1     M         1.363   1.432   1.444   1.635   1.725   1.738   1.448   1.519   1.546
2     S         1.363   1.432   1.444   1.270   1.372   1.399   1.448   1.519   1.546
3     A        -0.103  -0.281  -0.239  -0.492  -0.693  -0.629  -0.178  -0.439  -0.388
4     V        -1.347  -1.304  -1.270  -1.456  -1.376  -1.394  -1.262  -1.148  -1.097
5     A        -0.103  -0.281  -0.239  -0.442  -0.614  -0.545  -0.178  -0.439  -0.388
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    T        -2.251  -2.007  -1.994  -2.151  -1.882  -1.772  -1.804  -1.470  -1.441
11    Y        -1.347  -1.304  -1.270  -0.973  -0.979  -0.908  -1.262  -1.148  -1.097
12    L         1.363   1.432   1.444   1.254   1.329   1.384   1.448   1.519   1.546
13    K        -0.103  -0.281  -0.239  -0.012  -0.262  -0.200  -0.178  -0.439  -0.388
14    T        -1.347  -1.304  -1.270  -1.464  -1.395  -1.400  -1.262  -1.148  -1.097
15    L        -0.103   0.161  -0.153  -0.049   0.342  -0.131  -0.178   0.217  -0.253
16    T        -1.347  -1.267  -1.265  -1.636  -1.436  -1.430  -1.262  -1.113  -1.092
17    A        -1.347  -1.272  -1.262  -1.568  -1.353  -1.349  -1.262  -1.118  -1.088
18    R         1.363   1.432   1.444   1.534   1.633   1.644   1.448   1.519   1.546
19    R         1.363   1.432   1.444   1.534   1.633   1.644   1.448   1.519   1.546
20    T         1.363   1.432   1.444   1.254   1.366   1.384   1.448   1.519   1.546
21    I        -0.103  -0.281  -0.239   0.042  -0.159  -0.121  -0.178  -0.439  -0.388
22    Y         1.363   1.432   1.444   1.534   1.640   1.644   1.448   1.519   1.546
23    A        -0.103  -0.281  -0.239  -0.457  -0.618  -0.570  -0.178  -0.439  -0.388
24    L         1.363   1.432   1.444   1.254   1.329   1.384   1.448   1.519   1.546
25    K        -0.103  -0.281  -0.239  -0.059  -0.342  -0.281  -0.178  -0.439  -0.388
26    P        -0.103  -0.281  -0.239   0.024  -0.239  -0.208  -0.178  -0.439  -0.388
27    E        -0.103  -0.281  -0.239  -0.012  -0.283  -0.200  -0.178  -0.439  -0.388
28    L         1.363   1.432   1.444   1.254   1.329   1.384   1.448   1.519   1.546
29    P        -0.103  -0.281  -0.239   0.029  -0.230  -0.199  -0.178  -0.439  -0.388
30    G        -0.103   0.161  -0.153  -0.065   0.302  -0.137  -0.178   0.217  -0.253
31    E        -0.296  -0.197  -0.259  -0.302  -0.148  -0.257  -0.479  -0.308  -0.419
32    I        -1.347  -1.267  -1.265  -1.257  -1.186  -1.140  -1.262  -1.113  -1.092
33    T        -0.103   0.089  -0.163  -0.091   0.192  -0.182  -0.178   0.115  -0.269
34    I        -0.103  -0.281  -0.239  -0.049  -0.310  -0.277  -0.178  -0.439  -0.388
35    N        -0.103  -0.281  -0.239   0.109  -0.198  -0.140  -0.178  -0.439  -0.388
36    D        -0.103  -0.281  -0.239   0.150  -0.091  -0.036  -0.178  -0.439  -0.388
37    I        -0.444  -0.310  -0.252  -0.605  -0.369  -0.296  -0.720  -0.486  -0.409
38    Q        -0.103  -0.281  -0.239   0.117  -0.142  -0.085  -0.178  -0.439  -0.388
39    S        -0.444  -0.290  -0.241  -0.611  -0.378  -0.284  -0.720  -0.453  -0.392
40    V        -1.347  -1.272  -1.262  -1.257  -1.143  -1.134  -1.262  -1.118  -1.088
41    V        -0.103   0.153  -0.156  -0.073   0.280  -0.149  -0.178   0.205  -0.258
42    Q        -0.103  -0.281  -0.239   0.063  -0.233  -0.177  -0.178  -0.439  -0.388
43    T        -1.347  -1.267  -1.265  -1.636  -1.454  -1.430  -1.262  -1.113  -1.092
