.607  -0.692  -0.688
61    V        -1.681  -1.648  -1.602  -0.953  -0.939  -0.844  -1.471  -1.423  -1.351
62    S        -0.518  -0.578  -0.578  -1.247  -1.389  -1.387  -0.607  -0.692  -0.688
63    N        -0.518  -0.424  -0.545   0.139   0.263   0.096  -0.607  -0.464  -0.639
64    S        -0.518  -0.578  -0.578  -0.338  -0.502  -0.568  -0.607  -0.692  -0.688
65    D        -0.518  -0.578  -0.578   0.065  -0.022  -0.027  -0.607  -0.692  -0.688
66    A         1.084   1.091   1.101   1.035   1.050   1.060   1.122   1.128   1.139
67    T        -0.518  -0.578  -0.578  -1.324  -1.443  -1.422  -0.607  -0.692  -0.688
68    Y         1.084   1.091   1.101   1.575   1.579   1.578   1.122   1.128   1.139
69    T        -0.518  -0.578  -0.578  -0.578  -0.728  -0.756  -0.607  -0.692  -0.688
70    K         1.084   1.091   1.101   1.505   1.509   1.510   1.122   1.128   1.139
71    V        -0.518  -0.578  -0.578  -0.862  -0.934  -0.883  -0.607  -0.692  -0.688
72    V        -1.681  -1.648  -1.602  -0.932  -0.922  -0.824  -1.471  -1.423  -1.351
73    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
74    E        -0.518  -0.490  -0.560   0.175   0.215   0.094  -0.607  -0.561  -0.661
75    G        -0.518  -0.490  -0.560  -0.140  -0.097  -0.250  -0.607  -0.561  -0.661
76    P         1.084   1.091   1.101   1.645   1.647   1.644   1.122   1.128   1.139
77    D        -0.518  -0.490  -0.560   0.185   0.221   0.132  -0.607  -0.561  -0.661
78    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
79    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
80    S        -0.518  -0.490  -0.560  -0.835  -0.795  -0.794  -0.607  -0.561  -0.661
81    E        -1.681  -1.648  -1.602  -0.953  -0.881  -0.844  -1.471  -1.423  -1.351
82    K        -0.518  -0.490  -0.560  -0.338  -0.284  -0.506  -0.607  -0.561  -0.661
83    S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
84    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
85    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
86    K        -0.518  -0.578  -0.578  -0.829  -0.858  -0.785  -0.607  -0.692  -0.688
87    T        -0.518  -0.578  -0.578  -0.281  -0.441  -0.491  -0.607  -0.692  -0.688
88    L        -1.681  -1.648  -1.602  -0.981  -0.914  -0.871  -1.471  -1.423  -1.351
89    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
90    L        -0.518  -0.578  -0.578   0.097   0.011   0.005  -0.607  -0.692  -0.688
91    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
92    N         1.084   1.091   1.101   1.505   1.513   1.510   1.122   1.128   1.139
93    G        -0.518  -0.578  -0.578  -0.849  -0.883  -0.811  -0.607  -0.692  -0.688
94    S        -0.518  -0.578  -0.578  -0.338  -0.500  -0.568  -0.607  -0.692  -0.688
95    G        -0.518  -0.578  -0.578   0.081  -0.010  -0.020  -0.607  -0.692  -0.688
96    S        -0.518  -0.578  -0.578  -0.373  -0.543  -0.599  -0.607  -0.692  -0.688
97    S        -0.518  -0.578  -0.578  -0.809  -0.953  -0.991  -0.607  -0.692  -0.688
98    T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
99    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   Y         1.084   1.091   1.101   1.575   1.579   1.578   1.122   1.128   1.139
102   T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
103   K         1.084   1.091   1.101   1.505   1.509   1.510   1.122   1.128   1.139
104   T         1.084   1.091   1.101   0.619   0.625   0.661   1.122   1.128   1.139
105   V        -0.518  -0.578  -0.578  -0.036  -0.145  -0.170  -0.607  -0.692  -0.688
106   T        -0.518  -0.578  -0.578  -0.578  -0.728  -0.756  -0.607  -0.692  -0.688
107   Q        -0.518  -0.578  -0.578  -0.079  -0.140  -0.112  -0.607  -0.692  -0.688
108   A         1.084   1.091   1.101   1.035   1.050   1.060   1.122   1.128   1.139
109   V        -0.518  -0.578  -0.578  -0.047  -0.156  -0.180  -0.607  -0.692  -0.688
110   E        -0.518  -0.578  -0.578  -0.776  -0.794  -0.720  -0.607  -0.692  -0.688
111   S        -0.518  -0.424  -0.545  -1.324  -1.142  -1.357  -0.607  -0.464  -0.639
112   S        -0.518  -0.424  -0.545  -0.829  -0.723  -0.781  -0.607  -0.464  -0.639
113   T        -0.518  -0.578  -0.578  -1.324  -1.443  -1.422  -0.607  -0.692  -0.688
