1     M         1.277   1.278   1.293   1.570   1.570   1.589   1.334   1.334   1.351
2     L        -1.245  -1.244  -1.219  -1.284  -1.280  -1.237  -1.118  -1.118  -1.074
3     K        -0.184  -0.185  -0.235  -0.388  -0.390  -0.458  -0.301  -0.303  -0.378
4     R        -0.314  -0.314  -0.292  -0.213  -0.213  -0.177  -0.505  -0.505  -0.468
5     R        -0.314  -0.314  -0.292  -0.700  -0.699  -0.658  -0.505  -0.505  -0.468
6     S        -1.245  -1.244  -1.219  -1.124  -1.124  -1.079  -1.118  -1.118  -1.074
7     N        -1.245  -1.244  -1.219  -1.214  -1.215  -1.168  -1.118  -1.118  -1.074
8     A        -1.245  -1.244  -1.219  -1.237  -1.240  -1.191  -1.118  -1.118  -1.074
9     L        -1.245  -1.244  -1.219  -1.323  -1.319  -1.276  -1.118  -1.118  -1.074
10    I        -1.245  -1.244  -1.219  -1.088  -1.088  -1.043  -1.118  -1.118  -1.074
11    T         1.277   1.278   1.293   1.367   1.366   1.389   1.334   1.334   1.351
12    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    R        -0.184  -0.188  -0.237  -0.329  -0.339  -0.467  -0.301  -0.308  -0.382
29    R         1.277   1.278   1.293   1.379   1.380   1.401   1.334   1.334   1.351
30    L        -0.184  -0.185  -0.235  -0.478  -0.479  -0.522  -0.301  -0.303  -0.378
31    L        -0.184  -0.188  -0.237  -0.502  -0.508  -0.554  -0.301  -0.308  -0.382
32    -        -0.314  -0.314  -0.292  -0.253  -0.253  -0.216  -0.505  -0.505  -0.468
33    -        -0.314  -0.314  -0.292  -0.344  -0.344  -0.306  -0.505  -0.505  -0.468
34    -        -0.314  -0.314  -0.292  -0.279  -0.279  -0.242  -0.505  -0.505  -0.468
35    -         1.277   1.278   1.293   1.386   1.386   1.407   1.334   1.334   1.351
36    -        -0.314  -0.314  -0.292  -0.305  -0.305  -0.268  -0.505  -0.505  -0.468
37    -        -0.314  -0.314  -0.292  -0.344  -0.344  -0.306  -0.505  -0.505  -0.468
38    N         1.277   1.278   1.293   1.415   1.416   1.436   1.334   1.334   1.351
39    Q        -1.245  -1.244  -1.219  -1.245  -1.249  -1.199  -1.118  -1.118  -1.074
40    Q        -1.245  -1.244  -1.219  -0.973  -0.974  -0.930  -1.118  -1.118  -1.074
41    R        -1.245  -1.244  -1.219  -1.002  -1.000  -0.957  -1.118  -1.118  -1.074
42    R        -0.314  -0.314  -0.292  -0.444  -0.443  -0.405  -0.505  -0.505  -0.468
43    A        -0.314  -0.314  -0.292  -0.296  -0.296  -0.259  -0.505  -0.505  -0.468
44    V        -0.314  -0.314  -0.292  -0.610  -0.610  -0.570  -0.505  -0.505  -0.468
45    S        -0.314  -0.314  -0.292  -0.296  -0.296  -0.259  -0.505  -0.505  -0.468
46    T        -0.314  -0.314  -0.292  -0.444  -0.443  -0.405  -0.505  -0.505  -0.468
47    S         1.277   1.278   1.293   1.343   1.343   1.364   1.334   1.334   1.351
48    P         1.277   1.278   1.293   1.542   1.542   1.562   1.334   1.334   1.351
49    K        -0.314  -0.314  -0.292  -0.703  -0.703  -0.662  -0.505  -0.505  -0.468
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    K        -0.314  -0.314  -0.292  -0.571  -0.571  -0.531  -0.505  -0.505  -0.468
54    E        -0.184  -0.188  -0.237  -0.460  -0.468  -0.568  -0.301  -0.308  -0.382
55    I         1.277   1.278   1.293   1.427   1.428   1.448   1.334   1.334   1.351
56    K        -0.184  -0.185  -0.235  -0.388  -0.390  -0.458  -0.301  -0.303  -0.378
57    S        -0.184  -0.178  -0.234  -0.163  -0.153  -0.257  -0.301  -0.292  -0.377
58    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
59    E         1.277   1.278   1.293   1.157   1.157   1.180   1.334   1.334   1.351
60    D         1.277   1.278   1.293   1.511   1.511   1.531   1.334   1.334   1.351