44    I        -0.103  -0.281  -0.239  -0.177  -0.512  -0.501  -0.178  -0.439  -0.388
45    I        -1.347  -1.267  -1.265  -1.257  -1.186  -1.140  -1.262  -1.113  -1.092
46    K        -0.103  -0.281  -0.239  -0.015  -0.269  -0.204  -0.178  -0.439  -0.388
47    E        -1.347  -1.304  -1.270  -1.056  -0.960  -0.910  -1.262  -1.148  -1.097
48    T        -0.103  -0.281  -0.239  -0.094  -0.374  -0.311  -0.178  -0.439  -0.388
49    P         1.363   1.432   1.444   1.368   1.497   1.489   1.448   1.519   1.546
50    T        -0.103  -0.281  -0.239  -0.091  -0.364  -0.306  -0.178  -0.439  -0.388
51    A        -0.444  -0.290  -0.241  -0.936  -0.587  -0.534  -0.720  -0.453  -0.392
52    F         1.363   1.432   1.444   1.416   1.511   1.534   1.448   1.519   1.546
53    N         1.363   1.432   1.444   1.455   1.559   1.571   1.448   1.519   1.546
54    S        -0.103   0.089  -0.163   0.060   0.312   0.021  -0.178   0.115  -0.269
55    Q         1.363   1.432   1.444   1.408   1.504   1.527   1.448   1.519   1.546
56    P        -2.251  -2.007  -1.994  -1.973  -1.623  -1.607  -1.804  -1.470  -1.441
57    N         1.363   1.432   1.444   1.455   1.559   1.571   1.448   1.519   1.546
58    R         1.363   1.432   1.444   1.534   1.633   1.644   1.448   1.519   1.546
59    A        -0.103  -0.281  -0.239  -0.494  -0.704  -0.634  -0.178  -0.439  -0.388
60    V        -0.103   0.089  -0.163  -0.073   0.198  -0.160  -0.178   0.115  -0.269
61    I        -0.103  -0.281  -0.239  -0.046  -0.316  -0.272  -0.178  -0.439  -0.388
62    L         1.363   1.432   1.444   1.254   1.329   1.384   1.448   1.519   1.546
63    T        -0.103  -0.281  -0.239  -0.097  -0.388  -0.315  -0.178  -0.439  -0.388
64    G         1.363   1.432   1.444   1.303   1.409   1.429   1.448   1.519   1.546
65    E        -0.103  -0.281  -0.239  -0.193  -0.571  -0.515  -0.178  -0.439  -0.388
66    T        -0.103  -0.281  -0.239  -0.086  -0.367  -0.297  -0.178  -0.439  -0.388
67    H         1.363   1.432   1.444   1.558   1.658   1.666   1.448   1.519   1.546
68    K        -0.103  -0.281  -0.239  -0.054  -0.344  -0.271  -0.178  -0.439  -0.388
69    K        -0.103   0.089  -0.163  -0.059   0.218  -0.154  -0.178   0.115  -0.269
70    V        -0.103  -0.281  -0.239  -0.089  -0.399  -0.309  -0.178  -0.439  -0.388
71    W         1.363   1.432   1.444   1.573   1.670   1.680   1.448   1.519   1.546
72    D         1.363   1.432   1.444   1.416   1.516   1.534   1.448   1.519   1.546
73    E        -1.347  -1.267  -1.265  -1.236  -1.124  -1.117  -1.262  -1.113  -1.092
74    V        -0.103  -0.281  -0.239  -0.089  -0.378  -0.309  -0.178  -0.439  -0.388
75    T        -1.347  -1.049  -1.206  -1.460  -0.949  -1.263  -1.262  -0.842  -1.025
76    K        -1.347  -1.267  -1.265  -1.083  -1.021  -1.003  -1.262  -1.113  -1.092
77    A        -0.103  -0.281  -0.239  -0.497  -0.697  -0.639  -0.178  -0.439  -0.388
78    I        -0.103  -0.281  -0.239  -0.049  -0.330  -0.277  -0.178  -0.439  -0.388
79    E        -1.347  -1.272  -1.262  -1.418  -1.292  -1.339  -1.262  -1.118  -1.088
80    S        -2.251  -2.007  -1.994  -2.176  -1.918  -1.795  -1.804  -1.470  -1.441
81    P        -1.347  -1.304  -1.270  -1.097  -1.025  -0.992  -1.262  -1.148  -1.097
82    A        -1.347  -1.304  -1.270  -1.548  -1.417  -1.325  -1.262  -1.148  -1.097
83    G        -0.103  -0.281  -0.239  -0.012  -0.258  -0.214  -0.178  -0.439  -0.388
