1     M         1.599   1.608   1.654   1.821   1.832   1.898   1.733   1.743   1.809
2     D         0.409   0.446   0.330   0.485   0.541   0.364   0.303   0.364   0.164
3     R        -0.726  -0.718  -0.676  -0.960  -0.953  -0.877  -0.809  -0.793  -0.727
4     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     T        -0.602  -0.618  -0.615  -0.435  -0.480  -0.459  -0.650  -0.669  -0.650
7     L         0.409   0.453   0.345   0.184   0.248   0.094   0.303   0.374   0.188
8     R        -1.335  -1.322  -1.286  -1.060  -1.051  -0.977  -1.126  -1.106  -1.044
9     T         0.409   0.340   0.303   0.476   0.345   0.259   0.303   0.188   0.116
10    Y         1.599   1.608   1.654   1.750   1.757   1.828   1.733   1.743   1.809
11    R         0.409   0.437   0.338   0.299   0.346   0.160   0.303   0.349   0.177
12    G         0.409   0.446   0.330   0.528   0.580   0.422   0.303   0.364   0.164
13    L         0.409   0.453   0.345   0.172   0.241   0.077   0.303   0.374   0.188
14    I        -1.335  -1.322  -1.286  -1.243  -1.209  -1.160  -1.126  -1.106  -1.044
15    R         1.599   1.608   1.654   1.533   1.542   1.611   1.733   1.743   1.809
16    A        -0.602  -0.622  -0.627  -0.547  -0.600  -0.591  -0.650  -0.674  -0.666
17    I         0.132   0.143   0.185  -0.160  -0.154  -0.086  -0.173  -0.155  -0.090
18    L        -0.602  -0.622  -0.627  -0.676  -0.702  -0.736  -0.650  -0.674  -0.666
19    K         0.409   0.437   0.338   0.162   0.224   0.051   0.303   0.349   0.177
20    Y        -1.335  -1.322  -1.286  -0.984  -0.987  -0.902  -1.126  -1.106  -1.044
21    E        -0.602  -0.628  -0.626  -0.516  -0.566  -0.537  -0.650  -0.681  -0.664
22    R        -0.602  -0.628  -0.626  -0.734  -0.770  -0.789  -0.650  -0.681  -0.664
23    P        -0.602  -0.628  -0.626  -0.290  -0.350  -0.323  -0.650  -0.681  -0.664
24    S        -0.602  -0.622  -0.627  -0.458  -0.508  -0.502  -0.650  -0.674  -0.666
25    K        -0.602  -0.618  -0.615  -0.692  -0.682  -0.682  -0.650  -0.669  -0.650
26    I        -0.602  -0.618  -0.615  -0.551  -0.572  -0.585  -0.650  -0.669  -0.650
27    V         0.132   0.142   0.186  -0.023  -0.006   0.062  -0.173  -0.156  -0.089
28    N        -0.602  -0.622  -0.627  -0.412  -0.440  -0.429  -0.650  -0.674  -0.666
29    W        -0.602  -0.622  -0.627  -0.615  -0.639  -0.603  -0.650  -0.674  -0.666
30    G        -1.335  -1.322  -1.286  -1.050  -1.040  -0.967  -1.126  -1.106  -1.044
31    N        -1.335  -1.322  -1.286  -1.207  -1.159  -1.124  -1.126  -1.106  -1.044
32    L        -1.335  -1.322  -1.286  -1.536  -1.488  -1.452  -1.126  -1.106  -1.044
33    R        -1.335  -1.322  -1.286  -1.137  -1.125  -1.054  -1.126  -1.106  -1.044
34    K         0.409   0.340   0.303   0.184   0.101   0.025   0.303   0.188   0.116
35    A        -1.335  -1.322  -1.286  -1.420  -1.405  -1.337  -1.126  -1.106  -1.044
36    M        -1.335  -1.322  -1.286  -1.017  -1.002  -0.934  -1.126  -1.106  -1.044
37    I         0.409   0.340   0.303   0.514   0.400   0.331   0.303   0.188   0.116
38    T         0.409   0.446   0.330   0.514   0.555   0.399   0.303   0.364   0.164
39    K         0.409   0.437   0.338   0.088   0.157  -0.046   0.303   0.349   0.177
