1     M         1.067   1.076   1.132   1.325   1.337   1.404   1.131   1.142   1.223
2     G         0.038   0.088  -0.010  -0.114  -0.037  -0.209  -0.149  -0.068  -0.265
3     S         0.038   0.057  -0.013  -0.036  -0.005  -0.149  -0.149  -0.119  -0.270
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     F         0.038   0.057  -0.013   0.041   0.073  -0.052  -0.149  -0.119  -0.270
8     H        -0.182  -0.185  -0.062  -0.334  -0.370  -0.173  -0.541  -0.549  -0.361
9     H         1.067   1.076   1.132   1.244   1.257   1.330   1.131   1.142   1.223
10    A         1.067   1.076   1.132   0.975   0.973   1.083   1.131   1.142   1.223
11    D         1.067   1.076   1.132   1.031   1.052   1.134   1.131   1.142   1.223
12    H        -0.390  -0.441  -0.652  -0.075  -0.162  -0.492  -0.402  -0.476  -0.746
13    V        -0.682  -0.598  -0.701  -0.720  -0.596  -0.758  -0.820  -0.708  -0.814
14    N        -0.682  -0.717  -0.716  -0.639  -0.670  -0.664  -0.820  -0.852  -0.835
15    Y        -0.682  -0.597  -0.702  -0.571  -0.434  -0.635  -0.820  -0.712  -0.816
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    S        -1.044  -1.011  -1.178  -0.903  -0.886  -1.118  -0.959  -0.927  -1.072
18    S        -1.769  -1.700  -1.619  -1.764  -1.684  -1.519  -1.517  -1.452  -1.294
19    N        -1.406  -1.408  -1.245  -1.422  -1.412  -1.177  -1.377  -1.364  -1.142
20    L        -1.470  -1.439  -1.259  -1.708  -1.678  -1.374  -1.430  -1.391  -1.154
21    N        -1.769  -1.769  -1.623  -1.725  -1.708  -1.493  -1.517  -1.505  -1.298
22    K        -0.028   0.062  -0.013  -0.025   0.108   0.003  -0.262  -0.112  -0.270
23    E        -0.682  -0.627  -0.709  -0.752  -0.674  -0.794  -0.820  -0.755  -0.827
24    E         0.317   0.383   0.063   0.371   0.463  -0.004   0.295   0.391  -0.137
25    I        -1.270  -1.251  -1.220  -1.348  -1.345  -1.255  -1.238  -1.212  -1.119
26    L        -0.028  -0.110  -0.046  -0.206  -0.320  -0.206  -0.262  -0.412  -0.331
27    E        -0.682  -0.691  -0.712  -0.667  -0.661  -0.736  -0.820  -0.814  -0.828
28    Q        -1.632  -1.575  -1.603  -1.377  -1.292  -1.367  -1.377  -1.319  -1.280
29    L        -0.770  -0.797  -0.724  -1.040  -1.043  -0.868  -0.959  -0.973  -0.846
30    L        -1.044  -1.038  -1.193  -1.102  -1.105  -1.346  -0.959  -0.953  -1.088
31    L        -1.044  -1.013  -1.190  -0.962  -0.912  -1.224  -0.959  -0.924  -1.086
32    S        -0.390  -0.559  -0.671  -0.256  -0.492  -0.663  -0.402  -0.627  -0.772
33    Y        -0.390  -0.559  -0.671  -0.134  -0.397  -0.648  -0.402  -0.627  -0.772
34    E         0.317   0.398   0.067   0.371   0.481   0.003   0.295   0.413  -0.129
35    G        -0.028  -0.056  -0.033  -0.229  -0.297  -0.263  -0.262  -0.315  -0.307
36    L         1.067   1.076   1.132   0.901   0.921   1.015   1.131   1.142   1.223
37    S        -1.366  -1.407  -1.239  -1.506  -1.562  -1.292  -1.335  -1.362  -1.136
38    D        -1.366  -1.271  -1.231  -1.237  -1.110  -1.025  -1.335  -1.240  -1.129
39    G        -0.907  -0.887  -0.754  -1.154  -1.116  -0.910  -1.099  -1.070  -0.880
40    Q        -0.028   0.013  -0.022  -0.007   0.059  -0.024  -0.262  -0.194  -0.287
41    V        -1.270  -1.240  -1.217  -1.084  -1.009  -1.043  -1.238  -1.193  -1.115
42    N         1.067   1.076   1.132   1.099   1.112   1.197   1.131   1.142   1.223
43    W         1.067   1.076   1.132   1.269   1.291   1.352   1.131   1.142   1.223
44    V         1.067   1.076   1.132   0.931   0.938   1.043   1.131   1.142   1.223
45    C        -0.182  -0.174  -0.063  -0.347  -0.350  -0.178  -0.541  -0.530  -0.361
46    N         1.067   1.076   1.132   1.099   1.112   1.197   1.131   1.142   1.223
47    L         1.067   1.076   1.132   0.901   0.921   1.015   1.131   1.142   1.223
