1     M         1.792   1.794   1.810   1.950   1.954   1.981   1.925   1.928   1.948
2     T        -0.052  -0.051  -0.036  -0.343  -0.341  -0.317  -0.247  -0.245  -0.221
3     D        -0.052  -0.051  -0.036  -0.148  -0.146  -0.121  -0.247  -0.245  -0.221
4     P        -0.052  -0.051  -0.036  -0.173  -0.171  -0.147  -0.247  -0.245  -0.221
5     H        -0.052  -0.051  -0.036   0.063   0.066   0.090  -0.247  -0.245  -0.221
6     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -0.052  -0.051  -0.036  -0.303  -0.302  -0.277  -0.247  -0.245  -0.221
13    T        -0.052  -0.051  -0.036   0.002   0.004   0.029  -0.247  -0.245  -0.221
14    S         1.792   1.794   1.810   1.490   1.494   1.520   1.925   1.928   1.948
15    P        -0.052  -0.051  -0.036  -0.135  -0.133  -0.109  -0.247  -0.245  -0.221
16    T         1.792   1.794   1.810   1.881   1.885   1.912   1.925   1.928   1.948
17    F        -0.052  -0.051  -0.036   0.051   0.053   0.078  -0.247  -0.245  -0.221
18    E        -0.052  -0.051  -0.036  -0.148  -0.146  -0.121  -0.247  -0.245  -0.221
19    R        -1.130  -1.128  -1.116  -1.272  -1.269  -1.248  -0.971  -0.968  -0.945
20    S         0.099   0.086   0.066  -0.290  -0.309  -0.341  -0.006  -0.026  -0.057
21    Q        -1.130  -1.128  -1.116  -0.768  -0.763  -0.743  -0.971  -0.968  -0.945
22    D        -1.130  -1.128  -1.116  -1.387  -1.390  -1.363  -0.971  -0.968  -0.945
23    F         0.099   0.086   0.066   0.309   0.288   0.255  -0.006  -0.026  -0.057
24    L        -1.130  -1.128  -1.116  -0.817  -0.813  -0.792  -0.971  -0.968  -0.945
25    N         0.099   0.086   0.066   0.144   0.127   0.103  -0.006  -0.026  -0.057
26    I         0.099   0.086   0.045   0.291   0.271   0.205  -0.006  -0.026  -0.091
27    D        -1.130  -1.128  -1.116  -1.072  -1.069  -1.047  -0.971  -0.968  -0.945
28    E         0.099   0.086   0.045   0.013  -0.011  -0.081  -0.006  -0.026  -0.091
29    P         0.099   0.086   0.066   0.151   0.136   0.105  -0.006  -0.026  -0.057
30    P         1.792   1.794   1.810   1.782   1.790   1.812   1.925   1.928   1.948
31    C        -1.130  -1.128  -1.116  -0.900  -0.907  -0.875  -0.971  -0.968  -0.945
32    A         0.099   0.086   0.045   0.240   0.221   0.141  -0.006  -0.026  -0.091
33    Q         0.099   0.130   0.068   0.164   0.210   0.117  -0.006   0.044  -0.054
34    E         0.099   0.086   0.045   0.020  -0.005  -0.074  -0.006  -0.026  -0.091
35    T        -0.052  -0.051  -0.036  -0.343  -0.341  -0.317  -0.247  -0.245  -0.221
36    P         1.792   1.794   1.810   1.689   1.693   1.719   1.925   1.928   1.948
37    S        -0.052  -0.051  -0.036  -0.343  -0.341  -0.317  -0.247  -0.245  -0.221
38    V        -0.052  -0.051  -0.036   0.027   0.029   0.054  -0.247  -0.245  -0.221
39    S        -0.052  -0.051  -0.036  -0.277  -0.275  -0.251  -0.247  -0.245  -0.221
40    T        -0.052  -0.051  -0.036  -0.060  -0.058  -0.033  -0.247  -0.245  -0.221
41    F        -0.052  -0.051  -0.036   0.088   0.090   0.114  -0.247  -0.245  -0.221