40    L         0.409   0.340   0.303   0.184   0.082   0.030   0.303   0.188   0.116
41    E        -0.602  -0.622  -0.627  -0.587  -0.645  -0.661  -0.650  -0.674  -0.666
42    Y         1.599   1.608   1.654   1.750   1.757   1.828   1.733   1.743   1.809
43    A        -1.335  -1.322  -1.286  -1.212  -1.217  -1.129  -1.126  -1.106  -1.044
44    K        -0.602  -0.622  -0.627  -0.717  -0.749  -0.772  -0.650  -0.674  -0.666
45    K         0.409   0.446   0.330   0.444   0.513   0.286   0.303   0.364   0.164
46    Q         1.599   1.608   1.654   1.597   1.609   1.676   1.733   1.743   1.809
47    N        -0.726  -0.717  -0.676  -0.871  -0.855  -0.788  -0.809  -0.792  -0.727
48    Q         0.252   0.233   0.233   0.187   0.153   0.143   0.039   0.004  -0.005
49    R         1.599   1.608   1.654   1.546   1.560   1.624   1.733   1.743   1.809
50    D         0.252   0.259   0.235   0.219   0.230   0.177   0.039   0.051  -0.002
51    S         0.252   0.233   0.233   0.187   0.153   0.146   0.039   0.004  -0.005
52    H        -0.726  -0.717  -0.676  -0.472  -0.457  -0.391  -0.809  -0.792  -0.727
53    E         0.252   0.290   0.246   0.252   0.310   0.244   0.039   0.103   0.017
54    N        -0.726  -0.717  -0.676  -0.722  -0.714  -0.640  -0.809  -0.792  -0.727
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -0.726  -0.710  -0.676  -1.130  -1.099  -1.047  -0.809  -0.784  -0.727
69    -        -0.726  -0.710  -0.676  -0.868  -0.853  -0.785  -0.809  -0.784  -0.727
70    -        -0.726  -0.710  -0.676  -0.852  -0.822  -0.770  -0.809  -0.784  -0.727
71    I        -1.335  -1.322  -1.286  -1.264  -1.228  -1.180  -1.126  -1.106  -1.044
72    N        -0.602  -0.622  -0.627  -0.283  -0.315  -0.319  -0.650  -0.674  -0.666
73    R        -0.602  -0.551  -0.604  -0.811  -0.727  -0.802  -0.650  -0.580  -0.637
74    Q        -0.602  -0.628  -0.626  -0.660  -0.701  -0.716  -0.650  -0.681  -0.664
75    L        -0.602  -0.551  -0.604  -0.607  -0.512  -0.628  -0.650  -0.580  -0.637
76    E         1.599   1.608   1.654   1.552   1.557   1.630   1.733   1.743   1.809
77    K         0.409   0.437   0.338   0.213   0.275   0.117   0.303   0.349   0.177
78    W         0.409   0.446   0.330   0.287   0.339   0.208   0.303   0.364   0.164
79    K         0.409   0.340   0.303   0.247   0.174   0.114   0.303   0.188   0.116
80    K         0.132   0.143   0.185  -0.125  -0.084  -0.028  -0.173  -0.155  -0.090
81    L        -0.726  -0.717  -0.676  -0.933  -0.942  -0.850  -0.809  -0.792  -0.727
82    D         1.599   1.608   1.654   1.629   1.642   1.707   1.733   1.743   1.809
83    P         1.599   1.608   1.654   1.777   1.788   1.855   1.733   1.743   1.809
84    V        -1.335  -1.322  -1.286  -1.404  -1.390  -1.320  -1.126  -1.106  -1.044
85    S        -1.335  -1.322  -1.286  -1.327  -1.290  -1.244  -1.126  -1.106  -1.044
86    D         0.132   0.143   0.185   0.037   0.057   0.120  -0.173  -0.155  -0.090
87    R         0.252   0.233   0.233  -0.127  -0.156  -0.157   0.039   0.004  -0.005
88    S        -0.726  -0.717  -0.676  -0.795  -0.780  -0.713  -0.809  -0.792  -0.727
89    L         0.252   0.290   0.246  -0.038   0.017  -0.039   0.039   0.103   0.017