61    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
62    A        -0.184  -0.188  -0.237  -0.020  -0.029  -0.120  -0.301  -0.308  -0.382
63    N        -1.245  -1.244  -1.219  -1.284  -1.284  -1.237  -1.118  -1.118  -1.074
64    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
65    D        -1.245  -1.244  -1.219  -1.081  -1.082  -1.036  -1.118  -1.118  -1.074
66    S        -0.184  -0.188  -0.237  -0.197  -0.204  -0.285  -0.301  -0.308  -0.382
67    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
68    D        -0.184  -0.188  -0.237  -0.091  -0.100  -0.212  -0.301  -0.308  -0.382
69    G        -0.184  -0.185  -0.235   0.118   0.116   0.019  -0.301  -0.303  -0.378
70    V         1.277   1.278   1.293   1.475   1.475   1.496   1.334   1.334   1.351
71    D         1.277   1.278   1.293   1.511   1.511   1.531   1.334   1.334   1.351
72    T        -0.184  -0.178  -0.234   0.055   0.065  -0.044  -0.301  -0.292  -0.377
73    E        -0.184  -0.185  -0.235  -0.460  -0.462  -0.563  -0.301  -0.303  -0.378
74    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
75    I         1.277   1.278   1.293   1.427   1.428   1.448   1.334   1.334   1.351
76    R        -1.245  -1.244  -1.219  -1.363  -1.364  -1.315  -1.118  -1.118  -1.074
77    D        -1.245  -1.244  -1.219  -1.222  -1.223  -1.176  -1.118  -1.118  -1.074
78    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
79    I         1.277   1.278   1.293   1.427   1.428   1.448   1.334   1.334   1.351
80    N         1.277   1.278   1.293   1.415   1.416   1.436   1.334   1.334   1.351
81    E        -0.184  -0.185  -0.235  -0.254  -0.255  -0.317  -0.301  -0.303  -0.378
82    H        -0.184  -0.178  -0.234  -0.300  -0.292  -0.353  -0.301  -0.292  -0.377
83    T         1.277   1.278   1.293   1.367   1.366   1.389   1.334   1.334   1.351
84    T        -1.245  -1.244  -1.219  -1.016  -1.015  -0.972  -1.118  -1.118  -1.074
85    K        -0.184  -0.178  -0.234  -0.460  -0.448  -0.561  -0.301  -0.292  -0.377
86    L        -0.184  -0.188  -0.237  -0.478  -0.484  -0.525  -0.301  -0.308  -0.382
87    N         1.277   1.278   1.293   1.415   1.416   1.436   1.334   1.334   1.351
88    I        -0.184  -0.188  -0.237  -0.075  -0.083  -0.171  -0.301  -0.308  -0.382
89    K        -0.184  -0.188  -0.237  -0.312  -0.318  -0.371  -0.301  -0.308  -0.382
90    K        -1.245  -1.244  -1.219  -1.199  -1.196  -1.153  -1.118  -1.118  -1.074
91    E         1.277   1.278   1.293   1.157   1.157   1.180   1.334   1.334   1.351
92    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
93    D        -1.245  -1.244  -1.219  -1.124  -1.127  -1.079  -1.118  -1.118  -1.074
94    M        -0.184  -0.188  -0.237  -0.146  -0.157  -0.294  -0.301  -0.308  -0.382
95    L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
96    K         1.277   1.278   1.293   1.081   1.080   1.105   1.334   1.334   1.351
97    K        -1.245  -1.244  -1.219  -1.260  -1.258  -1.214  -1.118  -1.118  -1.074
98    F        -1.245  -1.244  -1.219  -1.192  -1.192  -1.146  -1.118  -1.118  -1.074
99    S        -0.184  -0.178  -0.234  -0.009   0.002  -0.112  -0.301  -0.292  -0.377
100   Q        -1.245  -1.244  -1.219  -0.856  -0.856  -0.813  -1.118  -1.118  -1.074
101   E         1.277   1.278   1.293   1.157   1.157   1.180   1.334   1.334   1.351
102   E        -0.184  -0.188  -0.237  -0.242  -0.248  -0.307  -0.301  -0.308  -0.382
103   E        -1.245  -1.244  -1.219  -1.081  -1.078  -1.036  -1.118  -1.118  -1.074
104   S        -1.245  -1.244  -1.219  -1.363  -1.362  -1.315  -1.118  -1.118  -1.074