42    N        -0.052  -0.051  -0.036  -0.277  -0.275  -0.251  -0.247  -0.245  -0.221
43    L        -0.052  -0.051  -0.036  -0.060  -0.058  -0.033  -0.247  -0.245  -0.221
44    P        -0.052  -0.051  -0.036  -0.212  -0.210  -0.186  -0.247  -0.245  -0.221
45    G        -0.052  -0.051  -0.036   0.136   0.138   0.162  -0.247  -0.245  -0.221
46    P        -0.052  -0.051  -0.036  -0.212  -0.210  -0.186  -0.247  -0.245  -0.221
47    S        -0.052  -0.051  -0.036  -0.343  -0.341  -0.317  -0.247  -0.245  -0.221
48    A        -0.052  -0.051  -0.036  -0.277  -0.275  -0.251  -0.247  -0.245  -0.221
49    P         1.792   1.794   1.810   1.689   1.693   1.719   1.925   1.928   1.948
50    A        -0.052  -0.051  -0.036   0.002   0.004   0.029  -0.247  -0.245  -0.221
51    Q         0.099   0.086   0.045   0.170   0.146   0.070  -0.006  -0.026  -0.091
52    S        -1.130  -1.128  -1.116  -1.253  -1.237  -1.229  -0.971  -0.968  -0.945
53    V        -1.130  -1.128  -1.116  -0.850  -0.852  -0.825  -0.971  -0.968  -0.945
54    D        -1.130  -1.128  -1.116  -1.272  -1.272  -1.248  -0.971  -0.968  -0.945
55    K        -1.130  -1.128  -1.116  -0.858  -0.852  -0.833  -0.971  -0.968  -0.945
56    P         1.792   1.794   1.810   1.782   1.790   1.812   1.925   1.928   1.948
57    V        -1.130  -1.128  -1.116  -0.900  -0.902  -0.875  -0.971  -0.968  -0.945
58    P         0.099   0.086   0.066   0.125   0.109   0.076  -0.006  -0.026  -0.057
59    M        -1.130  -1.128  -1.116  -0.800  -0.795  -0.775  -0.971  -0.968  -0.945
60    I        -0.052  -0.051  -0.036   0.054   0.056   0.081  -0.247  -0.245  -0.221
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    R         1.792   1.794   1.810   1.724   1.729   1.754   1.925   1.928   1.948
63    R         1.792   1.794   1.810   1.724   1.729   1.754   1.925   1.928   1.948
64    R         1.792   1.794   1.810   1.724   1.729   1.754   1.925   1.928   1.948
65    S         1.792   1.794   1.810   1.430   1.435   1.459   1.925   1.928   1.948
66    T         0.099   0.086   0.066   0.046   0.021  -0.031  -0.006  -0.026  -0.057
67    N         1.792   1.794   1.810   1.739   1.743   1.769   1.925   1.928   1.948
68    Y         1.792   1.794   1.810   1.909   1.908   1.939   1.925   1.928   1.948
69    M        -1.130  -1.128  -1.116  -0.776  -0.772  -0.751  -0.971  -0.968  -0.945
70    D         0.099   0.086   0.045   0.013  -0.010  -0.081  -0.006  -0.026  -0.091
71    A         0.099   0.086   0.045   0.309   0.291   0.221  -0.006  -0.026  -0.091
72    L         1.792   1.794   1.810   1.964   1.967   1.995   1.925   1.928   1.948
73    N        -1.130  -1.128  -1.116  -1.416  -1.417  -1.392  -0.971  -0.968  -0.945
74    S         0.099   0.086   0.045  -0.283  -0.302  -0.365  -0.006  -0.026  -0.091
75    R         0.099   0.130   0.068   0.073   0.124   0.016  -0.006   0.044  -0.054
76    E        -1.130  -1.128  -1.116  -1.072  -1.065  -1.047  -0.971  -0.968  -0.945
77    Q        -1.130  -1.128  -1.116  -0.950  -0.950  -0.926  -0.971  -0.968  -0.945
