1     M         0.929   0.935   0.991   1.066   1.076   1.152   0.989   0.996   1.072
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     F         0.321   0.355   0.021   0.584   0.627   0.123   0.297   0.349  -0.225
5     A        -1.869  -1.840  -1.746  -1.802  -1.754  -1.641  -1.583  -1.556  -1.381
6     R         0.321   0.340   0.022   0.460   0.485   0.008   0.297   0.326  -0.223
7     L        -1.309  -1.236  -1.440  -1.119  -1.015  -1.315  -1.187  -1.103  -1.257
8     -        -1.591  -1.570  -1.471  -1.483  -1.460  -1.290  -1.473  -1.448  -1.284
9     -        -1.218  -1.245  -1.124  -1.143  -1.167  -0.971  -1.297  -1.317  -1.131
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    -        -1.670  -1.668  -1.486  -1.817  -1.830  -1.541  -1.543  -1.536  -1.296
18    -         0.929   0.935   0.991   0.884   0.893   0.982   0.989   0.996   1.072
19    -         0.121   0.082  -0.011  -0.072  -0.129  -0.242  -0.024  -0.091  -0.286
20    -        -1.222  -1.242  -1.129  -1.003  -1.031  -0.875  -1.290  -1.308  -1.134
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    -         0.121   0.067  -0.019   0.200   0.114  -0.062  -0.024  -0.117  -0.300
29    -        -0.605  -0.618  -0.653  -0.846  -0.868  -0.916  -0.783  -0.798  -0.838
30    -        -1.222  -1.211  -1.129  -1.259  -1.241  -1.121  -1.290  -1.273  -1.135
31    -         0.121   0.095  -0.010   0.170   0.130  -0.081  -0.024  -0.069  -0.283
32    -        -1.670  -1.668  -1.486  -1.611  -1.596  -1.348  -1.543  -1.536  -1.296
33    -        -1.222  -1.211  -1.129  -1.099  -1.083  -0.970  -1.290  -1.273  -1.135
34    -        -1.222  -1.210  -1.125  -1.325  -1.311  -1.188  -1.290  -1.272  -1.131
35    -        -1.670  -1.668  -1.486  -1.844  -1.841  -1.566  -1.543  -1.536  -1.296
36    A        -1.574  -1.565  -1.472  -1.657  -1.648  -1.455  -1.465  -1.453  -1.285
37    N        -1.574  -1.541  -1.467  -1.594  -1.549  -1.418  -1.465  -1.433  -1.281
38    P        -1.589  -1.560  -1.469  -1.707  -1.682  -1.489  -1.484  -1.457  -1.284
39    A        -1.030  -1.029  -1.104  -1.050  -1.032  -1.219  -1.088  -1.075  -1.110
40    H        -2.149  -2.158  -1.997  -1.978  -2.003  -1.752  -1.681  -1.683  -1.461
41    F        -1.484  -1.501  -1.459  -1.211  -1.236  -1.216  -1.385  -1.397  -1.275
42    K        -1.869  -1.832  -1.748  -1.941  -1.902  -1.724  -1.583  -1.551  -1.383
43    P         0.929   0.935   0.991   0.998   1.007   1.089   0.989   0.996   1.072
44    L        -2.429  -2.424  -2.209  -2.096  -2.089  -1.802  -1.780  -1.772  -1.518
45    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    H        -1.670  -1.666  -1.486  -1.648  -1.650  -1.383  -1.543  -1.534  -1.296
49    I        -1.453  -1.485  -1.459  -1.245  -1.305  -1.294  -1.336  -1.364  -1.274
50    T        -1.133  -1.107  -1.107  -1.386  -1.350  -1.319  -1.207  -1.174  -1.113
51    R        -2.213  -2.212  -2.003  -2.099  -2.086  -1.804  -1.724  -1.717  -1.465
52    A        -1.574  -1.540  -1.470  -1.735  -1.696  -1.530  -1.465  -1.433  -1.283
53    A        -1.133  -1.109  -1.110  -1.257  -1.236  -1.194  -1.207  -1.181  -1.116
54    K        -1.204  -1.202  -1.123  -1.377  -1.375  -1.264  -1.286  -1.282  -1.130
55    R         0.929   0.935   0.991   0.985   0.994   1.076   0.989   0.996   1.072
56    L        -1.589  -1.571  -1.468  -1.487  -1.457  -1.291  -1.484  -1.464  -1.283
57    Y         0.929   0.935   0.991   1.105   1.114   1.188   0.989   0.996   1.072
58    H         0.929   0.935   0.991   1.105   1.114   1.188   0.989   0.996   1.072
59    P        -0.644  -0.682  -0.659  -0.649  -0.697  -0.677  -0.890  -0.923  -0.850
60    K         0.321   0.256   0.019   0.317   0.240  -0.087   0.297   0.197  -0.230
61    V         0.929   0.935   0.991   0.842   0.844   0.943   0.989   0.996   1.072
