1     M         1.856   1.915   2.005   2.111   2.183   2.331   2.033   2.120   2.283
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -         0.698   0.638   0.688   0.560   0.450   0.512   0.514   0.387   0.433
64    -        -0.285  -0.208  -0.171  -0.542  -0.414  -0.390  -0.499  -0.389  -0.351
65    -        -0.999  -0.958  -0.837  -1.202  -1.135  -0.965  -1.006  -0.947  -0.800
66    L        -0.112  -0.133  -0.143  -0.192  -0.248  -0.289  -0.282  -0.318  -0.324
67    S        -0.774  -0.816  -0.759  -0.778  -0.867  -0.746  -0.778  -0.810  -0.720
68    R         0.545   0.574   0.630   0.454   0.490   0.528   0.232   0.266   0.318
69    I        -0.882  -0.767  -0.769  -1.067  -0.918  -0.898  -0.893  -0.766  -0.733
70    Q        -0.703  -0.808  -0.760  -0.654  -0.863  -0.788  -0.668  -0.784  -0.716
71    N        -0.227  -0.294  -0.174  -0.357  -0.471  -0.285  -0.443  -0.514  -0.364
72    Y        -1.358  -1.367  -1.265  -1.337  -1.291  -1.190  -1.118  -1.111  -0.981
73    T        -0.406  -0.371  -0.246  -0.669  -0.630  -0.430  -0.668  -0.616  -0.457
74    S        -0.882  -0.918  -0.788  -0.923  -0.987  -0.787  -0.893  -0.911  -0.752
75    G        -0.774  -0.811  -0.747  -0.896  -0.980  -0.846  -0.778  -0.804  -0.709
76    L         1.011   1.068   0.862   0.968   1.061   0.774   1.041   1.126   0.758
77    V        -0.520  -0.610  -0.694  -0.416  -0.557  -0.687  -0.448  -0.556  -0.640
78    S        -1.743  -1.608  -1.612  -1.495  -1.319  -1.295  -1.275  -1.136  -1.101
79    K         0.216   0.127  -0.046   0.249   0.141  -0.084   0.214   0.076  -0.171
80    A        -1.336  -1.273  -1.231  -1.368  -1.300  -1.230  -1.109  -1.033  -0.954
81    N        -0.928  -0.964  -0.810  -0.821  -0.848  -0.637  -0.944  -0.954  -0.775
82    L        -1.336  -1.319  -1.235  -1.326  -1.277  -1.173  -1.109  -1.078  -0.958
83    L        -0.520  -0.628  -0.698  -0.421  -0.567  -0.666  -0.448  -0.576  -0.645
84    S        -1.336  -1.225  -1.226  -1.370  -1.188  -1.214  -1.109  -0.991  -0.950
85    S        -0.774  -0.778  -0.756  -0.576  -0.551  -0.544  -0.778  -0.768  -0.717
86    K        -0.212  -0.294  -0.173  -0.219  -0.279  -0.122  -0.448  -0.522  -0.365
87    A        -0.520  -0.555  -0.692  -0.453  -0.549  -0.730  -0.448  -0.493  -0.638
88    L        -0.774  -0.700  -0.741  -0.815  -0.711  -0.760  -0.778  -0.701  -0.705
89    Y         1.856   1.915   2.005   1.839   1.934   2.060   2.033   2.120   2.283
90    Y         0.449   0.496   0.597   0.419   0.498   0.641   0.048   0.115   0.254
91    G        -0.112  -0.232  -0.143  -0.321  -0.528  -0.389  -0.282  -0.426  -0.322
92    K         1.856   1.915   2.005   1.658   1.760   1.881   2.033   2.120   2.283
93    V         1.856   1.915   2.005   1.749   1.825   1.972   2.033   2.120   2.283
94    G        -0.774  -0.824  -0.750  -0.813  -0.915  -0.801  -0.778  -0.814  -0.712
95    A         1.011   1.053   0.853   0.969   1.003   0.735   1.041   1.103   0.742
96    E         1.856   1.915   2.005   1.940   2.020   2.161   2.033   2.120   2.283
97    I        -0.112   0.043  -0.102  -0.291  -0.050  -0.276  -0.282  -0.067  -0.264
98    S         0.449   0.470   0.585   0.067   0.063   0.250   0.048   0.064   0.229
99    K         1.011   0.847   0.805   0.948   0.764   0.693   1.041   0.762   0.654
100   Q        -0.112  -0.138  -0.149  -0.129  -0.192  -0.211  -0.282  -0.333  -0.334
101   I         0.449   0.522   0.606   0.161   0.273   0.392   0.048   0.167   0.270
102   Y         1.011   0.847   0.805   1.115   0.913   0.836   1.041   0.762   0.654
103   L        -1.336  -1.332  -1.252  -1.410  -1.350  -1.253  -1.109  -1.088  -0.971