78    A        -0.052  -0.051  -0.036   0.027   0.029   0.054  -0.247  -0.245  -0.221
79    R         1.792   1.794   1.810   1.795   1.799   1.825   1.925   1.928   1.948
80    E         1.792   1.794   1.810   1.881   1.885   1.912   1.925   1.928   1.948
81    R        -0.052  -0.051  -0.036  -0.085  -0.083  -0.058  -0.247  -0.245  -0.221
82    E         1.792   1.794   1.810   1.881   1.885   1.912   1.925   1.928   1.948
83    S        -0.052  -0.051  -0.036  -0.343  -0.341  -0.317  -0.247  -0.245  -0.221
84    S        -0.052  -0.051  -0.036  -0.277  -0.275  -0.251  -0.247  -0.245  -0.221
85    I        -0.052  -0.051  -0.036  -0.047  -0.045  -0.020  -0.247  -0.245  -0.221
86    G        -0.052  -0.051  -0.036  -0.072  -0.070  -0.045  -0.247  -0.245  -0.221
87    E        -0.052  -0.051  -0.036  -0.186  -0.184  -0.160  -0.247  -0.245  -0.221
88    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    E         0.099   0.086   0.045   0.144   0.124   0.071  -0.006  -0.026  -0.091
94    R        -1.130  -1.128  -1.116  -1.198  -1.196  -1.173  -0.971  -0.968  -0.945
95    R        -1.130  -1.128  -1.116  -1.358  -1.359  -1.334  -0.971  -0.968  -0.945
96    S        -1.130  -1.128  -1.116  -1.207  -1.191  -1.183  -0.971  -0.968  -0.945
97    S         0.099   0.086   0.066  -0.269  -0.285  -0.317  -0.006  -0.026  -0.057
98    G        -1.130  -1.128  -1.116  -1.125  -1.127  -1.101  -0.971  -0.968  -0.945
99    P        -1.130  -1.128  -1.116  -1.319  -1.320  -1.295  -0.971  -0.968  -0.945
100   M         0.099   0.086   0.045   0.291   0.271   0.205  -0.006  -0.026  -0.091
101   D         1.792   1.794   1.810   1.753   1.756   1.783   1.925   1.928   1.948
102   F        -1.130  -1.128  -1.116  -0.917  -0.917  -0.892  -0.971  -0.968  -0.945
103   Q         0.099   0.086   0.045   0.170   0.146   0.070  -0.006  -0.026  -0.091
104   N         0.099   0.086   0.045   0.079   0.058  -0.002  -0.006  -0.026  -0.091
105   T         0.099   0.086   0.066   0.291   0.273   0.241  -0.006  -0.026  -0.057
106   I        -1.130  -1.128  -1.116  -0.976  -0.979  -0.951  -0.971  -0.968  -0.945
107   H         0.099   0.086   0.045   0.377   0.358   0.288  -0.006  -0.026  -0.091
108   N         0.099   0.086   0.066   0.086   0.066   0.038  -0.006  -0.026  -0.057
109   M         0.099   0.130   0.068   0.303   0.353   0.254  -0.006   0.044  -0.054
110   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   A        -1.130  -1.128  -1.116  -1.116  -1.119  -1.092  -0.971  -0.968  -0.945
123   G         0.099   0.130   0.068  -0.184  -0.138  -0.221  -0.006   0.044  -0.054
124   V        -1.130  -1.128  -1.116  -0.776  -0.775  -0.751  -0.971  -0.968  -0.945
125   D        -1.130  -1.128  -1.116  -1.387  -1.390  -1.363  -0.971  -0.968  -0.945
126   M         0.099   0.130   0.068   0.266   0.315   0.218  -0.006   0.044  -0.054
127   G        -1.130  -1.128  -1.116  -1.143  -1.146  -1.119  -0.971  -0.968  -0.945
128   D         1.792   1.794   1.810   1.753   1.756   1.783   1.925   1.928   1.948
