1     M         0.842   0.877   0.926   1.019   1.073   1.115   0.875   0.922   0.992
2     R         0.842   0.877   0.926   0.838   0.870   0.968   0.875   0.922   0.992
3     Q        -1.322  -1.039  -1.145  -1.284  -0.872  -1.021  -1.491  -1.111  -1.169
4     L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
5     T         0.842   0.877   0.926   0.795   0.847   0.932   0.875   0.922   0.992
6     E         0.005  -0.070  -0.332   0.119   0.039  -0.360   0.003  -0.103  -0.537
7     E         0.005  -0.275  -0.347   0.093  -0.300  -0.462   0.003  -0.413  -0.563
8     E         0.842   0.877   0.926   0.834   0.896   0.964   0.875   0.922   0.992
9     T         0.005  -0.275  -0.347   0.087  -0.280  -0.391   0.003  -0.413  -0.563
10    K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
11    V        -1.322  -1.140  -1.158  -1.600  -1.347  -1.281  -1.491  -1.268  -1.185
12    V        -0.792  -0.727  -1.119  -0.721  -0.641  -1.195  -0.744  -0.663  -1.136
13    F         0.842   0.877   0.926   0.860   0.925   0.985   0.875   0.922   0.992
14    E         0.842   0.877   0.926   0.834   0.896   0.964   0.875   0.922   0.992
15    K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
16    L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
17    A         0.842   0.877   0.926   0.773   0.845   0.914   0.875   0.922   0.992
18    G        -1.322  -1.236  -1.157  -1.380  -1.172  -1.076  -1.491  -1.318  -1.183
19    Y         0.842   0.877   0.926   0.938   0.987   1.049   0.875   0.922   0.992
20    I        -0.792  -1.014  -1.142  -0.583  -0.864  -1.090  -0.744  -1.033  -1.164
21    G         0.005  -0.275  -0.347   0.036  -0.356  -0.503   0.003  -0.413  -0.563
22    R        -0.792  -1.124  -1.151  -0.623  -1.136  -1.196  -0.744  -1.160  -1.175
23    N         0.005  -0.275  -0.347   0.203  -0.222  -0.438   0.003  -0.413  -0.563
24    I         0.005  -0.275  -0.347   0.098  -0.280  -0.467   0.003  -0.413  -0.563
25    S        -1.542  -1.346  -1.688  -1.336  -1.097  -1.655  -1.367  -1.138  -1.446
26    F        -2.091  -2.074  -1.735  -2.124  -2.148  -1.633  -1.989  -1.904  -1.491
27    L        -0.792  -1.014  -1.142  -0.833  -1.162  -1.304  -0.744  -1.033  -1.164
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    V        -1.322  -1.376  -1.165  -1.593  -1.651  -1.351  -1.491  -1.480  -1.193
31    D         0.005   0.063  -0.327   0.174   0.235  -0.313   0.003   0.084  -0.529
32    N        -0.792  -1.124  -1.151  -0.484  -0.982  -1.085  -0.744  -1.160  -1.175
33    K        -1.946  -1.970  -1.730  -2.001  -2.015  -1.667  -1.865  -1.819  -1.486
34    E        -1.322  -1.028  -1.140  -1.456  -1.008  -1.158  -1.491  -1.094  -1.164
35    L        -2.624  -2.447  -2.174  -2.550  -2.314  -1.965  -2.224  -2.019  -1.665
36    P         0.005  -0.275  -0.347   0.207  -0.193  -0.365   0.003  -0.413  -0.563
37    H         0.005  -0.275  -0.347   0.251  -0.141  -0.302   0.003  -0.413  -0.563
38    V         0.005  -0.070  -0.332   0.043  -0.040  -0.364   0.003  -0.103  -0.537
39    F         0.842   0.877   0.926   0.860   0.925   0.985   0.875   0.922   0.992
40    R         0.842   0.877   0.926   0.838   0.870   0.968   0.875   0.922   0.992
41    L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
42    Q         0.005  -0.275  -0.347   0.306  -0.074  -0.254   0.003  -0.413  -0.563
43    K         0.005  -0.275  -0.347   0.053  -0.302  -0.432   0.003  -0.413  -0.563
44    D         0.005  -0.275  -0.347   0.161  -0.251  -0.388   0.003  -0.413  -0.563
45    R         0.842   0.877   0.926   0.838   0.870   0.968   0.875   0.922   0.992
46    V         0.842   0.877   0.926   0.733   0.788   0.881   0.875   0.922   0.992
47    Y         0.842   0.877   0.926   0.938   0.987   1.049   0.875   0.922   0.992