62    I        -0.190  -0.186  -0.074  -0.430  -0.424  -0.245  -0.593  -0.585  -0.405
63    D         0.321   0.320   0.035   0.495   0.497   0.083   0.297   0.297  -0.200
64    H         0.929   0.935   0.991   1.105   1.114   1.188   0.989   0.996   1.072
65    Y         0.929   0.935   0.991   1.105   1.114   1.188   0.989   0.996   1.072
66    T        -1.204  -1.210  -1.129  -1.223  -1.234  -1.086  -1.286  -1.290  -1.136
67    N         0.321   0.275   0.017   0.521   0.466   0.069   0.297   0.226  -0.233
68    P         0.929   0.935   0.991   0.998   1.007   1.089   0.989   0.996   1.072
69    R         0.929   0.935   0.991   0.985   0.994   1.076   0.989   0.996   1.072
70    N         0.929   0.935   0.991   1.037   1.047   1.125   0.989   0.996   1.072
71    V         0.929   0.935   0.991   0.842   0.844   0.943   0.989   0.996   1.072
72    G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
73    S        -0.139  -0.158  -0.075  -0.361  -0.402  -0.275  -0.495  -0.531  -0.406
74    M        -0.139  -0.117  -0.057  -0.283  -0.248  -0.153  -0.495  -0.453  -0.372
75    D        -0.644  -0.680  -0.666  -0.588  -0.626  -0.598  -0.890  -0.919  -0.860
76    K         0.929   0.935   0.991   0.825   0.834   0.927   0.989   0.996   1.072
77    S        -2.149  -2.159  -1.994  -1.932  -1.958  -1.755  -1.681  -1.683  -1.459
78    L        -0.644  -0.624  -0.657  -0.712  -0.674  -0.718  -0.890  -0.859  -0.847
79    A        -2.149  -2.126  -1.988  -2.018  -1.974  -1.826  -1.681  -1.659  -1.456
80    N        -0.644  -0.669  -0.662  -0.610  -0.637  -0.633  -0.890  -0.908  -0.854
81    V         0.929   0.935   0.991   0.842   0.844   0.943   0.989   0.996   1.072
82    G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
83    T        -0.259  -0.364  -0.620  -0.135  -0.271  -0.646  -0.297  -0.440  -0.793
84    G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
85    I        -0.259  -0.217  -0.595  -0.182  -0.129  -0.688  -0.297  -0.239  -0.758
86    V         0.929   0.935   0.991   0.842   0.844   0.943   0.989   0.996   1.072
87    G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
88    A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
89    P         0.929   0.935   0.991   0.998   1.007   1.089   0.989   0.996   1.072
90    A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
91    C         0.929   0.935   0.991   1.121   1.129   1.203   0.989   0.996   1.072
92    G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
93    D         0.929   0.935   0.991   1.008   1.018   1.098   0.989   0.996   1.072
94    V         0.929   0.935   0.991   0.842   0.844   0.943   0.989   0.996   1.072
95    I         0.021   0.048  -0.024   0.120   0.165   0.003  -0.198  -0.150  -0.310
96    K        -0.190  -0.185  -0.072  -0.440  -0.426  -0.238  -0.593  -0.584  -0.400
97    L         0.929   0.935   0.991   0.869   0.879   0.968   0.989   0.996   1.072
98    Q        -0.259  -0.364  -0.620   0.063  -0.082  -0.525  -0.297  -0.440  -0.793
99    I         0.929   0.935   0.991   0.956   0.967   1.049   0.989   0.996   1.072
100   Q        -0.525  -0.584  -0.656  -0.337  -0.431  -0.602  -0.692  -0.770  -0.846
101   V         0.929   0.935   0.991   0.842   0.844   0.943   0.989   0.996   1.072
102   N        -0.190  -0.187  -0.075  -0.270  -0.265  -0.096  -0.593  -0.588  -0.407
103   D        -0.804  -0.890  -1.085  -0.533  -0.655  -0.983  -0.791  -0.892  -1.088
104   K        -0.934  -0.959  -1.081  -0.714  -0.748  -0.966  -0.949  -0.978  -1.084
105   S        -0.357  -0.305  -0.634  -0.273  -0.204  -0.683  -0.432  -0.358  -0.812
106   G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
107   I        -0.259  -0.202  -0.615  -0.212  -0.145  -0.752  -0.297  -0.217  -0.786
