1     M         1.690   1.697   1.710   2.019   2.028   2.050   1.805   1.813   1.830
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     I         0.026   0.074  -0.001  -0.553  -0.478  -0.587  -0.076  -0.000  -0.118
4     P        -1.183  -1.175  -1.162  -0.989  -0.987  -0.954  -1.017  -1.005  -0.981
5     Y         0.026  -0.012  -0.035  -0.073  -0.161  -0.239  -0.076  -0.134  -0.171
6     Q         0.026   0.035  -0.006   0.142   0.159   0.088  -0.076  -0.062  -0.125
7     E         0.026   0.074  -0.001   0.142   0.224   0.095  -0.076  -0.000  -0.118
8     W        -1.183  -1.175  -1.162  -0.728  -0.714  -0.693  -1.017  -1.005  -0.981
9     H        -1.183  -1.175  -1.162  -0.802  -0.792  -0.767  -1.017  -1.005  -0.981
10    S        -1.183  -1.175  -1.162  -0.980  -0.957  -0.945  -1.017  -1.005  -0.981
11    Q         1.690   1.697   1.710   1.808   1.817   1.839   1.805   1.813   1.830
12    L         1.690   1.697   1.710   1.110   1.122   1.142   1.805   1.813   1.830
13    Q        -1.183  -1.175  -1.162  -0.860  -0.836  -0.826  -1.017  -1.005  -0.981
14    S        -0.122  -0.118  -0.102  -0.310  -0.301  -0.276  -0.312  -0.304  -0.278
15    L        -0.122  -0.118  -0.102  -0.708  -0.700  -0.674  -0.312  -0.304  -0.278
16    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    S        -0.122  -0.118  -0.102  -0.103  -0.094  -0.069  -0.312  -0.304  -0.278
19    Q        -0.122  -0.118  -0.102  -0.074  -0.066  -0.041  -0.312  -0.304  -0.278
20    I        -0.122  -0.118  -0.102  -0.708  -0.700  -0.674  -0.312  -0.304  -0.278
21    F        -0.122  -0.118  -0.102  -0.003   0.005   0.030  -0.312  -0.304  -0.278
22    H        -0.122  -0.118  -0.102  -0.117  -0.109  -0.084  -0.312  -0.304  -0.278
23    N        -0.122  -0.118  -0.102  -0.003   0.005   0.030  -0.312  -0.304  -0.278
24    W         1.690   1.697   1.710   1.951   1.959   1.981   1.805   1.813   1.830
25    A        -0.122  -0.118  -0.102  -0.003   0.005   0.030  -0.312  -0.304  -0.278
26    L        -0.122  -0.118  -0.102  -0.512  -0.503  -0.478  -0.312  -0.304  -0.278
27    C        -0.122  -0.118  -0.102   0.243   0.252   0.276  -0.312  -0.304  -0.278
28    Q        -0.122  -0.118  -0.102  -0.279  -0.271  -0.246  -0.312  -0.304  -0.278
29    D        -0.122  -0.118  -0.102  -0.103  -0.094  -0.069  -0.312  -0.304  -0.278
30    V         1.690   1.697   1.710   1.793   1.802   1.824   1.805   1.813   1.830
31    H        -0.122  -0.118  -0.102   0.025   0.033   0.058  -0.312  -0.304  -0.278
32    L         1.690   1.697   1.710   1.164   1.172   1.195   1.805   1.813   1.830
33    N        -0.122  -0.118  -0.102  -0.190  -0.182  -0.156  -0.312  -0.304  -0.278
34    D        -0.122  -0.118  -0.102  -0.117  -0.109  -0.084  -0.312  -0.304  -0.278
35    E         1.690   1.697   1.710   1.733   1.742   1.764   1.805   1.813   1.830
36    K        -0.122  -0.118  -0.102  -0.190  -0.182  -0.156  -0.312  -0.304  -0.278
37    D        -0.122  -0.118  -0.102  -0.325  -0.316  -0.291  -0.312  -0.304  -0.278
38    G        -0.122  -0.118  -0.102  -0.017  -0.009   0.016  -0.312  -0.304  -0.278
39    L        -0.122  -0.118  -0.102  -0.402  -0.393  -0.368  -0.312  -0.304  -0.278
40    L        -0.122  -0.118  -0.102  -0.708  -0.700  -0.674  -0.312  -0.304  -0.278
41    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    R         0.026  -0.012  -0.035  -0.156  -0.246  -0.319  -0.076  -0.134  -0.171
43    L         0.026  -0.012  -0.035  -0.507  -0.556  -0.577  -0.076  -0.134  -0.171
44    I        -1.183  -1.175  -1.162  -0.971  -0.960  -0.937  -1.017  -1.005  -0.981
45    P        -1.183  -1.175  -1.162  -0.810  -0.793  -0.775  -1.017  -1.005  -0.981
