1     M         1.520   1.522   1.538   1.819   1.821   1.844   1.605   1.607   1.627
2     S        -0.010  -0.033  -0.062  -0.094  -0.148  -0.178  -0.130  -0.166  -0.211
3     F        -0.146  -0.145  -0.127  -0.452  -0.453  -0.420  -0.347  -0.345  -0.316
4     A        -0.146  -0.145  -0.127  -0.109  -0.116  -0.078  -0.347  -0.345  -0.316
5     S        -0.146  -0.145  -0.127  -0.316  -0.314  -0.285  -0.347  -0.345  -0.316
6     R        -0.146  -0.145  -0.127  -0.211  -0.220  -0.180  -0.347  -0.345  -0.316
7     N        -0.146  -0.145  -0.127  -0.147  -0.129  -0.116  -0.347  -0.345  -0.316
8     I        -0.146  -0.145  -0.127  -0.535  -0.538  -0.503  -0.347  -0.345  -0.316
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    G        -0.146  -0.145  -0.127  -0.084  -0.064  -0.053  -0.347  -0.345  -0.316
11    R        -0.146  -0.145  -0.127  -0.122  -0.129  -0.091  -0.347  -0.345  -0.316
12    K        -0.146  -0.145  -0.127  -0.303  -0.274  -0.272  -0.347  -0.345  -0.316
13    I        -0.010  -0.002  -0.055   0.035   0.064  -0.043  -0.130  -0.118  -0.200
14    A        -1.121  -1.119  -1.102  -1.363  -1.346  -1.329  -0.998  -0.994  -0.963
15    G        -0.010  -0.033  -0.062   0.058   0.008  -0.047  -0.130  -0.166  -0.211
16    V        -0.010  -0.033  -0.062   0.018  -0.002  -0.076  -0.130  -0.166  -0.211
17    G        -0.010  -0.033  -0.062   0.098   0.055  -0.000  -0.130  -0.166  -0.211
18    V        -1.121  -1.119  -1.102  -0.864  -0.854  -0.831  -0.998  -0.994  -0.963
19    D         1.520   1.522   1.538   1.647   1.645   1.672   1.605   1.607   1.627
20    I        -0.010   0.011  -0.040   0.029   0.064  -0.023  -0.130  -0.097  -0.177
21    V         1.520   1.522   1.538   1.597   1.623   1.622   1.605   1.607   1.627
22    Y        -1.121  -1.119  -1.102  -0.886  -0.891  -0.853  -0.998  -0.994  -0.963
23    L         1.520   1.522   1.538   1.097   1.118   1.123   1.605   1.607   1.627
24    P         1.520   1.522   1.538   1.697   1.696   1.722   1.605   1.607   1.627
25    R         1.520   1.522   1.538   1.597   1.596   1.622   1.605   1.607   1.627
26    F        -1.121  -1.119  -1.102  -0.827  -0.818  -0.794  -0.998  -0.994  -0.963
27    A        -1.121  -1.119  -1.102  -0.968  -0.972  -0.935  -0.998  -0.994  -0.963
28    H        -1.121  -1.119  -1.102  -1.029  -1.040  -0.996  -0.998  -0.994  -0.963
29    I        -0.010  -0.002  -0.055  -0.428  -0.405  -0.485  -0.130  -0.118  -0.200
30    L         1.520   1.522   1.538   1.097   1.118   1.123   1.605   1.607   1.627
31    E        -1.121  -1.119  -1.102  -0.879  -0.879  -0.845  -0.998  -0.994  -0.963
32    K        -0.010  -0.033  -0.062  -0.041  -0.087  -0.126  -0.130  -0.166  -0.211
33    Y        -0.010  -0.033  -0.062   0.137   0.105   0.052  -0.130  -0.166  -0.211
34    S        -0.010   0.011  -0.040  -0.064  -0.046  -0.110  -0.130  -0.097  -0.177
35    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    C        -0.146  -0.145  -0.127  -0.137  -0.140  -0.106  -0.347  -0.345  -0.316