105   G        -1.245  -1.244  -1.219  -1.268  -1.272  -1.222  -1.118  -1.118  -1.074
106   H        -1.245  -1.244  -1.219  -0.904  -0.904  -0.861  -1.118  -1.118  -1.074
107   E         1.277   1.278   1.293   1.157   1.157   1.180   1.334   1.334   1.351
108   I        -1.245  -1.244  -1.219  -1.044  -1.044  -1.000  -1.118  -1.118  -1.074
109   P        -0.184  -0.185  -0.235   0.023   0.021  -0.083  -0.301  -0.303  -0.378
110   V        -0.184  -0.178  -0.234  -0.508  -0.501  -0.558  -0.301  -0.292  -0.377
111   K         1.277   1.278   1.293   1.081   1.080   1.105   1.334   1.334   1.351
112   R        -0.184  -0.185  -0.235  -0.248  -0.250  -0.363  -0.301  -0.303  -0.378
113   F         1.277   1.278   1.293   1.534   1.534   1.554   1.334   1.334   1.351
114   I        -1.245  -1.244  -1.219  -1.044  -1.045  -1.000  -1.118  -1.118  -1.074
115   R         1.277   1.278   1.293   1.379   1.380   1.401   1.334   1.334   1.351
116   P         1.277   1.278   1.293   1.570   1.569   1.589   1.334   1.334   1.351
117   L        -0.184  -0.185  -0.235  -0.502  -0.504  -0.551  -0.301  -0.303  -0.378
118   W         1.277   1.278   1.293   1.546   1.546   1.566   1.334   1.334   1.351
119   M        -0.184  -0.178  -0.234   0.017   0.027  -0.056  -0.301  -0.292  -0.377
120   F         1.277   1.278   1.293   1.534   1.534   1.554   1.334   1.334   1.351
121   I        -0.184  -0.185  -0.235  -0.283  -0.285  -0.416  -0.301  -0.303  -0.378
122   L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
123   M         1.277   1.278   1.293   1.570   1.570   1.589   1.334   1.334   1.351
124   G        -0.184  -0.188  -0.237   0.149   0.142   0.052  -0.301  -0.308  -0.382
125   S         1.277   1.278   1.293   1.294   1.295   1.316   1.334   1.334   1.351
126   S        -1.245  -1.244  -1.219  -1.154  -1.153  -1.109  -1.118  -1.118  -1.074
127   V        -0.184  -0.188  -0.237   0.044   0.037  -0.040  -0.301  -0.308  -0.382
128   Y         1.277   1.278   1.293   1.605   1.604   1.624   1.334   1.334   1.351
129   L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
130   L        -1.245  -1.244  -1.219  -1.315  -1.310  -1.268  -1.118  -1.118  -1.074
131   L        -1.245  -1.244  -1.219  -1.139  -1.135  -1.094  -1.118  -1.118  -1.074
132   H         1.277   1.278   1.293   1.558   1.558   1.578   1.334   1.334   1.351
133   F        -1.245  -1.244  -1.219  -1.169  -1.172  -1.123  -1.118  -1.118  -1.074
134   S        -0.184  -0.178  -0.234  -0.064  -0.053  -0.163  -0.301  -0.292  -0.377
135   W         1.277   1.278   1.293   1.546   1.546   1.566   1.334   1.334   1.351
136   W         1.277   1.278   1.293   1.546   1.546   1.566   1.334   1.334   1.351
137   K         1.277   1.278   1.293   1.081   1.080   1.105   1.334   1.334   1.351
138   L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
139   E        -1.245  -1.244  -1.219  -1.110  -1.107  -1.065  -1.118  -1.118  -1.074
140   H        -0.184  -0.178  -0.234   0.170   0.179   0.085  -0.301  -0.292  -0.377
141   E         1.277   1.278   1.293   1.157   1.157   1.180   1.334   1.334   1.351
142   E        -0.184  -0.188  -0.237  -0.460  -0.468  -0.568  -0.301  -0.308  -0.382
143   R        -0.184  -0.178  -0.234  -0.388  -0.379  -0.457  -0.301  -0.292  -0.377
144   E         1.277   1.278   1.293   1.157   1.157   1.180   1.334   1.334   1.351
145   S        -1.245  -1.244  -1.219  -1.411  -1.410  -1.363  -1.118  -1.118  -1.074
146   Q        -0.184  -0.178  -0.234  -0.242  -0.234  -0.302  -0.301  -0.292  -0.377
147   L        -0.184  -0.185  -0.235  -0.442  -0.443  -0.480  -0.301  -0.303  -0.378
