1     M         1.707   1.771   1.808   2.008   2.114   2.176   1.893   1.980   2.043
2     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -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    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    R         0.438   0.487   0.380   0.574   0.655   0.478   0.339   0.417   0.226
32    I         0.438   0.487   0.380   0.309   0.384   0.227   0.339   0.417   0.226
33    V        -0.638  -0.696  -0.665  -0.735  -0.824  -0.794  -0.696  -0.752  -0.703
34    V         0.143   0.188   0.233  -0.133  -0.054   0.028  -0.178  -0.104  -0.036
35    K         0.438   0.487   0.380   0.460   0.537   0.355   0.339   0.417   0.226
36    A        -1.420  -1.372  -1.352  -1.279  -1.188  -1.156  -1.214  -1.131  -1.090
37    I         0.438   0.319   0.334   0.473   0.238   0.261   0.339   0.131   0.145
38    E         0.438   0.319   0.334   0.369   0.174   0.209   0.339   0.131   0.145
39    P        -0.638  -0.696  -0.665  -0.712  -0.804  -0.733  -0.696  -0.752  -0.703
40    K        -0.638  -0.640  -0.642  -0.770  -0.780  -0.781  -0.696  -0.685  -0.673
41    D         1.707   1.771   1.808   1.714   1.819   1.878   1.893   1.980   2.043
42    E        -0.638  -0.696  -0.665  -0.829  -0.945  -0.897  -0.696  -0.752  -0.703
43    E         0.143   0.188   0.233  -0.023   0.061   0.140  -0.178  -0.104  -0.036
44    A        -0.638  -0.647  -0.648  -0.726  -0.754  -0.750  -0.696  -0.694  -0.680
45    W         0.438   0.319   0.334   0.596   0.373   0.379   0.339   0.131   0.145
46    N        -1.420  -1.372  -1.352  -1.450  -1.335  -1.330  -1.214  -1.131  -1.090
47    K        -1.420  -1.372  -1.352  -1.089  -0.993  -0.963  -1.214  -1.131  -1.090
48    L         0.438   0.319   0.334   0.345   0.158   0.191   0.339   0.131   0.145
49    W        -0.638  -0.640  -0.642  -0.512  -0.519  -0.534  -0.696  -0.685  -0.673
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    K        -0.638  -0.471  -0.598  -0.730  -0.432  -0.660  -0.696  -0.451  -0.616
54    E         0.143   0.206   0.247  -0.163  -0.063   0.003  -0.178  -0.072  -0.012
55    Y         0.438   0.319   0.334   0.375   0.162   0.173   0.339   0.131   0.145
56    Q        -1.420  -1.372  -1.352  -1.306  -1.249  -1.183  -1.214  -1.131  -1.090
57    G        -0.638  -0.537  -0.612  -0.775  -0.603  -0.726  -0.696  -0.541  -0.633
58    F         1.707   1.771   1.808   1.823   1.933   1.989   1.893   1.980   2.043
59    Q        -0.638  -0.696  -0.665  -0.634  -0.743  -0.661  -0.696  -0.752  -0.703
60    K         0.438   0.577   0.404   0.437   0.667   0.397   0.339   0.565   0.268
61    T        -0.638  -0.696  -0.665  -0.434  -0.481  -0.458  -0.696  -0.752  -0.703
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    V        -1.420  -1.372  -1.352  -1.328  -1.207  -1.205  -1.214  -1.131  -1.090
65    M        -1.420  -1.372  -1.352  -1.180  -1.150  -1.055  -1.214  -1.131  -1.090
66    P        -0.638  -0.696  -0.665  -0.647  -0.753  -0.684  -0.696  -0.752  -0.703
67    P         0.438   0.319   0.334   0.609   0.390   0.420   0.339   0.131   0.145
68    E         0.438   0.319   0.334   0.339   0.144   0.164   0.339   0.131   0.145
69    V         0.143   0.188   0.233  -0.133  -0.054   0.028  -0.178  -0.104  -0.036
70    A        -1.420  -1.372  -1.352  -1.253  -1.156  -1.129  -1.214  -1.131  -1.090