84    Q        -1.347  -1.267  -1.265  -1.176  -1.106  -1.051  -1.262  -1.113  -1.092
85    K        -0.103  -0.281  -0.239  -0.012  -0.262  -0.200  -0.178  -0.439  -0.388
86    R        -0.103  -0.281  -0.239   0.180  -0.131  -0.087  -0.178  -0.439  -0.388
87    P        -0.103  -0.281  -0.239   0.066  -0.175  -0.138  -0.178  -0.439  -0.388
88    A        -0.103   0.153  -0.156  -0.486  -0.096  -0.511  -0.178   0.205  -0.258
89    S         1.363   1.432   1.444   1.270   1.372   1.399   1.448   1.519   1.546
90    A        -1.347  -1.272  -1.262  -1.648  -1.465  -1.443  -1.262  -1.118  -1.088
91    R        -0.103  -0.281  -0.239   0.053  -0.327  -0.309  -0.178  -0.439  -0.388
92    D        -0.103  -0.281  -0.239   0.076  -0.213  -0.162  -0.178  -0.439  -0.388
93    E        -0.103  -0.281  -0.239  -0.054  -0.352  -0.271  -0.178  -0.439  -0.388
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   A         1.363   1.432   1.444   0.846   0.994   1.006   1.448   1.519   1.546
101   F        -1.347  -1.272  -1.262  -1.190  -1.222  -1.111  -1.262  -1.118  -1.088
102   G         1.363   1.432   1.444   1.303   1.409   1.429   1.448   1.519   1.546
103   S        -0.103  -0.281  -0.239  -0.081  -0.362  -0.302  -0.178  -0.439  -0.388
104   V        -0.444  -0.290  -0.241  -0.605  -0.331  -0.276  -0.720  -0.453  -0.392
105   I        -0.103  -0.281  -0.239  -0.049  -0.330  -0.277  -0.178  -0.439  -0.388
106   F         1.363   1.432   1.444   1.416   1.511   1.534   1.448   1.519   1.546
107   F        -0.103   0.089  -0.163   0.060   0.323  -0.053  -0.178   0.115  -0.269
108   T        -0.103  -0.281  -0.239  -0.086  -0.367  -0.297  -0.178  -0.439  -0.388
109   D         1.363   1.432   1.444   1.416   1.516   1.534   1.448   1.519   1.546
110   D        -0.103  -0.281  -0.239   0.071  -0.235  -0.171  -0.178  -0.439  -0.388
111   K        -0.103  -0.281  -0.239  -0.065  -0.345  -0.290  -0.178  -0.439  -0.388
112   V        -0.444  -0.310  -0.252  -0.641  -0.428  -0.332  -0.720  -0.486  -0.409
113   T        -0.103  -0.281  -0.239  -0.094  -0.374  -0.311  -0.178  -0.439  -0.388
114   E        -0.103  -0.281  -0.239  -0.054  -0.352  -0.271  -0.178  -0.439  -0.388
115   K        -0.103  -0.281  -0.239  -0.049  -0.322  -0.262  -0.178  -0.439  -0.388
116   L        -0.103  -0.281  -0.239   0.029  -0.198  -0.101  -0.178  -0.439  -0.388
117   K        -0.103   0.161  -0.153   0.063   0.428  -0.028  -0.178   0.217  -0.253
118   A        -0.103  -0.281  -0.239  -0.486  -0.696  -0.619  -0.178  -0.439  -0.388
119   D        -0.103  -0.281  -0.239   0.109  -0.162  -0.105  -0.178  -0.439  -0.388
120   F         1.363   1.432   1.444   1.416   1.511   1.534   1.448   1.519   1.546
121   P        -0.103  -0.281  -0.239  -0.113  -0.452  -0.447  -0.178  -0.439  -0.388
122   A        -0.103  -0.281  -0.239  -0.494  -0.704  -0.634  -0.178  -0.439  -0.388
123   Y        -0.444  -0.310  -0.252  -0.216  -0.013   0.054  -0.720  -0.486  -0.409
124   A        -0.444  -0.310  -0.252  -0.936  -0.731  -0.644  -0.720  -0.486  -0.409
125   A        -0.103  -0.281  -0.239  -0.439  -0.606  -0.540  -0.178  -0.439  -0.388
126   A        -1.347  -1.304  -1.270  -1.490  -1.261  -1.256  -1.262  -1.148  -1.097
127   F         1.363   1.432   1.444   1.416   1.511   1.534   1.448   1.519   1.546
128   P         1.363   1.432   1.444   1.368   1.497   1.489   1.448   1.519   1.546