148   K        -0.184  -0.185  -0.235  -0.394  -0.396  -0.465  -0.301  -0.303  -0.378
149   K        -0.184  -0.178  -0.234  -0.080  -0.068  -0.202  -0.301  -0.292  -0.377
150   E        -0.184  -0.178  -0.234  -0.496  -0.486  -0.587  -0.301  -0.292  -0.377
151   V         1.277   1.278   1.293   1.475   1.475   1.496   1.334   1.334   1.351
152   E        -1.245  -1.244  -1.219  -1.066  -1.063  -1.021  -1.118  -1.118  -1.074
153   I        -1.245  -1.244  -1.219  -1.052  -1.051  -1.007  -1.118  -1.118  -1.074
154   L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
155   E         1.277   1.278   1.293   1.157   1.157   1.180   1.334   1.334   1.351
156   H        -1.245  -1.244  -1.219  -1.073  -1.074  -1.029  -1.118  -1.118  -1.074
157   Q        -1.245  -1.244  -1.219  -1.169  -1.170  -1.123  -1.118  -1.118  -1.074
158   L         1.277   1.278   1.293   0.898   0.899   0.924   1.334   1.334   1.351
159   N        -1.245  -1.244  -1.219  -1.214  -1.216  -1.168  -1.118  -1.118  -1.074
160   E        -1.245  -1.244  -1.219  -1.110  -1.107  -1.065  -1.118  -1.118  -1.074
161   L        -0.184  -0.188  -0.237  -0.508  -0.514  -0.561  -0.301  -0.308  -0.382
162   I        -1.245  -1.244  -1.219  -0.959  -0.958  -0.916  -1.118  -1.118  -1.074
163   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   K        -0.184  -0.185  -0.235  -0.496  -0.498  -0.588  -0.301  -0.303  -0.378
167   T        -1.245  -1.244  -1.219  -1.199  -1.201  -1.153  -1.118  -1.118  -1.074
168   H        -0.184  -0.188  -0.237  -0.080  -0.089  -0.210  -0.301  -0.308  -0.382
169   N        -0.184  -0.188  -0.237  -0.031  -0.038  -0.116  -0.301  -0.308  -0.382
170   T        -0.184  -0.185  -0.235  -0.163  -0.166  -0.258  -0.301  -0.303  -0.378
171   S        -0.184  -0.188  -0.237  -0.080  -0.086  -0.146  -0.301  -0.308  -0.382
172   R        -1.245  -1.244  -1.219  -0.952  -0.951  -0.909  -1.118  -1.118  -1.074
173   G        -1.245  -1.244  -1.219  -1.037  -1.039  -0.993  -1.118  -1.118  -1.074
174   K        -1.245  -1.244  -1.219  -1.237  -1.234  -1.191  -1.118  -1.118  -1.074
175   G        -1.245  -1.244  -1.219  -0.723  -0.723  -0.682  -1.118  -1.118  -1.074
176   S        -1.245  -1.244  -1.219  -1.339  -1.338  -1.291  -1.118  -1.118  -1.074
177   N         1.277   1.278   1.293   1.415   1.416   1.436   1.334   1.334   1.351
178   E        -1.245  -1.244  -1.219  -1.511  -1.510  -1.462  -1.118  -1.118  -1.074
179   S        -0.314  -0.314  -0.292  -0.632  -0.632  -0.591  -0.505  -0.505  -0.468
180   T        -0.314  -0.314  -0.292  -0.323  -0.323  -0.285  -0.505  -0.505  -0.468
181   H        -0.314  -0.314  -0.292  -0.360  -0.360  -0.322  -0.505  -0.505  -0.468
182   M        -0.314  -0.314  -0.292  -0.298  -0.298  -0.261  -0.505  -0.505  -0.468
183   K        -0.184  -0.185  -0.235  -0.388  -0.390  -0.458  -0.301  -0.303  -0.378
184   P        -1.245  -1.244  -1.219  -1.237  -1.239  -1.191  -1.118  -1.118  -1.074
185   W         1.277   1.278   1.293   1.546   1.546   1.566   1.334   1.334   1.351
186   Y         1.277   1.278   1.293   1.605   1.604   1.624   1.334   1.334   1.351
187   R        -0.184  -0.178  -0.234  -0.388  -0.379  -0.457  -0.301  -0.292  -0.377
188   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   F         1.277   1.278   1.293   1.534   1.534   1.554   1.334   1.334   1.351
191   W         1.277   1.278   1.293   1.546   1.546   1.566   1.334   1.334   1.351
* 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/Q02888
Output conservation file - output/Q02888
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