40    G         1.520   1.522   1.538   1.620   1.619   1.645   1.605   1.607   1.627
41    R        -0.010  -0.002  -0.055  -0.088  -0.089  -0.159  -0.130  -0.118  -0.200
42    S        -0.010   0.011  -0.040  -0.088  -0.068  -0.136  -0.130  -0.097  -0.177
43    T        -1.121  -1.119  -1.102  -0.946  -0.950  -0.912  -0.998  -0.994  -0.963
44    L        -0.010   0.011  -0.040  -0.377  -0.334  -0.409  -0.130  -0.097  -0.177
45    N        -1.121  -1.119  -1.102  -0.842  -0.834  -0.809  -0.998  -0.994  -0.963
46    K        -0.010  -0.002  -0.055   0.000   0.006  -0.084  -0.130  -0.118  -0.200
47    I        -0.010   0.011  -0.040   0.029   0.064  -0.023  -0.130  -0.097  -0.177
48    T        -1.121  -1.119  -1.102  -1.304  -1.291  -1.269  -0.998  -0.994  -0.963
49    R        -1.121  -1.119  -1.102  -1.155  -1.166  -1.121  -0.998  -0.994  -0.963
50    K         1.520   1.522   1.538   1.508   1.503   1.534   1.605   1.607   1.627
51    F         1.520   1.522   1.538   1.684   1.683   1.709   1.605   1.607   1.627
52    M         1.520   1.522   1.538   1.819   1.821   1.844   1.605   1.607   1.627
53    H         1.520   1.522   1.538   1.660   1.657   1.685   1.605   1.607   1.627
54    E        -0.010  -0.002  -0.055   0.160   0.166   0.083  -0.130  -0.118  -0.200
55    K        -1.121  -1.119  -1.102  -1.014  -1.019  -0.980  -0.998  -0.994  -0.963
56    E         1.520   1.522   1.538   1.660   1.658   1.685   1.605   1.607   1.627
57    R        -0.010  -0.033  -0.062   0.035  -0.013  -0.056  -0.130  -0.166  -0.211
58    F        -1.121  -1.119  -1.102  -1.022  -1.035  -0.988  -0.998  -0.994  -0.963
59    H        -0.146  -0.145  -0.127  -0.034  -0.039  -0.004  -0.347  -0.345  -0.316
60    F         1.520   1.522   1.538   1.631   1.628   1.656   1.605   1.607   1.627
61    S        -0.146  -0.145  -0.127  -0.343  -0.342  -0.312  -0.347  -0.345  -0.316
62    N        -1.121  -1.119  -1.102  -0.976  -0.964  -0.942  -0.998  -0.994  -0.963
63    L         1.520   1.522   1.538   1.097   1.118   1.123   1.605   1.607   1.627
64    L        -1.121  -1.119  -1.102  -1.262  -1.230  -1.227  -0.998  -0.994  -0.963
65    I        -1.121  -1.119  -1.102  -0.968  -0.943  -0.935  -0.998  -0.994  -0.963
66    E        -1.121  -1.119  -1.102  -1.029  -1.045  -0.996  -0.998  -0.994  -0.963
67    E        -0.010  -0.002  -0.055   0.148   0.158   0.072  -0.130  -0.118  -0.200
68    N        -1.121  -1.119  -1.102  -1.076  -1.074  -1.042  -0.998  -0.994  -0.963
69    C        -0.010  -0.002  -0.055   0.018   0.017  -0.038  -0.130  -0.118  -0.200
70    L         1.520   1.522   1.538   1.097   1.118   1.123   1.605   1.607   1.627
71    T        -1.121  -1.119  -1.102  -1.139  -1.151  -1.105  -0.998  -0.994  -0.963
72    P        -1.121  -1.119  -1.102  -0.946  -0.947  -0.912  -0.998  -0.994  -0.963
73    R        -1.121  -1.119  -1.102  -1.014  -1.023  -0.980  -0.998  -0.994  -0.963