108   I         0.929   0.935   0.991   0.956   0.967   1.049   0.989   0.996   1.072
109   E        -1.030  -1.030  -1.103  -0.920  -0.916  -1.035  -1.088  -1.079  -1.109
110   N        -0.525  -0.496  -0.635  -0.381  -0.334  -0.546  -0.692  -0.644  -0.816
111   V         0.321   0.320   0.035   0.287   0.281  -0.178   0.297   0.297  -0.200
112   K         0.929   0.935   0.991   0.825   0.834   0.927   0.989   0.996   1.072
113   F         0.929   0.935   0.991   1.105   1.113   1.188   0.989   0.996   1.072
114   K         0.929   0.935   0.991   0.825   0.834   0.927   0.989   0.996   1.072
115   T         0.929   0.935   0.991   0.889   0.898   0.987   0.989   0.996   1.072
116   F         0.929   0.935   0.991   1.105   1.113   1.188   0.989   0.996   1.072
117   G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
118   C         0.929   0.935   0.991   1.121   1.129   1.203   0.989   0.996   1.072
119   G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
120   S         0.929   0.935   0.991   0.889   0.898   0.987   0.989   0.996   1.072
121   A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
122   I         0.929   0.935   0.991   0.956   0.967   1.049   0.989   0.996   1.072
123   A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
124   S         0.929   0.935   0.991   0.889   0.898   0.987   0.989   0.996   1.072
125   S         0.929   0.935   0.991   0.889   0.898   0.987   0.989   0.996   1.072
126   S         0.929   0.935   0.991   0.889   0.898   0.987   0.989   0.996   1.072
127   Y         0.929   0.935   0.991   1.105   1.114   1.188   0.989   0.996   1.072
128   M        -1.204  -1.175  -1.119  -1.329  -1.295  -1.218  -1.286  -1.249  -1.125
129   T         0.929   0.935   0.991   0.889   0.898   0.987   0.989   0.996   1.072
130   E         0.321   0.256   0.019   0.475   0.393   0.005   0.297   0.197  -0.230
131   L         0.321   0.256   0.019   0.365   0.290  -0.037   0.297   0.197  -0.230
132   V         0.321   0.337   0.019   0.322   0.337  -0.108   0.297   0.322  -0.230
133   R        -0.525  -0.546  -0.647  -0.461  -0.500  -0.648  -0.692  -0.722  -0.833
134   G         0.929   0.935   0.991   0.922   0.930   1.018   0.989   0.996   1.072
135   M        -0.644  -0.655  -0.658  -0.725  -0.735  -0.703  -0.890  -0.904  -0.851
136   S         0.021   0.067  -0.046  -0.072   0.001  -0.217  -0.198  -0.117  -0.350
137   L         0.021   0.039  -0.037  -0.070  -0.040  -0.182  -0.198  -0.166  -0.334
138   D        -0.525  -0.472  -0.653  -0.448  -0.365  -0.702  -0.692  -0.614  -0.841
139   E        -0.525  -0.559  -0.641  -0.375  -0.414  -0.530  -0.692  -0.729  -0.824
140   A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
141   V        -1.869  -1.846  -1.748  -1.907  -1.868  -1.734  -1.583  -1.558  -1.383
142   K         0.321   0.337   0.019   0.313   0.334  -0.100   0.297   0.322  -0.230
143   I         0.321   0.275   0.017   0.419   0.363  -0.061   0.297   0.226  -0.233
144   K         0.929   0.935   0.991   0.825   0.834   0.927   0.989   0.996   1.072
145   N         0.929   0.935   0.991   1.037   1.047   1.125   0.989   0.996   1.072
146   T         0.321   0.320   0.035   0.369   0.370  -0.039   0.297   0.297  -0.200
147   E        -1.309  -1.308  -1.448  -1.075  -1.064  -1.362  -1.187  -1.183  -1.264
148   I         0.929   0.935   0.991   0.956   0.967   1.049   0.989   0.996   1.072
149   A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
150   K         0.321   0.340   0.022   0.309   0.334  -0.104   0.297   0.326  -0.223
151   E         0.929   0.935   0.991   1.005   1.014   1.095   0.989   0.996   1.072
152   L         0.929   0.935   0.991   0.869   0.879   0.968   0.989   0.996   1.072
153   S         0.021  -0.040  -0.056   0.004  -0.087  -0.105  -0.198  -0.307  -0.370