90    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    L         1.599   1.608   1.654   1.300   1.314   1.379   1.733   1.743   1.809
92    F         1.599   1.608   1.654   1.859   1.874   1.936   1.733   1.743   1.809
93    I        -1.335  -1.322  -1.286  -0.849  -0.833  -0.767  -1.126  -1.106  -1.044
94    A        -1.335  -1.322  -1.286  -1.253  -1.217  -1.170  -1.126  -1.106  -1.044
95    D        -0.602  -0.628  -0.626  -0.367  -0.405  -0.387  -0.650  -0.681  -0.664
96    S         0.409   0.453   0.345   0.447   0.509   0.338   0.303   0.374   0.188
97    K        -0.602  -0.618  -0.615  -0.713  -0.712  -0.706  -0.650  -0.669  -0.650
98    S        -1.335  -1.322  -1.286  -1.207  -1.191  -1.124  -1.126  -1.106  -1.044
99    L         0.409   0.453   0.345   0.172   0.241   0.077   0.303   0.374   0.188
100   R         0.409   0.437   0.338   0.299   0.346   0.160   0.303   0.349   0.177
101   S        -0.602  -0.622  -0.627  -0.520  -0.558  -0.567  -0.650  -0.674  -0.666
102   I         0.409   0.340   0.303   0.577   0.475   0.421   0.303   0.188   0.116
103   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   V         0.409   0.340   0.303   0.525   0.438   0.388   0.303   0.188   0.116
114   A        -1.335  -1.322  -1.286  -1.162  -1.148  -1.079  -1.126  -1.106  -1.044
115   Q        -0.602  -0.622  -0.627  -0.500  -0.538  -0.536  -0.650  -0.674  -0.666
116   G        -0.602  -0.557  -0.604  -0.500  -0.417  -0.524  -0.650  -0.588  -0.637
117   Q        -1.335  -1.322  -1.286  -1.466  -1.412  -1.382  -1.126  -1.106  -1.044
118   N        -1.335  -1.322  -1.286  -1.036  -1.004  -0.953  -1.126  -1.106  -1.044
119   V        -0.602  -0.622  -0.627  -0.531  -0.566  -0.581  -0.650  -0.674  -0.666
120   D        -1.335  -1.322  -1.286  -1.012  -1.008  -0.930  -1.126  -1.106  -1.044
121   E         0.132   0.142   0.186  -0.097  -0.093  -0.011  -0.173  -0.156  -0.089
122   I        -0.602  -0.622  -0.627  -0.504  -0.546  -0.540  -0.650  -0.674  -0.666
123   F        -1.335  -1.322  -1.286  -1.327  -1.281  -1.244  -1.126  -1.106  -1.044
124   E        -0.602  -0.551  -0.604  -0.567  -0.495  -0.571  -0.650  -0.580  -0.637
125   H         1.599   1.608   1.654   1.838   1.851   1.916   1.733   1.743   1.809
126   A         0.132   0.142   0.186  -0.202  -0.182  -0.105  -0.173  -0.156  -0.089
127   L        -0.602  -0.622  -0.627  -0.949  -0.961  -0.995  -0.650  -0.674  -0.666
128   D         0.409   0.453   0.345   0.531   0.604   0.435   0.303   0.374   0.188
129   I         0.409   0.340   0.303   0.600   0.503   0.453   0.303   0.188   0.116
130   I        -1.335  -1.322  -1.286  -1.338  -1.353  -1.255  -1.126  -1.106  -1.044
131   K        -1.335  -1.322  -1.286  -1.382  -1.382  -1.298  -1.126  -1.106  -1.044
132   F         1.599   1.608   1.654   1.856   1.870   1.933   1.733   1.743   1.809
133   L         0.409   0.437   0.338   0.172   0.219   0.067   0.303   0.349   0.177
134   D        -1.335  -1.322  -1.286  -1.152  -1.143  -1.069  -1.126  -1.106  -1.044
135   N         1.599   1.608   1.654   1.688   1.696   1.766   1.733   1.743   1.809
136   Q         1.599   1.608   1.654   1.597   1.609   1.676   1.733   1.743   1.809