114   -         1.084   1.091   1.101   1.462   1.468   1.469   1.122   1.128   1.139
115   -        -0.661  -0.647  -0.604  -0.087  -0.069  -0.015  -0.823  -0.797  -0.728
116   -        -0.661  -0.647  -0.604  -0.855  -0.831  -0.750  -0.823  -0.797  -0.728
117   -        -0.661  -0.647  -0.604  -0.855  -0.831  -0.750  -0.823  -0.797  -0.728
118   S        -0.518  -0.490  -0.560  -0.776  -0.737  -0.723  -0.607  -0.561  -0.661
119   S        -0.518  -0.490  -0.560  -1.324  -1.268  -1.387  -0.607  -0.561  -0.661
120   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
121   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
122   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
123   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
124   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
125   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
126   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
127   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
128   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
129   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
130   A         1.084   1.091   1.101   1.035   1.044   1.060   1.122   1.128   1.139
131   S        -0.661  -0.647  -0.604  -0.767  -0.744  -0.666  -0.823  -0.797  -0.728
132   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
133   S         1.084   1.091   1.101   0.476   0.492   0.525   1.122   1.128   1.139
134   G        -0.518  -0.578  -0.578  -0.717  -0.767  -0.700  -0.607  -0.692  -0.688
135   A        -0.518  -0.578  -0.578  -1.092  -1.159  -1.119  -0.607  -0.692  -0.688
136   A        -0.518  -0.578  -0.578  -1.092  -1.159  -1.119  -0.607  -0.692  -0.688
137   P        -1.681  -1.648  -1.602  -1.234  -1.101  -1.114  -1.471  -1.423  -1.351
138   A        -0.518  -0.490  -0.560  -0.809  -0.745  -0.938  -0.607  -0.561  -0.661
139   A        -0.518  -0.578  -0.578  -1.092  -1.159  -1.119  -0.607  -0.692  -0.688
140   F        -0.518  -0.578  -0.578  -0.616  -0.648  -0.573  -0.607  -0.692  -0.688
141   Q        -0.518  -0.578  -0.578  -0.717  -0.731  -0.647  -0.607  -0.692  -0.688
142   G        -1.681  -1.648  -1.602  -1.413  -1.288  -1.285  -1.471  -1.423  -1.351
143   A        -0.518  -0.578  -0.578  -0.107  -0.223  -0.262  -0.607  -0.692  -0.688
144   S        -0.518  -0.578  -0.578  -0.809  -0.953  -0.991  -0.607  -0.692  -0.688
145   V        -0.518  -0.578  -0.578  -0.468  -0.552  -0.545  -0.607  -0.692  -0.688
146   G         1.084   1.091   1.101   1.469   1.470   1.476   1.122   1.128   1.139
147   A        -1.681  -1.648  -1.602  -1.587  -1.498  -1.452  -1.471  -1.423  -1.351
148   L         1.084   1.091   1.101   1.528   1.530   1.533   1.122   1.128   1.139
149   A        -0.518  -0.490  -0.560  -0.252  -0.213  -0.259  -0.607  -0.561  -0.661
150   L        -1.681  -1.648  -1.602  -0.981  -0.914  -0.871  -1.471  -1.423  -1.351
151   -         1.084   1.091   1.101   1.480   1.485   1.486   1.122   1.128   1.139
152   -        -0.661  -0.647  -0.604  -0.696  -0.674  -0.598  -0.823  -0.797  -0.728
153   -         1.084   1.091   1.101   1.480   1.485   1.486   1.122   1.128   1.139
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   -        -0.661  -0.647  -0.604  -0.284  -0.265  -0.203  -0.823  -0.797  -0.728
157   -        -0.661  -0.647  -0.604  -0.111  -0.093  -0.038  -0.823  -0.797  -0.728
158   -         1.084   1.091   1.101   0.988   0.997   1.015   1.122   1.128   1.139
159   G        -0.518  -0.424  -0.545  -0.140   0.017  -0.218  -0.607  -0.464  -0.639
160   L        -1.681  -1.648  -1.602  -1.249  -1.168  -1.128  -1.471  -1.423  -1.351
161   I        -1.681  -1.648  -1.602  -1.272  -1.181  -1.150  -1.471  -1.423  -1.351
162   S        -0.518  -0.578  -0.578  -0.809  -0.953  -0.991  -0.607  -0.692  -0.688
163   Y        -0.518  -0.578  -0.578   0.311   0.218   0.197  -0.607  -0.692  -0.688
164   L         1.084   1.091   1.101   1.528   1.530   1.533   1.122   1.128   1.139
165   L         1.084   1.091   1.101   1.528   1.530   1.533   1.122   1.128   1.139
* 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/Q08906
Output conservation file - output/Q08906
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