48    S        -0.182  -0.144  -0.058  -0.477  -0.413  -0.274  -0.541  -0.474  -0.352
49    N         1.067   1.076   1.132   1.099   1.112   1.197   1.131   1.142   1.223
50    A        -0.182  -0.179  -0.060  -0.393  -0.395  -0.185  -0.541  -0.538  -0.356
51    S        -0.182  -0.168  -0.057  -0.477  -0.466  -0.272  -0.541  -0.519  -0.351
52    S         0.317   0.205   0.062   0.361   0.200  -0.036   0.295   0.123  -0.138
53    L         0.317   0.241   0.044   0.236   0.145  -0.147   0.295   0.178  -0.170
54    I        -0.182  -0.167  -0.062  -0.528  -0.498  -0.314  -0.541  -0.516  -0.360
55    W         1.067   1.076   1.132   1.269   1.291   1.352   1.131   1.142   1.223
56    H         1.067   1.076   1.132   1.244   1.257   1.330   1.131   1.142   1.223
57    A        -0.390  -0.405  -0.665  -0.332  -0.378  -0.725  -0.402  -0.425  -0.764
58    Y        -0.390  -0.559  -0.671  -0.101  -0.339  -0.578  -0.402  -0.627  -0.772
59    K        -0.390  -0.339  -0.654  -0.222  -0.150  -0.589  -0.402  -0.335  -0.749
60    S         1.067   1.076   1.132   1.044   1.053   1.146   1.131   1.142   1.223
61    L         0.317   0.314   0.056   0.279   0.287  -0.025   0.295   0.290  -0.148
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    A        -1.270  -1.257  -1.224  -1.274  -1.280  -1.217  -1.238  -1.229  -1.122
66    V        -1.270  -1.356  -1.228  -1.364  -1.483  -1.264  -1.238  -1.311  -1.126
67    D        -0.770  -0.822  -0.721  -0.869  -0.920  -0.754  -0.959  -1.002  -0.842
68    I        -0.028  -0.037  -0.041  -0.237  -0.261  -0.263  -0.262  -0.282  -0.321
69    N         1.067   1.076   1.132   1.099   1.112   1.197   1.131   1.142   1.223
70    W         1.067   1.076   1.132   1.269   1.291   1.352   1.131   1.142   1.223
71    A        -0.682  -0.610  -0.698  -0.757  -0.655  -0.764  -0.820  -0.709  -0.810
72    G         1.067   1.076   1.132   0.974   0.982   1.082   1.131   1.142   1.223
73    F         1.067   1.076   1.132   1.188   1.214   1.278   1.131   1.142   1.223
74    Y         1.067   1.076   1.132   1.221   1.234   1.309   1.131   1.142   1.223
75    V        -0.784  -0.699  -0.717  -1.078  -0.935  -0.950  -0.955  -0.843  -0.835
76    T        -0.672  -0.728  -0.720  -0.628  -0.729  -0.779  -0.781  -0.857  -0.836
77    Q        -1.789  -1.790  -1.633  -1.524  -1.541  -1.361  -1.524  -1.518  -1.305
78    A        -1.789  -1.759  -1.631  -1.582  -1.532  -1.336  -1.524  -1.491  -1.303
79    S        -2.212  -2.170  -1.958  -2.082  -2.021  -1.717  -1.714  -1.672  -1.419
80    E        -1.366  -1.334  -1.236  -1.344  -1.290  -1.114  -1.335  -1.295  -1.134
81    E        -1.789  -1.790  -1.633  -1.717  -1.729  -1.490  -1.524  -1.518  -1.305
82    N        -1.206  -1.159  -1.210  -1.167  -1.092  -1.189  -1.145  -1.088  -1.106
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    T        -0.784  -0.766  -0.729  -0.842  -0.818  -0.733  -0.955  -0.937  -0.851
90    L         1.067   1.076   1.132   0.883   0.899   0.999   1.131   1.142   1.223
91    I         0.243   0.311   0.048   0.266   0.357  -0.078   0.183   0.286  -0.163
92    L         1.067   1.076   1.132   0.883   0.899   0.999   1.131   1.142   1.223
93    G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
94    P         1.067   1.076   1.132   1.248   1.258   1.334   1.131   1.142   1.223
95    F         1.067   1.076   1.132   1.182   1.205   1.273   1.131   1.142   1.223
96    Q         0.317   0.241   0.044   0.503   0.407   0.122   0.295   0.178  -0.170
97    G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
98    K         0.317   0.241   0.044   0.406   0.311   0.013   0.295   0.178  -0.170
99    V         1.067   1.076   1.132   0.931   0.938   1.043   1.131   1.142   1.223
100   A         1.067   1.076   1.132   0.975   0.973   1.083   1.131   1.142   1.223