48    Y         0.842   0.877   0.926   0.938   0.987   1.049   0.875   0.922   0.992
49    V         0.842   0.877   0.926   0.733   0.788   0.881   0.875   0.922   0.992
50    P        -2.476  -2.407  -2.165  -2.262  -2.243  -1.849  -2.114  -2.003  -1.658
51    D        -0.792  -0.895  -1.133  -0.651  -0.876  -1.227  -0.744  -0.904  -1.153
52    H        -3.006  -2.765  -2.514  -2.713  -2.437  -2.064  -2.363  -2.109  -1.769
53    V        -1.157  -1.271  -1.165  -1.225  -1.427  -1.294  -1.242  -1.370  -1.194
54    A         0.005  -0.070  -0.332   0.065  -0.000  -0.385   0.003  -0.103  -0.537
55    K        -0.627  -0.589  -0.409  -0.881  -0.807  -0.523  -0.993  -0.937  -0.669
56    L        -1.852  -1.727  -1.714  -1.948  -1.747  -1.646  -1.740  -1.549  -1.471
57    A         0.842   0.877   0.926   0.773   0.845   0.914   0.875   0.922   0.992
58    T         0.842   0.877   0.926   0.795   0.847   0.932   0.875   0.922   0.992
59    S         0.005   0.063  -0.327   0.182   0.247  -0.257   0.003   0.084  -0.529
60    V         0.842   0.877   0.926   0.733   0.788   0.881   0.875   0.922   0.992
61    A        -0.697  -0.602  -0.407  -1.053  -0.888  -0.568  -1.118  -0.961  -0.665
62    R         0.842   0.877   0.926   0.838   0.870   0.968   0.875   0.922   0.992
63    P        -2.476  -2.376  -2.157  -2.178  -2.074  -1.786  -2.114  -1.968  -1.652
64    N        -1.322  -1.400  -1.171  -1.283  -1.385  -1.083  -1.491  -1.512  -1.201
65    L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
66    M        -0.792  -1.014  -1.142  -0.472  -0.854  -1.134  -0.744  -1.033  -1.164
67    S         0.842   0.877   0.926   0.873   0.917   0.996   0.875   0.922   0.992
68    L        -1.157  -0.904  -1.141  -1.425  -1.068  -1.363  -1.242  -0.910  -1.165
69    G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
70    I        -1.322  -1.116  -1.160  -1.565  -1.259  -1.312  -1.491  -1.229  -1.188
71    C         0.842   0.877   0.926   1.136   1.163   1.210   0.875   0.922   0.992
72    L        -1.322  -1.116  -1.157  -1.613  -1.344  -1.250  -1.491  -1.229  -1.184
73    G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
74    K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
75    F         0.005  -0.275  -0.347   0.152  -0.206  -0.347   0.003  -0.413  -0.563
76    T         0.842   0.877   0.926   0.795   0.847   0.932   0.875   0.922   0.992
77    K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
78    T         0.842   0.877   0.926   0.795   0.847   0.932   0.875   0.922   0.992
79    G         0.005  -0.070  -0.332   0.062  -0.017  -0.403   0.003  -0.103  -0.537
80    K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
81    F         0.842   0.877   0.926   0.860   0.925   0.985   0.875   0.922   0.992
82    R         0.842   0.877   0.926   0.838   0.870   0.968   0.875   0.922   0.992
83    L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
84    H         0.842   0.877   0.926   0.972   1.018   1.077   0.875   0.922   0.992
85    I         0.842   0.877   0.926   0.843   0.917   0.971   0.875   0.922   0.992
86    T         0.842   0.877   0.926   0.795   0.847   0.932   0.875   0.922   0.992
87    S        -0.627  -0.413  -0.380  -0.928  -0.554  -0.530  -0.993  -0.636  -0.619
88    L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
89    T        -1.852  -1.632  -1.710  -1.715  -1.393  -1.554  -1.740  -1.461  -1.467
90    V        -1.946  -1.970  -1.730  -2.064  -2.076  -1.744  -1.865  -1.819  -1.486
91    L         0.005  -0.070  -0.332  -0.113  -0.207  -0.570   0.003  -0.103  -0.537
92    A         0.005  -0.275  -0.347   0.043  -0.329  -0.472   0.003  -0.413  -0.563
93    K        -1.852  -1.860  -1.717  -1.706  -1.713  -1.594  -1.740  -1.697  -1.474