154   L         0.929   0.935   0.991   0.869   0.879   0.968   0.989   0.996   1.072
155   P         0.929   0.935   0.991   0.998   1.007   1.089   0.989   0.996   1.072
156   P         0.929   0.935   0.991   0.998   1.007   1.089   0.989   0.996   1.072
157   V         0.929   0.935   0.991   0.842   0.844   0.943   0.989   0.996   1.072
158   K         0.929   0.935   0.991   0.825   0.834   0.927   0.989   0.996   1.072
159   L         0.929   0.935   0.991   0.869   0.879   0.968   0.989   0.996   1.072
160   H         0.929   0.935   0.991   1.105   1.114   1.188   0.989   0.996   1.072
161   C         0.929   0.935   0.991   1.121   1.129   1.203   0.989   0.996   1.072
162   S         0.929   0.935   0.991   0.889   0.898   0.987   0.989   0.996   1.072
163   M         0.929   0.935   0.991   1.066   1.076   1.152   0.989   0.996   1.072
164   L         0.929   0.935   0.991   0.869   0.879   0.968   0.989   0.996   1.072
165   A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
166   E         0.929   0.935   0.991   1.005   1.014   1.095   0.989   0.996   1.072
167   D         0.929   0.935   0.991   1.008   1.018   1.098   0.989   0.996   1.072
168   A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
169   I         0.929   0.935   0.991   0.956   0.967   1.049   0.989   0.996   1.072
170   K         0.929   0.935   0.991   0.825   0.834   0.927   0.989   0.996   1.072
171   A        -0.139  -0.141  -0.070  -0.518  -0.524  -0.397  -0.495  -0.497  -0.397
172   A         0.929   0.935   0.991   0.714   0.722   0.823   0.989   0.996   1.072
173   I        -0.190  -0.187  -0.076  -0.449  -0.451  -0.263  -0.593  -0.587  -0.408
174   K        -0.259  -0.236  -0.598  -0.214  -0.183  -0.699  -0.297  -0.263  -0.762
175   D         0.321   0.256   0.019   0.509   0.434   0.097   0.297   0.197  -0.230
176   Y         0.929   0.935   0.991   1.105   1.114   1.188   0.989   0.996   1.072
177   K        -1.204  -1.172  -1.118  -1.136  -1.089  -0.991  -1.286  -1.247  -1.124
178   T        -0.644  -0.633  -0.661  -0.835  -0.823  -0.872  -0.890  -0.876  -0.854
179   K         0.929   0.935   0.991   0.825   0.834   0.927   0.989   0.996   1.072
180   R        -0.259  -0.364  -0.620  -0.008  -0.139  -0.495  -0.297  -0.440  -0.793
181   N        -1.589  -1.594  -1.472  -1.593  -1.602  -1.401  -1.484  -1.482  -1.286
182   P        -1.309  -1.293  -1.437  -1.116  -1.092  -1.306  -1.187  -1.166  -1.254
183   -        -1.222  -1.250  -1.132  -1.426  -1.480  -1.301  -1.290  -1.316  -1.137
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   -         0.121   0.095  -0.015   0.050   0.009  -0.206  -0.024  -0.068  -0.292
189   -         0.121   0.091  -0.019   0.082   0.030  -0.219  -0.024  -0.074  -0.300
190   -        -1.222  -1.228  -1.133  -1.440  -1.457  -1.271  -1.290  -1.293  -1.138
191   -        -0.158  -0.134  -0.063  -0.336  -0.298  -0.187  -0.530  -0.485  -0.384
192   -         0.121   0.091  -0.019  -0.089  -0.136  -0.302  -0.024  -0.074  -0.300
193   -         0.121   0.095  -0.015  -0.089  -0.131  -0.296  -0.024  -0.068  -0.292
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
206   -        -1.222  -1.250  -1.132  -1.354  -1.388  -1.173  -1.290  -1.316  -1.137
207   -        -0.774  -0.789  -0.687  -1.029  -1.053  -0.881  -1.037  -1.050  -0.885
208   S        -0.525  -0.576  -0.658  -0.604  -0.687  -0.866  -0.692  -0.757  -0.848
209   V        -1.484  -1.450  -1.457  -1.501  -1.457  -1.433  -1.385  -1.352  -1.273
210   L        -0.818  -0.821  -0.697  -1.145  -1.153  -0.970  -1.088  -1.087  -0.898
211   H        -1.030  -0.980  -1.092  -1.122  -1.058  -1.194  -1.088  -1.025  -1.097
* 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/Q12056
Output conservation file - output/Q12056
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