129   S        -1.347  -1.272  -1.262  -1.200  -1.134  -1.069  -1.262  -1.118  -1.088
130   F        -0.103  -0.281  -0.239   0.162  -0.076  -0.015  -0.178  -0.439  -0.388
131   A         1.363   1.432   1.444   0.846   0.994   1.006   1.448   1.519   1.546
132   D        -1.347  -1.304  -1.270  -1.127  -1.121  -1.050  -1.262  -1.148  -1.097
133   H        -0.103  -0.281  -0.239   0.245  -0.041   0.004  -0.178  -0.439  -0.388
134   T        -1.347  -0.993  -1.198  -1.448  -0.856  -1.238  -1.262  -0.775  -1.016
135   S        -0.103  -0.281  -0.239  -0.028  -0.279  -0.212  -0.178  -0.439  -0.388
136   G        -0.103  -0.281  -0.239  -0.177  -0.533  -0.501  -0.178  -0.439  -0.388
137   A        -0.103  -0.281  -0.239  -0.360  -0.479  -0.406  -0.178  -0.439  -0.388
138   A        -0.103  -0.281  -0.239  -0.497  -0.720  -0.639  -0.178  -0.439  -0.388
139   Q         1.363   1.432   1.444   1.408   1.504   1.527   1.448   1.519   1.546
140   I        -0.103  -0.281  -0.239   0.050  -0.149  -0.108  -0.178  -0.439  -0.388
141   N        -1.347  -1.304  -1.270  -1.103  -1.081  -1.037  -1.262  -1.148  -1.097
142   S        -1.347  -1.304  -1.270  -1.271  -1.243  -1.167  -1.262  -1.148  -1.097
143   W         1.363   1.432   1.444   1.573   1.670   1.680   1.448   1.519   1.546
144   V        -1.347  -1.049  -1.206  -1.456  -0.956  -1.261  -1.262  -0.842  -1.025
145   A         1.363   1.432   1.444   0.846   0.994   1.006   1.448   1.519   1.546
146   L        -0.103   0.089  -0.163  -0.081   0.172  -0.167  -0.178   0.115  -0.269
147   E         1.363   1.432   1.444   1.286   1.367   1.414   1.448   1.519   1.546
148   A        -0.103   0.089  -0.163  -0.497  -0.190  -0.538  -0.178   0.115  -0.269
149   M        -1.347  -1.267  -1.265  -1.103  -1.073  -0.951  -1.262  -1.113  -1.092
150   G         1.363   1.432   1.444   1.303   1.409   1.429   1.448   1.519   1.546
151   L         1.363   1.432   1.444   1.254   1.329   1.384   1.448   1.519   1.546
152   G         1.363   1.432   1.444   1.303   1.409   1.429   1.448   1.519   1.546
153   G        -0.103  -0.281  -0.239  -0.177  -0.533  -0.501  -0.178  -0.439  -0.388
154   H        -0.103  -0.281  -0.239   0.259  -0.012   0.029  -0.178  -0.439  -0.388
155   L         1.363   1.432   1.444   1.254   1.329   1.384   1.448   1.519   1.546
156   Q         1.363   1.432   1.444   1.408   1.504   1.527   1.448   1.519   1.546
157   H         1.363   1.432   1.444   1.558   1.658   1.666   1.448   1.519   1.546
158   Y         1.363   1.432   1.444   1.534   1.640   1.644   1.448   1.519   1.546
159   N         1.363   1.432   1.444   1.455   1.559   1.571   1.448   1.519   1.546
160   G        -0.103  -0.281  -0.239  -0.012  -0.258  -0.214  -0.178  -0.439  -0.388
161   Y        -0.103  -0.281  -0.239   0.175  -0.148  -0.096  -0.178  -0.439  -0.388
162   I        -0.444  -0.310  -0.252  -0.605  -0.369  -0.296  -0.720  -0.486  -0.409
163   K        -0.103  -0.281  -0.239  -0.012  -0.262  -0.200  -0.178  -0.439  -0.388
164   A         1.363   1.432   1.444   0.846   0.994   1.006   1.448   1.519   1.546
165   A        -0.103  -0.281  -0.239  -0.486  -0.682  -0.619  -0.178  -0.439  -0.388
166   L        -0.103  -0.281  -0.239  -0.094  -0.407  -0.311  -0.178  -0.439  -0.388
167   P        -0.103  -0.281  -0.239  -0.113  -0.452  -0.447  -0.178  -0.439  -0.388