94    H        -0.697  -0.602  -0.408  -0.862  -0.715  -0.417  -1.118  -0.960  -0.667
95    A         0.842   0.877   0.926   0.773   0.845   0.914   0.875   0.922   0.992
96    K        -0.627  -0.611  -0.406  -0.951  -0.946  -0.589  -0.993  -0.975  -0.662
97    Y        -1.467  -1.365  -1.180  -1.502  -1.367  -1.108  -1.616  -1.479  -1.211
98    K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
99    I        -0.407  -0.196  -0.369  -0.521  -0.170  -0.525  -0.619  -0.291  -0.599
100   W         0.842   0.877   0.926   1.157   1.194   1.227   0.875   0.922   0.992
101   I        -0.407  -0.558  -0.408  -0.521  -0.823  -0.611  -0.619  -0.882  -0.666
102   K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
103   P        -2.236  -2.229  -2.158  -1.858  -1.939  -1.829  -1.865  -1.844  -1.653
104   N         0.842   0.877   0.926   0.968   1.026   1.073   0.875   0.922   0.992
105   G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
106   E         0.005  -0.275  -0.347   0.090  -0.300  -0.471   0.003  -0.413  -0.563
107   M         0.005  -0.275  -0.347   0.310  -0.063  -0.234   0.003  -0.413  -0.563
108   P         0.842   0.877   0.926   0.942   0.998   1.052   0.875   0.922   0.992
109   F         0.842   0.877   0.926   0.860   0.925   0.985   0.875   0.922   0.992
110   L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
111   Y         0.842   0.877   0.926   0.938   0.987   1.049   0.875   0.922   0.992
112   G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
113   N         0.005  -0.275  -0.347   0.238  -0.154  -0.332   0.003  -0.413  -0.563
114   H         0.005  -0.275  -0.347   0.255  -0.130  -0.290   0.003  -0.413  -0.563
115   V         0.842   0.877   0.926   0.733   0.788   0.881   0.875   0.922   0.992
116   L         0.005  -0.275  -0.347  -0.129  -0.541  -0.645   0.003  -0.413  -0.563
117   K         0.842   0.877   0.926   0.768   0.842   0.910   0.875   0.922   0.992
118   A         0.842   0.877   0.926   0.773   0.845   0.914   0.875   0.922   0.992
119   H         0.842   0.877   0.926   0.972   1.018   1.077   0.875   0.922   0.992
120   V        -0.627  -0.468  -0.391  -0.980  -0.704  -0.590  -0.993  -0.728  -0.636
121   G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
122   K        -0.697  -0.583  -0.403  -1.081  -0.887  -0.583  -1.118  -0.927  -0.658
123   M        -0.792  -1.124  -1.151  -0.389  -0.835  -0.945  -0.744  -1.160  -1.175
124   S        -0.407  -0.350  -0.386  -0.472  -0.403  -0.511  -0.619  -0.533  -0.629
125   D         0.005  -0.275  -0.347   0.155  -0.257  -0.404   0.003  -0.413  -0.563
126   D         0.842   0.877   0.926   0.890   0.925   1.010   0.875   0.922   0.992
127   I        -0.792  -1.124  -1.151  -0.573  -1.005  -1.078  -0.744  -1.160  -1.175
128   P         0.842   0.877   0.926   0.942   0.998   1.052   0.875   0.922   0.992
129   E         0.005  -0.070  -0.332   0.126   0.050  -0.339   0.003  -0.103  -0.537
130   H         0.842   0.877   0.926   0.972   1.018   1.077   0.875   0.922   0.992
131   A        -0.792  -1.124  -1.151  -0.648  -1.103  -1.137  -0.744  -1.160  -1.175
132   G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
133   V         0.005   0.191  -0.317  -0.033   0.206  -0.549   0.003   0.254  -0.511
134   I        -0.407  -0.558  -0.408  -0.521  -0.823  -0.611  -0.619  -0.882  -0.666
135   V        -0.407  -0.340  -0.385  -0.592  -0.488  -0.580  -0.619  -0.517  -0.627
136   F        -0.627  -0.421  -0.373  -0.790  -0.432  -0.409  -0.993  -0.650  -0.607
137   A         0.005   0.201  -0.316   0.129   0.365  -0.382   0.003   0.267  -0.510
138   M         0.842   0.877   0.926   1.019   1.073   1.115   0.875   0.922   0.992
139   N        -1.542  -1.611  -1.708  -1.182  -1.351  -1.513  -1.367  -1.447  -1.465
140   D         0.842   0.877   0.926   0.890   0.925   1.010   0.875   0.922   0.992