74    L        -1.121  -1.119  -1.102  -1.321  -1.319  -1.286  -0.998  -0.994  -0.963
75    H        -0.010  -0.002  -0.055   0.058   0.058  -0.014  -0.130  -0.118  -0.200
76    E        -0.146  -0.145  -0.127  -0.163  -0.167  -0.132  -0.347  -0.345  -0.316
77    Y         1.520   1.522   1.538   1.660   1.658   1.685   1.605   1.607   1.627
78    I         1.520   1.522   1.538   1.584   1.577   1.610   1.605   1.607   1.627
79    A         1.520   1.522   1.538   1.546   1.547   1.572   1.605   1.607   1.627
80    G         1.520   1.522   1.538   1.684   1.686   1.709   1.605   1.607   1.627
81    V        -0.010   0.011  -0.040   0.052   0.106   0.001  -0.130  -0.097  -0.177
82    W         1.520   1.522   1.538   1.880   1.881   1.904   1.605   1.607   1.627
83    A         1.520   1.522   1.538   1.546   1.547   1.572   1.605   1.607   1.627
84    L        -0.010  -0.033  -0.062  -0.494  -0.519  -0.572  -0.130  -0.166  -0.211
85    K         1.520   1.522   1.538   1.508   1.503   1.534   1.605   1.607   1.627
86    E         1.520   1.522   1.538   1.660   1.658   1.685   1.605   1.607   1.627
87    C        -1.121  -1.119  -1.102  -0.991  -1.001  -0.957  -0.998  -0.994  -0.963
88    S        -1.121  -1.119  -1.102  -1.451  -1.458  -1.416  -0.998  -0.994  -0.963
89    L        -0.010  -0.033  -0.062  -0.377  -0.393  -0.434  -0.130  -0.166  -0.211
90    K         1.520   1.522   1.538   1.508   1.503   1.534   1.605   1.607   1.627
91    A        -0.010  -0.033  -0.062   0.006  -0.035  -0.079  -0.130  -0.166  -0.211
92    L         1.520   1.522   1.538   1.097   1.118   1.123   1.605   1.607   1.627
93    C        -0.146  -0.145  -0.127   0.008   0.006   0.038  -0.347  -0.345  -0.316
94    C         1.520   1.522   1.538   1.785   1.786   1.809   1.605   1.607   1.627
95    C        -0.146  -0.145  -0.127  -0.137  -0.140  -0.106  -0.347  -0.345  -0.316
96    V        -0.146  -0.145  -0.127  -0.314  -0.305  -0.282  -0.347  -0.345  -0.316
97    S        -0.010  -0.002  -0.055   0.069   0.074  -0.022  -0.130  -0.118  -0.200
98    K        -1.121  -1.119  -1.102  -1.338  -1.319  -1.303  -0.998  -0.994  -0.963
99    H        -0.010  -0.033  -0.062   0.035  -0.019  -0.069  -0.130  -0.166  -0.211
100   D        -1.121  -1.119  -1.102  -1.053  -1.068  -1.019  -0.998  -0.994  -0.963
101   -        -0.146  -0.145  -0.127  -0.148  -0.146  -0.117  -0.347  -0.345  -0.316
102   L        -0.010  -0.033  -0.062  -0.422  -0.439  -0.487  -0.130  -0.166  -0.211
103   P         1.520   1.522   1.538   1.697   1.696   1.722   1.605   1.607   1.627
104   P        -0.010  -0.033  -0.062   0.069   0.016  -0.037  -0.130  -0.166  -0.211
105   A         1.520   1.522   1.538   1.546   1.547   1.572   1.605   1.607   1.627
106   Q        -1.121  -1.119  -1.102  -0.806  -0.816  -0.773  -0.998  -0.994  -0.963
107   V        -1.121  -1.119  -1.102  -0.931  -0.920  -0.897  -0.998  -0.994  -0.963
108   L        -0.010  -0.002  -0.055  -0.196  -0.183  -0.310  -0.130  -0.118  -0.200