104   K        -0.112  -0.127  -0.149  -0.378  -0.422  -0.458  -0.282  -0.323  -0.333
105   E         1.011   0.847   0.805   1.204   0.985   0.908   1.041   0.762   0.654
106   G         1.011   0.847   0.805   0.957   0.712   0.652   1.041   0.762   0.654
107   L         0.216   0.063  -0.044   0.316   0.141   0.002   0.214  -0.008  -0.168
108   Q        -0.928  -0.964  -0.805  -1.120  -1.147  -0.928  -0.944  -0.954  -0.771
109   P         1.856   1.915   2.005   2.013   2.094   2.234   2.033   2.120   2.283
110   P         1.856   1.915   2.005   2.013   2.094   2.234   2.033   2.120   2.283
111   T        -0.212  -0.129  -0.143  -0.307  -0.206  -0.181  -0.448  -0.337  -0.330
112   V        -1.182  -1.105  -1.181  -1.087  -0.968  -1.103  -0.944  -0.846  -0.902
113   A        -1.182  -1.026  -1.152  -1.089  -0.846  -1.062  -0.944  -0.763  -0.873
114   Q        -1.336  -1.347  -1.241  -0.991  -1.002  -0.827  -1.109  -1.099  -0.963
115   F         1.856   1.915   2.005   1.920   1.981   2.141   2.033   2.120   2.283
116   K        -0.366  -0.314  -0.228  -0.595  -0.499  -0.386  -0.613  -0.537  -0.432
117   S        -1.182  -1.222  -1.209  -1.026  -1.123  -1.069  -0.944  -0.974  -0.929
118   V         0.216   0.127  -0.046   0.302   0.171  -0.072   0.214   0.076  -0.171
119   Y         1.011   0.847   0.805   1.115   0.913   0.836   1.041   0.762   0.654
120   S        -1.182  -1.008  -1.150  -0.928  -0.664  -0.890  -0.944  -0.744  -0.871
121   N         0.216   0.367   0.012   0.495   0.712   0.187   0.214   0.430  -0.086
122   L        -0.112  -0.220  -0.140  -0.288  -0.428  -0.319  -0.282  -0.408  -0.313
123   Y        -0.774  -0.852  -0.767  -0.749  -0.864  -0.756  -0.778  -0.845  -0.730
124   K         0.216   0.299   0.012   0.258   0.393   0.011   0.214   0.334  -0.086
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   Q         0.825   0.842   0.766   0.850   0.874   0.730   0.736   0.754   0.580
128   S        -0.887  -0.803  -0.774  -1.061  -0.933  -0.911  -0.884  -0.775  -0.732
129   L        -0.101  -0.209  -0.162  -0.370  -0.552  -0.527  -0.236  -0.392  -0.338
130   N        -0.887  -0.729  -0.766  -0.938  -0.694  -0.765  -0.884  -0.686  -0.723
131   F         0.449   0.513   0.598   0.285   0.383   0.499   0.048   0.148   0.255
132   A        -0.366  -0.355  -0.232  -0.545  -0.547  -0.337  -0.613  -0.596  -0.438
133   L        -1.336  -1.332  -1.252  -1.321  -1.303  -1.145  -1.109  -1.088  -0.971
134   K        -0.520  -0.618  -0.690  -0.469  -0.571  -0.701  -0.448  -0.564  -0.635
135   P         1.011   0.847   0.805   1.257   1.020   0.935   1.041   0.762   0.654
136   T        -0.774  -0.790  -0.741  -0.787  -0.837  -0.746  -0.778  -0.784  -0.703
137   E        -0.774  -0.849  -0.759  -0.718  -0.843  -0.736  -0.778  -0.839  -0.722
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   V        -0.774  -0.816  -0.759  -0.776  -0.856  -0.746  -0.778  -0.810  -0.720
142   L        -0.112  -0.009  -0.115  -0.264  -0.097  -0.271  -0.282  -0.137  -0.282
143   S        -1.743  -1.740  -1.642  -1.329  -1.311  -1.191  -1.275  -1.252  -1.124
144   C        -1.182  -1.222  -1.209  -0.765  -0.807  -0.878  -0.944  -0.974  -0.929
145   L        -0.112  -0.177  -0.135  -0.316  -0.411  -0.371  -0.282  -0.343  -0.307
146   K        -0.520  -0.628  -0.698  -0.455  -0.575  -0.690  -0.448  -0.576  -0.645
147   N         0.216   0.276   0.012   0.486   0.580   0.171   0.214   0.303  -0.086
148   I         0.624   0.687   0.693   0.591   0.680   0.676   0.379   0.477   0.442