46    T        -1.183  -1.175  -1.162  -0.920  -0.894  -0.885  -1.017  -1.005  -0.981
47    R         1.690   1.697   1.710   1.794   1.800   1.825   1.805   1.813   1.830
48    Q         0.026   0.035  -0.006   0.142   0.159   0.088  -0.076  -0.062  -0.125
49    L         0.026  -0.012  -0.035  -0.424  -0.462  -0.478  -0.076  -0.134  -0.171
50    Q         0.026   0.035  -0.006   0.200   0.216   0.153  -0.076  -0.062  -0.125
51    K         0.026  -0.012  -0.035   0.321   0.264   0.229  -0.076  -0.134  -0.171
52    N        -1.183  -1.175  -1.162  -1.206  -1.230  -1.171  -1.017  -1.005  -0.981
53    T         0.026   0.035  -0.006  -0.156  -0.133  -0.244  -0.076  -0.062  -0.125
54    E        -0.122  -0.118  -0.102  -0.057  -0.049  -0.024  -0.312  -0.304  -0.278
55    R        -0.122  -0.118  -0.102  -0.615  -0.606  -0.580  -0.312  -0.304  -0.278
56    I        -0.122  -0.118  -0.102  -0.664  -0.655  -0.629  -0.312  -0.304  -0.278
57    E        -0.122  -0.118  -0.102  -0.128  -0.120  -0.095  -0.312  -0.304  -0.278
58    N        -0.122  -0.118  -0.102   0.108   0.117   0.142  -0.312  -0.304  -0.278
59    K        -0.122  -0.118  -0.102  -0.015  -0.007   0.018  -0.312  -0.304  -0.278
60    L         1.690   1.697   1.710   1.086   1.094   1.118   1.805   1.813   1.830
61    L        -0.122  -0.118  -0.102  -0.615  -0.606  -0.580  -0.312  -0.304  -0.278
62    N        -0.122  -0.118  -0.102   0.108   0.117   0.142  -0.312  -0.304  -0.278
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    H         1.690   1.697   1.710   1.912   1.921   1.943   1.805   1.813   1.830
82    I         1.690   1.697   1.710   1.663   1.671   1.695   1.805   1.813   1.830
83    E         1.690   1.697   1.710   1.751   1.763   1.782   1.805   1.813   1.830
84    L         1.690   1.697   1.710   1.110   1.122   1.142   1.805   1.813   1.830
85    Y        -1.183  -1.175  -1.162  -1.311  -1.292  -1.275  -1.017  -1.005  -0.981
86    L         0.026   0.074  -0.001  -0.284  -0.180  -0.359  -0.076  -0.000  -0.118
87    T         0.026  -0.012  -0.035   0.213   0.161   0.125  -0.076  -0.134  -0.171
88    Y         0.026   0.035  -0.006   0.296   0.312   0.250  -0.076  -0.062  -0.125
89    S         0.026  -0.012  -0.035  -0.032  -0.096  -0.131  -0.076  -0.134  -0.171
90    K         0.026   0.035  -0.006   0.252   0.265   0.197  -0.076  -0.062  -0.125
91    V         1.690   1.697   1.710   1.751   1.752   1.782   1.805   1.813   1.830
92    Y         1.690   1.697   1.710   1.879   1.888   1.910   1.805   1.813   1.830
93    N        -1.183  -1.175  -1.162  -0.869  -0.861  -0.834  -1.017  -1.005  -0.981
94    E         0.026  -0.012  -0.035   0.089   0.028  -0.013  -0.076  -0.134  -0.171
95    P         1.690   1.697   1.710   1.950   1.960   1.980   1.805   1.813   1.830
96    L         0.026  -0.012  -0.035  -0.569  -0.622  -0.651  -0.076  -0.134  -0.171
97    L         0.026  -0.012  -0.035  -0.553  -0.602  -0.632  -0.076  -0.134  -0.171
98    L         0.026  -0.012  -0.035  -0.484  -0.528  -0.550  -0.076  -0.134  -0.171
99    L        -1.183  -1.175  -1.162  -1.359  -1.303  -1.324  -1.017  -1.005  -0.981
100   R         1.690   1.697   1.710   1.794   1.800   1.825   1.805   1.813   1.830
101   I        -1.183  -1.175  -1.162  -1.500  -1.516  -1.465  -1.017  -1.005  -0.981
102   W         1.690   1.697   1.710   1.950   1.960   1.980   1.805   1.813   1.830
103   E         0.026   0.035  -0.006   0.181   0.198   0.139  -0.076  -0.062  -0.125
104   E        -1.183  -1.175  -1.162  -0.885  -0.856  -0.851  -1.017  -1.005  -0.981
105   K        -1.183  -1.175  -1.162  -0.802  -0.785  -0.767  -1.017  -1.005  -0.981