109   Y         1.520   1.522   1.538   1.660   1.658   1.685   1.605   1.607   1.627
110   A        -0.010  -0.002  -0.055   0.041   0.049  -0.041  -0.130  -0.118  -0.200
111   G        -0.010  -0.002  -0.055   0.000   0.004  -0.067  -0.130  -0.118  -0.200
112   M        -0.010  -0.002  -0.055  -0.307  -0.282  -0.346  -0.130  -0.118  -0.200
113   L        -0.010  -0.033  -0.062  -0.448  -0.466  -0.518  -0.130  -0.166  -0.211
114   Y        -0.010  -0.033  -0.062   0.137   0.094   0.052  -0.130  -0.166  -0.211
115   K        -0.010   0.011  -0.040  -0.041  -0.016  -0.091  -0.130  -0.097  -0.177
116   T        -1.121  -1.119  -1.102  -0.999  -1.013  -0.965  -0.998  -0.994  -0.963
117   Q        -1.121  -1.119  -1.102  -0.879  -0.866  -0.845  -0.998  -0.994  -0.963
118   T        -1.121  -1.119  -1.102  -0.968  -0.972  -0.935  -0.998  -0.994  -0.963
119   D        -1.121  -1.119  -1.102  -1.006  -1.011  -0.973  -0.998  -0.994  -0.963
120   T        -1.121  -1.119  -1.102  -0.916  -0.908  -0.882  -0.998  -0.994  -0.963
121   G         1.520   1.522   1.538   1.684   1.686   1.709   1.605   1.607   1.627
122   V        -0.010  -0.033  -0.062   0.000  -0.023  -0.097  -0.130  -0.166  -0.211
123   P         1.520   1.522   1.538   1.697   1.696   1.722   1.605   1.607   1.627
124   Q        -0.010  -0.033  -0.062   0.204   0.173   0.115  -0.130  -0.166  -0.211
125   L         1.520   1.522   1.538   1.097   1.118   1.123   1.605   1.607   1.627
126   E        -1.121  -1.119  -1.102  -1.220  -1.184  -1.186  -0.998  -0.994  -0.963
127   F        -0.010  -0.002  -0.055  -0.377  -0.352  -0.426  -0.130  -0.118  -0.200
128   D         1.520   1.522   1.538   1.647   1.645   1.672   1.605   1.607   1.627
129   K        -1.121  -1.119  -1.102  -0.931  -0.920  -0.897  -0.998  -0.994  -0.963
130   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   K         1.520   1.522   1.538   1.415   1.426   1.441   1.605   1.607   1.627
134   K        -0.146  -0.145  -0.127  -0.290  -0.287  -0.259  -0.347  -0.345  -0.316
135   Y        -0.146  -0.145  -0.127  -0.134  -0.142  -0.104  -0.347  -0.345  -0.316
136   P        -0.146  -0.145  -0.127  -0.303  -0.301  -0.272  -0.347  -0.345  -0.316
137   K        -0.146  -0.145  -0.127  -0.290  -0.287  -0.259  -0.347  -0.345  -0.316
138   Y        -0.146  -0.145  -0.127  -0.071  -0.077  -0.041  -0.347  -0.345  -0.316
139   Q        -0.010  -0.002  -0.055   0.160   0.166   0.090  -0.130  -0.118  -0.200
140   Q        -1.121  -1.119  -1.102  -0.923  -0.924  -0.890  -0.998  -0.994  -0.963
141   L        -0.010  -0.033  -0.062  -0.377  -0.380  -0.434  -0.130  -0.166  -0.211
142   S        -1.121  -1.119  -1.102  -1.107  -1.120  -1.074  -0.998  -0.994  -0.963
143   K        -1.121  -1.119  -1.102  -1.363  -1.344  -1.329  -0.998  -0.994  -0.963
144   N        -1.121  -1.119  -1.102  -0.893  -0.885  -0.860  -0.998  -0.994  -0.963
145   Y        -1.121  -1.119  -1.102  -0.727  -0.724  -0.695  -0.998  -0.994  -0.963
146   D        -1.121  -1.119  -1.102  -1.228  -1.192  -1.194  -0.998  -0.994  -0.963