129   S        -1.130  -1.128  -1.116  -1.063  -1.043  -1.038  -0.971  -0.968  -0.945
130   I        -1.130  -1.128  -1.116  -1.011  -1.015  -0.986  -0.971  -0.968  -0.945
131   S         0.099   0.086   0.045  -0.136  -0.150  -0.194  -0.006  -0.026  -0.091
132   H        -1.130  -1.128  -1.116  -0.950  -0.958  -0.926  -0.971  -0.968  -0.945
133   T         0.099   0.086   0.045   0.046   0.021  -0.078  -0.006  -0.026  -0.091
134   P         0.099   0.130   0.068  -0.269  -0.217  -0.314  -0.006   0.044  -0.054
135   I        -1.130  -1.128  -1.116  -1.019  -1.023  -0.995  -0.971  -0.968  -0.945
136   C         0.099   0.086   0.045   0.469   0.445   0.372  -0.006  -0.026  -0.091
137   S        -1.130  -1.128  -1.116  -1.235  -1.216  -1.210  -0.971  -0.968  -0.945
138   R        -1.130  -1.128  -1.116  -1.028  -1.022  -1.003  -0.971  -0.968  -0.945
139   A         0.099   0.086   0.066   0.347   0.328   0.298  -0.006  -0.026  -0.057
140   G         0.099   0.086   0.066   0.303   0.286   0.253  -0.006  -0.026  -0.057
141   N        -1.130  -1.128  -1.116  -1.397  -1.399  -1.373  -0.971  -0.968  -0.945
142   R        -1.130  -1.128  -1.116  -1.406  -1.408  -1.382  -0.971  -0.968  -0.945
143   P        -1.130  -1.128  -1.116  -0.976  -0.968  -0.951  -0.971  -0.968  -0.945
144   I         1.792   1.794   1.810   1.984   1.988   2.014   1.925   1.928   1.948
145   F        -0.052  -0.051  -0.036  -0.122  -0.120  -0.096  -0.247  -0.245  -0.221
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   K        -1.130  -1.128  -1.116  -1.338  -1.346  -1.314  -0.971  -0.968  -0.945
158   N        -1.130  -1.128  -1.116  -0.900  -0.889  -0.875  -0.971  -0.968  -0.945
159   S         0.099   0.130   0.068  -0.129  -0.068  -0.199  -0.006   0.044  -0.054
160   Y         1.792   1.794   1.810   1.909   1.908   1.939   1.925   1.928   1.948
161   L        -1.130  -1.128  -1.116  -0.925  -0.927  -0.900  -0.971  -0.968  -0.945
162   D        -1.130  -1.128  -1.116  -1.011  -1.005  -0.986  -0.971  -0.968  -0.945
163   N        -1.130  -1.128  -1.116  -1.189  -1.182  -1.164  -0.971  -0.968  -0.945
164   N         0.099   0.086   0.045  -0.007  -0.029  -0.102  -0.006  -0.026  -0.091
165   S        -1.130  -1.128  -1.116  -1.416  -1.402  -1.392  -0.971  -0.968  -0.945
166   N        -1.130  -1.128  -1.116  -0.900  -0.890  -0.875  -0.971  -0.968  -0.945
167   G        -1.130  -1.128  -1.116  -1.152  -1.158  -1.128  -0.971  -0.968  -0.945
168   N        -1.130  -1.128  -1.116  -1.081  -1.074  -1.056  -0.971  -0.968  -0.945
169   S        -1.130  -1.128  -1.116  -1.272  -1.258  -1.248  -0.971  -0.968  -0.945
170   A         0.099   0.086   0.066   0.303   0.283   0.250  -0.006  -0.026  -0.057
171   R         0.099   0.130   0.068   0.007   0.059  -0.049  -0.006   0.044  -0.054
172   V        -1.130  -1.128  -1.116  -1.028  -1.034  -1.003  -0.971  -0.968  -0.945
173   P         0.099   0.086   0.045   0.151   0.136   0.073  -0.006  -0.026  -0.091
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   H        -0.052  -0.051  -0.036   0.063   0.066   0.090  -0.247  -0.245  -0.221