101   C         1.067   1.076   1.132   1.199   1.209   1.288   1.131   1.142   1.223
102   Q         1.067   1.076   1.132   1.141   1.151   1.235   1.131   1.142   1.223
103   M        -1.769  -1.758  -1.622  -1.663  -1.629  -1.416  -1.517  -1.496  -1.297
104   I         1.067   1.076   1.132   1.082   1.093   1.181   1.131   1.142   1.223
105   Q        -1.769  -1.780  -1.626  -1.640  -1.662  -1.429  -1.517  -1.516  -1.300
106   F         0.317   0.241   0.044   0.488   0.393   0.020   0.295   0.178  -0.170
107   G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
108   K        -0.682  -0.631  -0.695  -0.567  -0.507  -0.549  -0.820  -0.766  -0.808
109   G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
110   V         1.067   1.076   1.132   0.931   0.938   1.043   1.131   1.142   1.223
111   C         1.067   1.076   1.132   1.199   1.209   1.288   1.131   1.142   1.223
112   G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
113   T        -1.632  -1.686  -1.610  -1.435  -1.561  -1.473  -1.377  -1.426  -1.286
114   A         1.067   1.076   1.132   0.975   0.973   1.083   1.131   1.142   1.223
115   A         1.067   1.076   1.132   0.975   0.973   1.083   1.131   1.142   1.223
116   S        -0.390  -0.559  -0.671  -0.296  -0.552  -0.746  -0.402  -0.627  -0.772
117   T        -1.270  -1.274  -1.219  -1.233  -1.240  -1.149  -1.238  -1.242  -1.117
118   K        -0.770  -0.761  -0.719  -0.857  -0.845  -0.768  -0.959  -0.941  -0.841
119   E        -1.769  -1.730  -1.617  -1.725  -1.644  -1.491  -1.517  -1.475  -1.293
120   T         1.067   1.076   1.132   1.166   1.184   1.258   1.131   1.142   1.223
121   Q         1.067   1.076   1.132   1.141   1.151   1.235   1.131   1.142   1.223
122   I         0.317   0.378   0.065   0.236   0.322  -0.112   0.295   0.384  -0.133
123   V         1.067   1.076   1.132   0.931   0.938   1.043   1.131   1.142   1.223
124   P         0.317   0.241   0.044   0.579   0.476   0.139   0.295   0.178  -0.170
125   D        -0.028  -0.065  -0.050  -0.136  -0.192  -0.193  -0.262  -0.331  -0.338
126   V         1.067   1.076   1.132   0.931   0.938   1.043   1.131   1.142   1.223
127   N        -0.907  -0.893  -0.755  -1.089  -1.059  -0.851  -1.099  -1.077  -0.881
128   K        -1.270  -1.302  -1.220  -1.298  -1.366  -1.222  -1.238  -1.269  -1.119
129   Y        -0.028   0.003  -0.033   0.057   0.116   0.023  -0.262  -0.212  -0.307
130   P         1.067   1.076   1.132   1.248   1.258   1.334   1.131   1.142   1.223
131   G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
132   H         1.067   1.076   1.132   1.244   1.257   1.330   1.131   1.142   1.223
133   I         1.067   1.076   1.132   1.082   1.093   1.181   1.131   1.142   1.223
134   A         1.067   1.076   1.132   0.975   0.973   1.083   1.131   1.142   1.223
135   C         1.067   1.076   1.132   1.199   1.209   1.288   1.131   1.142   1.223
136   D         1.067   1.076   1.132   1.031   1.052   1.134   1.131   1.142   1.223
137   G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
138   E        -0.390  -0.559  -0.671  -0.315  -0.561  -0.780  -0.402  -0.627  -0.772
139   T         0.317   0.205   0.062   0.494   0.347   0.096   0.295   0.123  -0.138
140   K         0.317   0.314   0.056   0.406   0.407   0.034   0.295   0.290  -0.148
141   S         1.067   1.076   1.132   1.044   1.053   1.146   1.131   1.142   1.223
142   E         1.067   1.076   1.132   1.039   1.058   1.142   1.131   1.142   1.223
143   I         1.067   1.076   1.132   1.082   1.093   1.181   1.131   1.142   1.223
144   V         1.067   1.076   1.132   0.931   0.938   1.043   1.131   1.142   1.223
145   V         1.067   1.076   1.132   0.931   0.938   1.043   1.131   1.142   1.223
146   P         1.067   1.076   1.132   1.248   1.258   1.334   1.131   1.142   1.223