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   Q        -1.182  -1.144  -1.206  -0.959  -0.923  -1.035  -0.944  -0.900  -0.926
152   K         1.011   0.847   0.805   0.948   0.764   0.693   1.041   0.762   0.654
153   N        -1.336  -1.210  -1.235  -0.929  -0.776  -0.753  -1.109  -0.980  -0.956
154   E        -0.928  -0.853  -0.794  -0.591  -0.505  -0.406  -0.944  -0.859  -0.760
155   L         0.216   0.152  -0.028   0.224   0.097  -0.168   0.214   0.108  -0.144
156   L        -0.774  -0.841  -0.754  -0.933  -1.027  -0.902  -0.778  -0.831  -0.717
157   K         0.216   0.063  -0.044   0.210  -0.001  -0.154   0.214  -0.008  -0.168
158   Y        -0.212  -0.134  -0.156  -0.390  -0.295  -0.286  -0.448  -0.345  -0.345
159   G         0.216   0.276   0.012   0.238   0.305  -0.059   0.214   0.303  -0.086
160   A        -0.774  -0.734  -0.746  -0.892  -0.868  -0.849  -0.778  -0.735  -0.710
161   Y         0.216   0.115  -0.044   0.369   0.222  -0.029   0.214   0.061  -0.168
162   G         0.624   0.587   0.615   0.356   0.261   0.273   0.379   0.290   0.289
163   I        -0.774  -0.824  -0.750  -0.807  -0.899  -0.764  -0.778  -0.814  -0.712
164   Q         1.011   0.847   0.805   1.132   0.921   0.856   1.041   0.762   0.654
165   L        -0.520  -0.600  -0.694  -0.353  -0.427  -0.554  -0.448  -0.545  -0.640
166   I         1.011   1.158   0.861   0.968   1.169   0.773   1.041   1.264   0.756
167   G         1.011   1.068   0.862   0.952   1.011   0.736   1.041   1.126   0.758
168   F         0.624   0.692   0.660   0.560   0.655   0.556   0.379   0.487   0.378
169   Y         0.449   0.539   0.615   0.285   0.433   0.535   0.048   0.199   0.289
170   S         0.624   0.561   0.613   0.477   0.355   0.427   0.379   0.240   0.284
171   V        -0.112  -0.216  -0.150  -0.269  -0.400  -0.341  -0.282  -0.403  -0.331
172   G         1.856   1.915   2.005   1.708   1.770   1.930   2.033   2.120   2.283
173   E         1.856   1.915   2.005   1.940   2.020   2.161   2.033   2.120   2.283
174   I        -0.112  -0.232  -0.143  -0.081  -0.221  -0.116  -0.282  -0.426  -0.322
175   I         1.856   1.915   2.005   1.866   1.945   2.088   2.033   2.120   2.283
176   G         1.856   1.915   2.005   1.708   1.770   1.930   2.033   2.120   2.283
177   R         1.856   1.915   2.005   1.993   2.061   2.214   2.033   2.120   2.283
178   R         1.011   0.847   0.805   1.300   1.089   1.048   1.041   0.762   0.654
179   K        -0.520  -0.466  -0.651  -0.479  -0.368  -0.662  -0.448  -0.368  -0.590
180   L        -0.212  -0.132  -0.145  -0.464  -0.355  -0.336  -0.448  -0.348  -0.334
181   V        -0.774  -0.679  -0.715  -0.720  -0.559  -0.609  -0.778  -0.648  -0.671
182   G         1.011   1.068   0.862   1.001   1.064   0.829   1.041   1.126   0.758
183   Y         1.856   1.915   2.005   1.839   1.934   2.060   2.033   2.120   2.283
184   K        -0.703  -0.765  -0.742  -0.550  -0.585  -0.546  -0.668  -0.738  -0.696
185   -        -0.887  -0.908  -0.803  -0.913  -0.980  -0.840  -0.884  -0.896  -0.765
186   -        -0.285  -0.321  -0.209  -0.234  -0.268  -0.120  -0.499  -0.549  -0.406
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.358  -1.247  -1.231  -1.436  -1.260  -1.254  -1.118  -0.989  -0.950
192   -        -0.882  -0.821  -0.781  -0.929  -0.858  -0.748  -0.893  -0.814  -0.743
193   H        -0.112  -0.140  -0.152   0.020  -0.068  -0.128  -0.282  -0.330  -0.337
194   H         1.856   1.915   2.005   2.098   2.179   2.318   2.033   2.120   2.283
* 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/Q12233
Output conservation file - output/Q12233
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