147   S        -1.121  -1.119  -1.102  -0.976  -0.984  -0.942  -0.998  -0.994  -0.963
148   L        -1.121  -1.119  -1.102  -1.220  -1.208  -1.186  -0.998  -0.994  -0.963
149   F        -0.010  -0.002  -0.055  -0.377  -0.352  -0.426  -0.130  -0.118  -0.200
150   S        -1.121  -1.119  -1.102  -1.060  -1.068  -1.027  -0.998  -0.994  -0.963
151   T        -1.121  -1.119  -1.102  -0.999  -1.013  -0.965  -0.998  -0.994  -0.963
152   H        -1.121  -1.119  -1.102  -0.991  -0.994  -0.957  -0.998  -0.994  -0.963
153   E        -1.121  -1.119  -1.102  -1.029  -1.035  -0.996  -0.998  -0.994  -0.963
154   F        -0.010  -0.033  -0.062   0.148   0.104   0.060  -0.130  -0.166  -0.211
155   L        -0.010  -0.033  -0.062  -0.390  -0.406  -0.449  -0.130  -0.166  -0.211
156   V        -1.121  -1.119  -1.102  -1.107  -1.101  -1.074  -0.998  -0.994  -0.963
157   S        -0.010   0.011  -0.040  -0.076  -0.056  -0.123  -0.130  -0.097  -0.177
158   L        -0.010  -0.033  -0.062  -0.428  -0.450  -0.495  -0.130  -0.166  -0.211
159   S         1.520   1.522   1.538   1.457   1.447   1.482   1.605   1.607   1.627
160   H         1.520   1.522   1.538   1.660   1.657   1.685   1.605   1.607   1.627
161   D         1.520   1.522   1.538   1.647   1.645   1.672   1.605   1.607   1.627
162   K        -1.121  -1.119  -1.102  -0.931  -0.920  -0.897  -0.998  -0.994  -0.963
163   D        -0.010   0.011  -0.040   0.115   0.141   0.064  -0.130  -0.097  -0.177
164   Y         1.520   1.522   1.538   1.660   1.658   1.685   1.605   1.607   1.627
165   L         1.520   1.522   1.538   1.097   1.118   1.123   1.605   1.607   1.627
166   I        -0.010   0.011  -0.040   0.029   0.064  -0.023  -0.130  -0.097  -0.177
167   A        -0.010  -0.033  -0.062   0.098   0.063   0.029  -0.130  -0.166  -0.211
168   V        -1.121  -1.119  -1.102  -0.983  -0.977  -0.950  -0.998  -0.994  -0.963
169   T        -0.010  -0.033  -0.062  -0.160  -0.207  -0.293  -0.130  -0.166  -0.211
170   N        -1.121  -1.119  -1.102  -1.245  -1.236  -1.211  -0.998  -0.994  -0.963
171   L        -0.010  -0.033  -0.062  -0.390  -0.407  -0.449  -0.130  -0.166  -0.211
172   V        -1.121  -1.119  -1.102  -1.329  -1.319  -1.294  -0.998  -0.994  -0.963
173   E        -1.121  -1.119  -1.102  -0.946  -0.952  -0.912  -0.998  -0.994  -0.963
174   R        -1.121  -1.119  -1.102  -0.968  -0.972  -0.935  -0.998  -0.994  -0.963
175   E        -1.121  -1.119  -1.102  -1.060  -1.066  -1.027  -0.998  -0.994  -0.963
176   -         1.520   1.522   1.538   1.659   1.662   1.684   1.605   1.607   1.627
177   -         1.520   1.522   1.538   1.067   1.069   1.094   1.605   1.607   1.627
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -         1.520   1.522   1.538   1.621   1.624   1.646   1.605   1.607   1.627
* 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/Q12036
Output conservation file - output/Q12036
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