71    T        -1.420  -1.372  -1.352  -1.394  -1.254  -1.272  -1.214  -1.131  -1.090
72    T        -0.638  -0.640  -0.642  -0.811  -0.827  -0.841  -0.696  -0.685  -0.673
73    T         0.438   0.319   0.334   0.405   0.202   0.207   0.339   0.131   0.145
74    F         0.438   0.319   0.334   0.492   0.275   0.279   0.339   0.131   0.145
75    A         0.438   0.589   0.401   0.421   0.644   0.355   0.339   0.584   0.263
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    R         0.438   0.319   0.334   0.473   0.267   0.289   0.339   0.131   0.145
78    F         1.707   1.771   1.808   1.823   1.933   1.989   1.893   1.980   2.043
79    I         0.143   0.206   0.247  -0.111   0.005   0.085  -0.178  -0.072  -0.012
80    D         1.707   1.771   1.808   1.714   1.819   1.878   1.893   1.980   2.043
81    P        -1.420  -1.372  -1.352  -1.377  -1.324  -1.255  -1.214  -1.131  -1.090
82    T        -1.420  -1.372  -1.352  -1.355  -1.303  -1.233  -1.214  -1.131  -1.090
83    V        -0.638  -0.696  -0.665  -0.843  -0.931  -0.897  -0.696  -0.752  -0.703
84    K         0.438   0.487   0.380   0.593   0.677   0.485   0.339   0.417   0.226
85    L         0.438   0.487   0.380   0.235   0.310   0.125   0.339   0.417   0.226
86    W        -1.420  -1.372  -1.352  -1.232  -1.159  -1.108  -1.214  -1.131  -1.090
87    G        -1.420  -1.372  -1.352  -1.190  -1.130  -1.066  -1.214  -1.131  -1.090
88    A        -0.638  -0.647  -0.648  -0.757  -0.782  -0.788  -0.696  -0.694  -0.680
89    L         0.438   0.487   0.380   0.235   0.310   0.125   0.339   0.417   0.226
90    A         0.438   0.319   0.334   0.473   0.272   0.311   0.339   0.131   0.145
91    F        -0.638  -0.696  -0.665  -0.735  -0.805  -0.741  -0.696  -0.752  -0.703
92    D         0.438   0.319   0.334   0.405   0.193   0.207   0.339   0.131   0.145
93    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    E         0.438   0.577   0.404   0.339   0.551   0.285   0.339   0.565   0.268
95    T        -0.638  -0.696  -0.665  -0.508  -0.576  -0.550  -0.696  -0.752  -0.703
96    G         0.438   0.319   0.334   0.427   0.241   0.248   0.339   0.131   0.145
97    D        -1.420  -1.372  -1.352  -1.232  -1.106  -1.108  -1.214  -1.131  -1.090
98    A        -1.420  -1.372  -1.352  -1.344  -1.249  -1.222  -1.214  -1.131  -1.090
99    I         0.438   0.319   0.334   0.524   0.301   0.339   0.339   0.131   0.145
100   G         1.707   1.771   1.808   1.704   1.816   1.868   1.893   1.980   2.043
101   F        -0.638  -0.640  -0.642  -0.471  -0.433  -0.462  -0.696  -0.685  -0.673
102   A         1.707   1.771   1.808   1.714   1.794   1.878   1.893   1.980   2.043
103   H        -1.420  -1.372  -1.352  -1.159  -1.060  -1.034  -1.214  -1.131  -1.090
104   Y         1.707   1.771   1.808   1.694   1.804   1.858   1.893   1.980   2.043
105   L        -0.638  -0.640  -0.642  -0.708  -0.711  -0.689  -0.696  -0.685  -0.673
106   N        -0.638  -0.647  -0.648  -0.609  -0.643  -0.646  -0.696  -0.694  -0.680
107   H         0.438   0.319   0.334   0.720   0.552   0.552   0.339   0.131   0.145
108   L        -0.638  -0.696  -0.665  -0.656  -0.750  -0.708  -0.696  -0.752  -0.703
109   T        -0.638  -0.696  -0.665  -0.500  -0.570  -0.546  -0.696  -0.752  -0.703
110   S         0.438   0.487   0.380   0.479   0.574   0.397   0.339   0.417   0.226