179   G        -0.052  -0.051  -0.036  -0.097  -0.095  -0.071  -0.247  -0.245  -0.221
180   S        -0.052  -0.051  -0.036  -0.356  -0.355  -0.330  -0.247  -0.245  -0.221
181   P        -0.052  -0.051  -0.036  -0.199  -0.197  -0.173  -0.247  -0.245  -0.221
182   P        -0.052  -0.051  -0.036  -0.290  -0.288  -0.264  -0.247  -0.245  -0.221
183   Q        -0.052  -0.051  -0.036  -0.035  -0.033  -0.008  -0.247  -0.245  -0.221
184   L         0.099   0.086   0.045   0.247   0.222   0.151  -0.006  -0.026  -0.091
185   G        -1.130  -1.128  -1.116  -0.784  -0.778  -0.759  -0.971  -0.968  -0.945
186   T        -1.130  -1.128  -1.116  -0.850  -0.847  -0.825  -0.971  -0.968  -0.945
187   R         0.099   0.086   0.045   0.027   0.005  -0.061  -0.006  -0.026  -0.091
188   R         1.792   1.794   1.810   1.724   1.729   1.754   1.925   1.928   1.948
189   K         0.099   0.130   0.068   0.027   0.077  -0.023  -0.006   0.044  -0.054
190   S         0.099   0.086   0.045  -0.269  -0.285  -0.348  -0.006  -0.026  -0.091
191   S         1.792   1.794   1.810   1.430   1.435   1.459   1.925   1.928   1.948
192   F         1.792   1.794   1.810   1.992   1.998   2.022   1.925   1.928   1.948
193   K        -1.130  -1.128  -1.116  -1.028  -1.029  -1.003  -0.971  -0.968  -0.945
194   Y         1.792   1.794   1.810   1.909   1.908   1.939   1.925   1.928   1.948
195   E         1.792   1.794   1.810   1.753   1.755   1.783   1.925   1.928   1.948
196   D         1.792   1.794   1.810   1.753   1.756   1.783   1.925   1.928   1.948
197   F         1.792   1.794   1.810   1.992   1.998   2.022   1.925   1.928   1.948
198   K         1.792   1.794   1.810   1.824   1.825   1.854   1.925   1.928   1.948
199   K         1.792   1.794   1.810   1.824   1.825   1.854   1.925   1.928   1.948
200   D         0.099   0.086   0.066   0.013  -0.010  -0.044  -0.006  -0.026  -0.057
201   I         0.099   0.086   0.045   0.322   0.303   0.241  -0.006  -0.026  -0.091
202   Y         1.792   1.794   1.810   1.909   1.908   1.939   1.925   1.928   1.948
203   N         0.099   0.086   0.045   0.007  -0.016  -0.087  -0.006  -0.026  -0.091
204   Q        -1.130  -1.128  -1.116  -1.045  -1.049  -1.021  -0.971  -0.968  -0.945
205   L         0.099   0.086   0.066   0.073   0.045  -0.005  -0.006  -0.026  -0.057
206   H         0.099   0.086   0.066   0.322   0.298   0.262  -0.006  -0.026  -0.057
207   M        -1.130  -1.128  -1.116  -0.809  -0.805  -0.784  -0.971  -0.968  -0.945
208   F         1.792   1.794   1.810   1.992   1.998   2.022   1.925   1.928   1.948
209   G        -0.052  -0.051  -0.036  -0.160  -0.159  -0.134  -0.247  -0.245  -0.221
210   E        -0.052  -0.051  -0.036  -0.186  -0.184  -0.160  -0.247  -0.245  -0.221
211   K        -1.130  -1.128  -1.116  -1.143  -1.146  -1.119  -0.971  -0.968  -0.945
* 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/P43598
Output conservation file - output/P43598
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