147   I         1.067   1.076   1.132   1.082   1.093   1.181   1.131   1.142   1.223
148   I         0.317   0.378   0.065   0.267   0.338  -0.086   0.295   0.384  -0.133
149   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   N        -1.769  -1.786  -1.624  -1.737  -1.797  -1.555  -1.517  -1.519  -1.298
151   D        -1.270  -1.222  -1.214  -1.262  -1.201  -1.179  -1.238  -1.192  -1.113
152   G         0.317   0.205   0.062   0.323   0.172  -0.055   0.295   0.123  -0.138
153   K        -1.270  -1.300  -1.215  -1.190  -1.196  -1.063  -1.238  -1.254  -1.113
154   T        -0.682  -0.775  -0.721  -0.721  -0.900  -0.852  -0.820  -0.939  -0.841
155   L        -1.270  -1.223  -1.209  -1.439  -1.342  -1.298  -1.238  -1.176  -1.108
156   G         0.317   0.205   0.062   0.314   0.154  -0.077   0.295   0.123  -0.138
157   V         0.317   0.205   0.062   0.267   0.113  -0.090   0.295   0.123  -0.138
158   I         0.317   0.314   0.056   0.387   0.385  -0.042   0.295   0.290  -0.148
159   D         1.067   1.076   1.132   1.031   1.052   1.134   1.131   1.142   1.223
160   I        -0.682  -0.696  -0.693  -0.807  -0.804  -0.852  -0.820  -0.816  -0.803
161   D         1.067   1.076   1.132   1.031   1.052   1.134   1.131   1.142   1.223
162   C         1.067   1.076   1.132   1.199   1.209   1.288   1.131   1.142   1.223
163   L        -0.028  -0.110  -0.046  -0.309  -0.464  -0.359  -0.262  -0.412  -0.331
164   D        -1.044  -1.190  -1.202  -0.907  -1.119  -1.151  -0.959  -1.123  -1.098
165   Y        -0.682  -0.552  -0.697  -0.760  -0.579  -0.727  -0.820  -0.648  -0.808
166   E        -0.028  -0.053  -0.035  -0.128  -0.168  -0.161  -0.262  -0.311  -0.312
167   G         1.067   1.076   1.132   0.996   1.007   1.103   1.131   1.142   1.223
168   F         1.067   1.076   1.132   1.182   1.205   1.273   1.131   1.142   1.223
169   D        -0.028   0.062  -0.013  -0.110   0.040  -0.094  -0.262  -0.112  -0.270
170   H        -1.769  -1.660  -1.617  -1.665  -1.513  -1.414  -1.517  -1.416  -1.293
171   V        -0.390  -0.339  -0.654  -0.419  -0.352  -0.829  -0.402  -0.335  -0.749
172   D         1.067   1.076   1.132   1.031   1.052   1.134   1.131   1.142   1.223
173   K        -0.770  -0.762  -0.720  -0.867  -0.854  -0.785  -0.959  -0.942  -0.841
174   E        -1.270  -1.356  -1.228  -1.304  -1.429  -1.235  -1.238  -1.311  -1.126
175   F        -1.270  -1.346  -1.224  -1.027  -1.115  -0.969  -1.238  -1.299  -1.122
176   L         1.067   1.076   1.132   0.901   0.921   1.015   1.131   1.142   1.223
177   E         1.067   1.076   1.132   1.039   1.058   1.142   1.131   1.142   1.223
178   K         0.317   0.314   0.056   0.406   0.407   0.034   0.295   0.290  -0.148
179   L         0.317   0.241   0.044   0.236   0.145  -0.147   0.295   0.178  -0.170
180   A         1.067   1.076   1.132   0.975   0.973   1.083   1.131   1.142   1.223
181   K        -2.131  -2.085  -1.938  -2.132  -2.055  -1.831  -1.656  -1.612  -1.406
182   L        -1.044  -0.984  -1.184  -1.073  -0.986  -1.284  -0.959  -0.892  -1.079
183   I        -0.682  -0.758  -0.715  -0.800  -0.940  -0.900  -0.820  -0.913  -0.834
184   N        -1.769  -1.662  -1.616  -1.780  -1.657  -1.525  -1.517  -1.422  -1.293
185   K        -1.044  -1.077  -1.183  -0.805  -0.842  -0.981  -0.959  -0.999  -1.078
186   S        -0.028   0.006  -0.035  -0.098  -0.046  -0.120  -0.262  -0.208  -0.310
187   C         0.317   0.398   0.067   0.505   0.611   0.081   0.295   0.413  -0.129
188   V        -0.784  -0.781  -0.726  -0.997  -0.975  -0.897  -0.955  -0.936  -0.846
189   F        -0.201  -0.168  -0.058  -0.213  -0.149   0.008  -0.576  -0.519  -0.353
190   K        -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/P36088
Output conservation file - output/P36088
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