111   W         1.707   1.771   1.808   1.931   2.039   2.098   1.893   1.980   2.043
112   H         0.438   0.487   0.380   0.517   0.616   0.449   0.339   0.417   0.226
113   V         0.438   0.319   0.334   0.322   0.147   0.173   0.339   0.131   0.145
114   E        -0.638  -0.640  -0.642  -0.757  -0.763  -0.753  -0.696  -0.685  -0.673
115   E        -0.638  -0.696  -0.665  -0.797  -0.925  -0.874  -0.696  -0.752  -0.703
116   V        -1.420  -1.372  -1.352  -1.445  -1.372  -1.324  -1.214  -1.131  -1.090
117   V        -1.420  -1.372  -1.352  -1.366  -1.293  -1.244  -1.214  -1.131  -1.090
118   Y         1.707   1.771   1.808   1.694   1.804   1.858   1.893   1.980   2.043
119   M         0.438   0.487   0.380   0.408   0.477   0.350   0.339   0.417   0.226
120   N         0.438   0.319   0.334   0.549   0.346   0.345   0.339   0.131   0.145
121   D         1.707   1.771   1.808   1.714   1.819   1.878   1.893   1.980   2.043
122   L         1.707   1.771   1.808   1.582   1.670   1.744   1.893   1.980   2.043
123   Y         0.438   0.577   0.404   0.453   0.677   0.409   0.339   0.565   0.268
124   V         1.707   1.771   1.808   1.551   1.650   1.713   1.893   1.980   2.043
125   T        -1.420  -1.372  -1.352  -1.328  -1.243  -1.205  -1.214  -1.131  -1.090
126   E        -1.420  -1.372  -1.352  -1.306  -1.204  -1.183  -1.214  -1.131  -1.090
127   R        -1.420  -1.372  -1.352  -1.344  -1.214  -1.222  -1.214  -1.131  -1.090
128   A        -1.420  -1.372  -1.352  -1.377  -1.275  -1.255  -1.214  -1.131  -1.090
129   R         1.707   1.771   1.808   1.754   1.846   1.919   1.893   1.980   2.043
130   V        -1.420  -1.372  -1.352  -1.508  -1.413  -1.388  -1.214  -1.131  -1.090
131   K        -0.638  -0.471  -0.598  -0.621  -0.340  -0.543  -0.696  -0.451  -0.616
132   G         1.707   1.771   1.808   1.704   1.816   1.868   1.893   1.980   2.043
133   V         0.438   0.319   0.334   0.272   0.080   0.096   0.339   0.131   0.145
134   G         1.707   1.771   1.808   1.704   1.816   1.868   1.893   1.980   2.043
135   R         0.438   0.319   0.334   0.517   0.326   0.357   0.339   0.131   0.145
136   K         0.438   0.319   0.334   0.382   0.200   0.201   0.339   0.131   0.145
137   L         1.707   1.771   1.808   1.582   1.670   1.744   1.893   1.980   2.043
138   I         0.438   0.319   0.334   0.482   0.247   0.276   0.339   0.131   0.145
139   E         0.438   0.319   0.334   0.382   0.198   0.229   0.339   0.131   0.145
140   F         0.143   0.188   0.233  -0.016   0.062   0.128  -0.178  -0.104  -0.036
141   V        -0.638  -0.647  -0.648  -0.843  -0.894  -0.850  -0.696  -0.694  -0.680
142   Y         0.438   0.319   0.334   0.418   0.218   0.239   0.339   0.131   0.145
143   S        -0.638  -0.696  -0.665  -0.617  -0.702  -0.643  -0.696  -0.752  -0.703
144   R         0.438   0.487   0.380   0.352   0.423   0.262   0.339   0.417   0.226
145   A         0.438   0.319   0.334   0.479   0.278   0.321   0.339   0.131   0.145
146   D         0.438   0.319   0.334   0.395   0.177   0.192   0.339   0.131   0.145
147   E        -0.638  -0.537  -0.612  -0.712  -0.539  -0.675  -0.696  -0.541  -0.633
148   L         0.438   0.319   0.334   0.339   0.140   0.181   0.339   0.131   0.145
149   G         0.438   0.577   0.404   0.411   0.648   0.351   0.339   0.565   0.268