106   S        -1.183  -1.175  -1.162  -1.379  -1.393  -1.344  -1.017  -1.005  -0.981
107   I        -1.183  -1.175  -1.162  -1.521  -1.498  -1.486  -1.017  -1.005  -0.981
108   D         1.690   1.697   1.710   1.722   1.730   1.753   1.805   1.813   1.830
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   G         0.026  -0.012  -0.035   0.283   0.222   0.168  -0.076  -0.134  -0.171
111   I         0.026  -0.012  -0.035   0.009  -0.054  -0.089  -0.076  -0.134  -0.171
112   P        -1.183  -1.175  -1.162  -0.989  -0.987  -0.954  -1.017  -1.005  -0.981
113   M        -1.183  -1.175  -1.162  -0.920  -0.922  -0.885  -1.017  -1.005  -0.981
114   T         0.026   0.074  -0.001   0.002   0.075  -0.038  -0.076  -0.000  -0.118
115   K         0.026   0.035  -0.006   0.258   0.272   0.204  -0.076  -0.062  -0.125
116   L         1.690   1.697   1.710   1.110   1.122   1.142   1.805   1.813   1.830
117   M        -1.183  -1.175  -1.162  -1.123  -1.149  -1.088  -1.017  -1.005  -0.981
118   L        -1.183  -1.175  -1.162  -1.159  -1.106  -1.125  -1.017  -1.005  -0.981
119   P        -1.183  -1.175  -1.162  -1.379  -1.403  -1.344  -1.017  -1.005  -0.981
120   T        -1.183  -1.175  -1.162  -0.963  -0.958  -0.928  -1.017  -1.005  -0.981
121   D         0.026   0.035  -0.006   0.063   0.079   0.011  -0.076  -0.062  -0.125
122   I        -1.183  -1.175  -1.162  -1.069  -1.053  -1.034  -1.017  -1.005  -0.981
123   E         0.026   0.035  -0.006   0.213   0.231   0.175  -0.076  -0.062  -0.125
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   S        -1.183  -1.175  -1.162  -0.963  -0.947  -0.928  -1.017  -1.005  -0.981
126   L        -1.183  -1.175  -1.162  -1.490  -1.450  -1.455  -1.017  -1.005  -0.981
127   L         0.026  -0.012  -0.035  -0.553  -0.602  -0.632  -0.076  -0.134  -0.171
128   D        -1.183  -1.175  -1.162  -1.087  -1.076  -1.052  -1.017  -1.005  -0.981
129   V        -1.183  -1.175  -1.162  -0.971  -0.953  -0.937  -1.017  -1.005  -0.981
130   Q        -1.183  -1.175  -1.162  -1.263  -1.277  -1.227  -1.017  -1.005  -0.981
131   G        -1.183  -1.175  -1.162  -0.860  -0.846  -0.826  -1.017  -1.005  -0.981
132   K        -1.183  -1.175  -1.162  -0.937  -0.937  -0.902  -1.017  -1.005  -0.981
133   F         0.026   0.035  -0.006  -0.005   0.016  -0.096  -0.076  -0.062  -0.125
134   Q        -1.183  -1.175  -1.162  -1.051  -1.044  -1.016  -1.017  -1.005  -0.981
135   L         0.026  -0.012  -0.035  -0.507  -0.556  -0.577  -0.076  -0.134  -0.171
136   G         0.026  -0.012  -0.035   0.245   0.178   0.122  -0.076  -0.134  -0.171
137   L         1.690   1.697   1.710   1.110   1.122   1.142   1.805   1.813   1.830
138   D         0.026  -0.012  -0.035   0.009  -0.059  -0.102  -0.076  -0.134  -0.171
139   T         0.026  -0.012  -0.035   0.076   0.010  -0.039  -0.076  -0.134  -0.171
140   I         0.026  -0.012  -0.035  -0.005  -0.065  -0.105  -0.076  -0.134  -0.171
141   I        -1.183  -1.175  -1.162  -1.359  -1.323  -1.324  -1.017  -1.005  -0.981
142   N        -1.183  -1.175  -1.162  -0.920  -0.909  -0.885  -1.017  -1.005  -0.981
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   L         0.026  -0.012  -0.035  -0.484  -0.525  -0.550  -0.076  -0.134  -0.171
150   E        -1.183  -1.175  -1.162  -0.911  -0.888  -0.876  -1.017  -1.005  -0.981
151   G         0.026  -0.012  -0.035   0.296   0.238   0.183  -0.076  -0.134  -0.171
152   S        -1.183  -1.175  -1.162  -0.989  -0.979  -0.954  -1.017  -1.005  -0.981
153   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   W         1.690   1.697   1.710   1.950   1.960   1.980   1.805   1.813   1.830