137   R         0.409   0.437   0.338   0.393   0.429   0.284   0.303   0.349   0.177
138   E         0.409   0.340   0.303   0.402   0.288   0.230   0.303   0.188   0.116
139   Y         1.599   1.608   1.654   1.750   1.757   1.828   1.733   1.743   1.809
140   E         0.409   0.340   0.303   0.318   0.194   0.109   0.303   0.188   0.116
141   E        -0.602  -0.628  -0.626  -0.571  -0.614  -0.602  -0.650  -0.681  -0.664
142   L         1.599   1.608   1.654   1.316   1.334   1.394   1.733   1.743   1.809
143   V        -0.602  -0.622  -0.627  -0.607  -0.661  -0.676  -0.650  -0.674  -0.666
144   D        -0.602  -0.622  -0.627  -0.559  -0.603  -0.590  -0.650  -0.674  -0.666
145   R         1.599   1.608   1.654   1.533   1.542   1.611   1.733   1.743   1.809
146   Y         1.599   1.608   1.654   1.750   1.757   1.828   1.733   1.743   1.809
147   N         1.599   1.608   1.654   1.688   1.696   1.766   1.733   1.743   1.809
148   P         1.599   1.608   1.654   1.777   1.788   1.855   1.733   1.743   1.809
149   G         1.599   1.608   1.654   1.786   1.805   1.863   1.733   1.743   1.809
150   N        -1.335  -1.322  -1.286  -1.489  -1.442  -1.405  -1.126  -1.106  -1.044
151   K         0.409   0.340   0.303   0.203   0.129   0.052   0.303   0.188   0.116
152   L         0.132   0.143   0.185  -0.050  -0.013   0.051  -0.173  -0.155  -0.090
153   T        -0.602  -0.622  -0.627  -0.477  -0.526  -0.509  -0.650  -0.674  -0.666
154   Q         0.409   0.340   0.303   0.467   0.364   0.302   0.303   0.188   0.116
155   D        -0.602  -0.628  -0.626  -0.527  -0.570  -0.573  -0.650  -0.681  -0.664
156   E         1.599   1.608   1.654   1.552   1.557   1.630   1.733   1.743   1.809
157   K         0.409   0.340   0.303   0.162   0.073  -0.006   0.303   0.188   0.116
158   V         1.599   1.608   1.654   1.588   1.609   1.666   1.733   1.743   1.809
159   K        -0.602  -0.628  -0.626  -0.824  -0.852  -0.846  -0.650  -0.681  -0.664
160   R        -0.602  -0.628  -0.626  -0.859  -0.917  -0.937  -0.650  -0.681  -0.664
161   T         0.409   0.340   0.303   0.569   0.452   0.392   0.303   0.188   0.116
162   A         1.599   1.608   1.654   1.625   1.628   1.703   1.733   1.743   1.809
163   N         0.409   0.340   0.303   0.517   0.396   0.331   0.303   0.188   0.116
164   V        -0.602  -0.622  -0.627  -0.828  -0.845  -0.853  -0.650  -0.674  -0.666
165   V         1.599   1.608   1.654   1.588   1.609   1.666   1.733   1.743   1.809
166   G         1.599   1.608   1.654   1.786   1.805   1.863   1.733   1.743   1.809
167   L         1.599   1.608   1.654   1.316   1.334   1.394   1.733   1.743   1.809
168   D        -0.602  -0.562  -0.597  -0.571  -0.516  -0.557  -0.650  -0.594  -0.627
169   V         0.409   0.453   0.345   0.467   0.537   0.373   0.303   0.374   0.188
170   P         1.599   1.608   1.654   1.777   1.788   1.855   1.733   1.743   1.809
171   T        -1.335  -1.322  -1.286  -1.084  -1.081  -1.001  -1.126  -1.106  -1.044
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -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/P40491
Output conservation file - output/P40491
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