150   T        -0.638  -0.696  -0.665  -0.410  -0.520  -0.488  -0.696  -0.752  -0.703
151   P        -1.420  -1.372  -1.352  -1.383  -1.284  -1.261  -1.214  -1.131  -1.090
152   A        -0.638  -0.696  -0.665  -0.708  -0.799  -0.744  -0.696  -0.752  -0.703
153   V        -1.420  -1.372  -1.352  -1.399  -1.359  -1.278  -1.214  -1.131  -1.090
154   Y         0.438   0.319   0.334   0.418   0.229   0.239   0.339   0.131   0.145
155   W         1.707   1.771   1.808   1.931   2.039   2.098   1.893   1.980   2.043
156   V        -0.638  -0.471  -0.598  -0.656  -0.414  -0.570  -0.696  -0.451  -0.616
157   T         0.438   0.319   0.334   0.385   0.177   0.177   0.339   0.131   0.145
158   D        -0.638  -0.696  -0.665  -0.524  -0.677  -0.609  -0.696  -0.752  -0.703
159   H        -0.638  -0.647  -0.648  -0.426  -0.447  -0.449  -0.696  -0.694  -0.680
160   Y        -1.420  -1.372  -1.352  -1.306  -1.178  -1.183  -1.214  -1.131  -1.090
161   N         1.707   1.771   1.808   1.863   1.983   2.029   1.893   1.980   2.043
162   H         0.438   0.319   0.334   0.750   0.582   0.598   0.339   0.131   0.145
163   R         1.707   1.771   1.808   1.754   1.846   1.919   1.893   1.980   2.043
164   A         1.707   1.771   1.808   1.714   1.794   1.878   1.893   1.980   2.043
165   Q         0.438   0.319   0.334   0.701   0.491   0.524   0.339   0.131   0.145
166   L         0.438   0.319   0.334   0.275   0.053   0.084   0.339   0.131   0.145
167   L         0.438   0.319   0.334   0.255   0.027   0.053   0.339   0.131   0.145
168   Y         1.707   1.771   1.808   1.694   1.804   1.858   1.893   1.980   2.043
169   T         0.438   0.319   0.334   0.405   0.202   0.207   0.339   0.131   0.145
170   K         1.707   1.771   1.808   1.664   1.779   1.827   1.893   1.980   2.043
171   V        -0.638  -0.640  -0.642  -0.784  -0.810  -0.771  -0.696  -0.685  -0.673
172   A         0.438   0.487   0.380   0.427   0.513   0.330   0.339   0.417   0.226
173   Y        -1.420  -1.372  -1.352  -1.585  -1.488  -1.466  -1.214  -1.131  -1.090
174   K         0.438   0.319   0.334   0.469   0.314   0.334   0.339   0.131   0.145
175   T        -1.420  -1.372  -1.352  -1.377  -1.289  -1.255  -1.214  -1.131  -1.090
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     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   D        -0.638  -0.647  -0.648  -0.708  -0.720  -0.729  -0.696  -0.694  -0.680
191   K        -0.638  -0.696  -0.665  -0.609  -0.717  -0.671  -0.696  -0.752  -0.703
192   V         0.143   0.188   0.233  -0.301  -0.236  -0.153  -0.178  -0.104  -0.036
193   L        -0.638  -0.640  -0.642  -0.820  -0.838  -0.821  -0.696  -0.685  -0.673
194   Y         0.438   0.319   0.334   0.418   0.229   0.239   0.339   0.131   0.145
195   K        -0.638  -0.471  -0.598  -0.779  -0.480  -0.714  -0.696  -0.451  -0.616
196   R         0.438   0.319   0.334   0.434   0.202   0.229   0.339   0.131   0.145
197   N         0.438   0.487   0.380   0.655   0.740   0.570   0.339   0.417   0.226
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   G        -0.771  -0.738  -0.696  -0.859  -0.775  -0.730  -0.869  -0.802  -0.742
200   Y        -0.771  -0.738  -0.696  -0.908  -0.833  -0.780  -0.869  -0.802  -0.742
* 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/P39979
Output conservation file - output/P39979
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