155   Y         1.690   1.697   1.710   1.879   1.888   1.910   1.805   1.813   1.830
156   S         0.026  -0.012  -0.035   0.082   0.030   0.005  -0.076  -0.134  -0.171
157   F         0.026   0.074  -0.001   0.181   0.246   0.145  -0.076  -0.000  -0.118
158   H         0.026  -0.012  -0.035   0.365   0.308   0.269  -0.076  -0.134  -0.171
159   P         0.026  -0.012  -0.035   0.353   0.296   0.257  -0.076  -0.134  -0.171
160   C         1.690   1.697   1.710   2.061   2.071   2.091   1.805   1.813   1.830
161   D         1.690   1.697   1.710   1.722   1.730   1.753   1.805   1.813   1.830
162   T         1.690   1.697   1.710   1.794   1.805   1.825   1.805   1.813   1.830
163   S        -1.183  -1.175  -1.162  -1.105  -1.090  -1.070  -1.017  -1.005  -0.981
164   C        -1.183  -1.175  -1.162  -0.752  -0.742  -0.718  -1.017  -1.005  -0.981
165   I         0.026  -0.012  -0.035   0.096   0.043   0.015  -0.076  -0.134  -0.171
166   V         1.690   1.697   1.710   1.751   1.752   1.782   1.805   1.813   1.830
167   G         1.690   1.697   1.710   1.978   1.992   2.008   1.805   1.813   1.830
168   D         0.026  -0.012  -0.035   0.082   0.025  -0.014  -0.076  -0.134  -0.171
169   Q        -1.183  -1.175  -1.162  -1.024  -1.009  -0.989  -1.017  -1.005  -0.981
170   A        -1.183  -1.175  -1.162  -0.802  -0.791  -0.767  -1.017  -1.005  -0.981
171   E         0.026   0.035  -0.006   0.109   0.129   0.059  -0.076  -0.062  -0.125
172   F        -0.122  -0.118  -0.102   0.026   0.035   0.060  -0.312  -0.304  -0.278
173   M        -0.122  -0.118  -0.102   0.068   0.076   0.101  -0.312  -0.304  -0.278
174   S        -0.122  -0.118  -0.102  -0.201  -0.192  -0.167  -0.312  -0.304  -0.278
175   T         0.026  -0.012  -0.035   0.148   0.090   0.048  -0.076  -0.134  -0.171
176   Y         1.690   1.697   1.710   1.879   1.888   1.910   1.805   1.813   1.830
177   L         1.690   1.697   1.710   1.110   1.122   1.142   1.805   1.813   1.830
178   R        -1.183  -1.175  -1.162  -1.429  -1.446  -1.394  -1.017  -1.005  -0.981
179   R         1.690   1.697   1.710   1.794   1.800   1.825   1.805   1.813   1.830
180   W         1.690   1.697   1.710   1.950   1.960   1.980   1.805   1.813   1.830
181   V         0.026  -0.012  -0.035   0.049  -0.022  -0.061  -0.076  -0.134  -0.171
182   S         1.690   1.697   1.710   1.634   1.638   1.665   1.805   1.813   1.830
183   I        -1.183  -1.175  -1.162  -1.500  -1.516  -1.465  -1.017  -1.005  -0.981
184   F         0.026  -0.012  -0.035   0.328   0.269   0.227  -0.076  -0.134  -0.171
185   I         0.026   0.074  -0.001  -0.553  -0.478  -0.587  -0.076  -0.000  -0.118
186   F        -1.183  -1.175  -1.162  -1.263  -1.248  -1.227  -1.017  -1.005  -0.981
187   S        -0.122  -0.118  -0.102  -0.402  -0.393  -0.368  -0.312  -0.304  -0.278
188   W         0.026  -0.012  -0.035   0.359   0.304   0.264  -0.076  -0.134  -0.171
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   L         1.690   1.697   1.710   1.164   1.172   1.195   1.805   1.813   1.830
193   G        -0.122  -0.118  -0.102   0.081   0.089   0.114  -0.312  -0.304  -0.278
194   Y        -0.122  -0.118  -0.102  -0.175  -0.167  -0.142  -0.312  -0.304  -0.278
195   E        -1.183  -1.175  -1.162  -0.877  -0.852  -0.842  -1.017  -1.005  -0.981
196   D        -1.183  -1.175  -1.162  -1.244  -1.255  -1.208  -1.017  -1.005  -0.981
197   S        -1.183  -1.175  -1.162  -1.141  -1.129  -1.106  -1.017  -1.005  -0.981
* 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/Q07879
Output conservation file - output/Q07879
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