168   S        -0.444  -0.290  -0.241  -0.611  -0.378  -0.284  -0.720  -0.453  -0.392
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   K        -1.347  -1.304  -1.270  -1.426  -1.343  -1.367  -1.262  -1.148  -1.097
172   I         1.363   1.432   1.444   1.303   1.432   1.429   1.448   1.519   1.546
173   P         1.363   1.432   1.444   1.368   1.497   1.489   1.448   1.519   1.546
174   E        -1.347  -1.049  -1.206  -1.362  -0.893  -1.166  -1.262  -0.842  -1.025
175   S        -0.103   0.089  -0.163  -0.070   0.197  -0.161  -0.178   0.115  -0.269
176   W         1.363   1.432   1.444   1.573   1.670   1.680   1.448   1.519   1.546
177   T        -1.347  -1.272  -1.262  -1.264  -1.160  -1.140  -1.262  -1.118  -1.088
178   V        -0.103  -0.281  -0.239  -0.089  -0.399  -0.309  -0.178  -0.439  -0.388
179   Q        -1.347  -1.272  -1.262  -0.940  -0.850  -0.808  -1.262  -1.118  -1.088
180   A        -0.103   0.153  -0.156  -0.492  -0.095  -0.519  -0.178   0.205  -0.258
181   Q         1.363   1.432   1.444   1.408   1.504   1.527   1.448   1.519   1.546
182   L         1.363   1.432   1.444   1.254   1.329   1.384   1.448   1.519   1.546
183   V         1.363   1.432   1.444   1.262   1.354   1.392   1.448   1.519   1.546
184   F         1.363   1.432   1.444   1.416   1.511   1.534   1.448   1.519   1.546
185   G         1.363   1.432   1.444   1.303   1.409   1.429   1.448   1.519   1.546
186   T        -2.251  -2.007  -1.994  -2.286  -1.836  -1.897  -1.804  -1.470  -1.441
187   P        -0.103  -0.281  -0.239   0.024  -0.239  -0.208  -0.178  -0.439  -0.388
188   A        -1.347  -1.272  -1.262  -1.628  -1.443  -1.419  -1.262  -1.118  -1.088
189   A        -0.103  -0.281  -0.239  -0.480  -0.671  -0.609  -0.178  -0.439  -0.388
190   P        -2.251  -2.007  -1.994  -2.127  -1.668  -1.750  -1.804  -1.470  -1.441
191   P        -0.444  -0.290  -0.241  -0.858  -0.628  -0.572  -0.720  -0.453  -0.392
192   G         1.363   1.432   1.444   1.303   1.409   1.429   1.448   1.519   1.546
193   E         1.363   1.432   1.444   1.286   1.367   1.414   1.448   1.519   1.546
194   K         1.363   1.432   1.444   1.286   1.391   1.414   1.448   1.519   1.546
195   T        -0.103  -0.281  -0.239  -0.226  -0.573  -0.542  -0.178  -0.439  -0.388
196   Y        -0.103  -0.281  -0.239   0.225  -0.052  -0.010  -0.178  -0.439  -0.388
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   I        -0.103  -0.281  -0.239  -0.046  -0.316  -0.272  -0.178  -0.439  -0.388
200   K        -1.347  -1.267  -1.265  -1.117  -1.053  -1.029  -1.262  -1.113  -1.092
201   N        -0.103  -0.281  -0.239   0.109  -0.198  -0.140  -0.178  -0.439  -0.388
202   D        -2.251  -2.007  -1.994  -1.889  -1.554  -1.529  -1.804  -1.470  -1.441
203   V        -0.103  -0.281  -0.239  -0.036  -0.297  -0.218  -0.178  -0.439  -0.388
204   E        -0.444  -0.290  -0.241  -0.599  -0.359  -0.275  -0.720  -0.453  -0.392
205   I        -0.103  -0.281  -0.239  -0.044  -0.306  -0.268  -0.178  -0.439  -0.388
206   F        -0.103   0.089  -0.163   0.060   0.323  -0.053  -0.178   0.115  -0.269
207   N        -0.103  -0.281  -0.239   0.114  -0.176  -0.131  -0.178  -0.439  -0.388
208   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
209   -        -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/Q96VH4
Output conservation file - output/Q96VH4
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