141   V        -2.476  -2.359  -2.157  -2.451  -2.301  -1.951  -2.114  -1.961  -1.653
142   P         0.842   0.877   0.926   0.942   0.998   1.052   0.875   0.922   0.992
143   L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
144   G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
145   F         0.842   0.877   0.926   0.860   0.925   0.985   0.875   0.922   0.992
146   G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
147   V         0.005   0.212  -0.317  -0.011   0.249  -0.489   0.003   0.281  -0.511
148   S        -0.407  -0.558  -0.408  -0.472  -0.791  -0.557  -0.619  -0.882  -0.666
149   A         0.842   0.877   0.926   0.773   0.845   0.914   0.875   0.922   0.992
150   K        -0.407  -0.558  -0.408  -0.559  -0.843  -0.598  -0.619  -0.882  -0.666
151   S         0.842   0.877   0.926   0.873   0.917   0.996   0.875   0.922   0.992
152   T         0.005   0.063  -0.327   0.065   0.142  -0.421   0.003   0.084  -0.529
153   S        -2.476  -2.289  -2.154  -2.571  -2.361  -2.057  -2.114  -1.903  -1.650
154   E         0.842   0.877   0.926   0.834   0.896   0.964   0.875   0.922   0.992
155   S        -1.946  -1.870  -1.724  -2.110  -2.004  -1.803  -1.865  -1.721  -1.480
156   R         0.005   0.191  -0.317   0.094   0.308  -0.411   0.003   0.254  -0.511
157   N        -1.946  -1.614  -1.709  -1.920  -1.490  -1.577  -1.865  -1.484  -1.467
158   M         0.005   0.201  -0.316  -0.087   0.142  -0.470   0.003   0.267  -0.510
159   Q        -1.852  -1.807  -1.725  -1.616  -1.649  -1.503  -1.740  -1.685  -1.482
160   P         0.842   0.877   0.926   0.942   0.998   1.052   0.875   0.922   0.992
161   T         0.842   0.877   0.926   0.795   0.847   0.932   0.875   0.922   0.992
162   G        -1.157  -0.979  -1.147  -1.253  -1.011  -1.241  -1.242  -1.019  -1.172
163   I         0.005   0.063  -0.327   0.134   0.235  -0.327   0.003   0.084  -0.529
164   V         0.842   0.877   0.926   0.733   0.788   0.881   0.875   0.922   0.992
165   A         0.005  -0.275  -0.347   0.082  -0.256  -0.357   0.003  -0.413  -0.563
166   F         0.842   0.877   0.926   0.860   0.925   0.985   0.875   0.922   0.992
167   R         0.005  -0.070  -0.332   0.123   0.013  -0.357   0.003  -0.103  -0.537
168   Q         0.842   0.877   0.926   1.023   1.076   1.118   0.875   0.922   0.992
169   A        -1.322  -1.400  -1.171  -1.572  -1.633  -1.280  -1.491  -1.512  -1.201
170   D         0.842   0.877   0.926   0.890   0.925   1.010   0.875   0.922   0.992
171   I        -1.157  -1.370  -1.172  -1.154  -1.440  -1.158  -1.242  -1.472  -1.202
172   G         0.842   0.877   0.926   0.777   0.838   0.917   0.875   0.922   0.992
173   E         0.842   0.877   0.926   0.834   0.896   0.964   0.875   0.922   0.992
174   Y         0.842   0.877   0.926   0.938   0.987   1.049   0.875   0.922   0.992
175   L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
176   R         0.842   0.877   0.926   0.838   0.870   0.968   0.875   0.922   0.992
177   D        -0.627  -0.468  -0.391  -0.846  -0.586  -0.488  -0.993  -0.728  -0.636
178   E         0.842   0.877   0.926   0.834   0.896   0.964   0.875   0.922   0.992
179   D         0.842   0.877   0.926   0.890   0.925   1.010   0.875   0.922   0.992
180   T         0.842   0.877   0.926   0.795   0.847   0.932   0.875   0.922   0.992
181   L         0.842   0.877   0.926   0.621   0.669   0.790   0.875   0.922   0.992
182   F         0.842   0.877   0.926   0.860   0.925   0.985   0.875   0.922   0.992
183   T        -0.675  -0.606  -0.406  -1.046  -0.955  -0.608  -1.077  -0.966  -0.664
184   -        -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/Q08962
Output conservation file - output/Q08962
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
