1     M         1.827   1.841   1.910   2.172   2.201   2.308   2.056   2.080   2.194
2     T        -0.359  -0.351  -0.303  -0.478  -0.437  -0.392  -0.576  -0.563  -0.493
3     N        -0.359  -0.351  -0.303  -0.647  -0.625  -0.564  -0.576  -0.563  -0.493
4     D        -0.359  -0.351  -0.303  -0.543  -0.518  -0.458  -0.576  -0.563  -0.493
5     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    S         0.831   0.819   0.736   0.808   0.787   0.680   0.792   0.770   0.608
17    E        -1.376  -1.371  -1.332  -1.124  -1.107  -1.050  -1.103  -1.095  -1.031
18    I        -0.064   0.023  -0.128  -0.072   0.047  -0.159  -0.155  -0.028  -0.244
19    K        -1.376  -1.371  -1.332  -1.166  -1.149  -1.093  -1.103  -1.095  -1.031
20    -         0.708   0.699   0.665   0.605   0.589   0.540   0.575   0.558   0.474
21    E        -1.376  -1.371  -1.332  -1.219  -1.217  -1.147  -1.103  -1.095  -1.031
22    I        -0.064  -0.062  -0.142   0.223   0.229   0.099  -0.155  -0.150  -0.263
23    K        -1.376  -1.371  -1.332  -1.253  -1.215  -1.181  -1.103  -1.095  -1.031
24    G         0.831   0.798   0.731   1.159   1.113   1.022   0.792   0.735   0.598
25    E        -0.932  -0.930  -0.883  -1.221  -1.210  -1.149  -0.906  -0.900  -0.829
26    L        -0.242  -0.252  -0.252  -0.351  -0.368  -0.364  -0.412  -0.424  -0.421
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    A        -0.242  -0.246  -0.236  -0.381  -0.386  -0.353  -0.412  -0.416  -0.400
34    N        -0.064  -0.062  -0.142  -0.276  -0.273  -0.398  -0.155  -0.150  -0.263
35    V        -0.242  -0.240  -0.236  -0.264  -0.258  -0.245  -0.412  -0.407  -0.400
36    K        -0.932  -0.928  -0.883  -0.929  -0.928  -0.852  -0.906  -0.898  -0.829
37    K         0.708   0.680   0.645   0.404   0.353   0.279   0.575   0.522   0.436
38    R         0.708   0.717   0.661   0.535   0.547   0.414   0.575   0.590   0.466
39    K         0.708   0.761   0.674   0.478   0.553   0.426   0.575   0.668   0.492
40    R         0.708   0.714   0.665   0.587   0.596   0.496   0.575   0.584   0.474
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    R        -1.376  -1.371  -1.332  -1.360  -1.315  -1.290  -1.103  -1.095  -1.031
50    S        -0.824  -0.835  -0.823  -1.209  -1.228  -1.220  -0.787  -0.796  -0.764
51    K        -1.376  -1.371  -1.332  -1.402  -1.397  -1.333  -1.103  -1.095  -1.031
52    K         0.831   0.819   0.736   0.587   0.569   0.422   0.792   0.770   0.608
53    I        -0.824  -0.784  -0.814  -0.604  -0.529  -0.597  -0.787  -0.738  -0.755
54    N        -0.824  -0.866  -0.837  -0.781  -0.864  -0.820  -0.787  -0.830  -0.780
55    K        -0.824  -0.866  -0.837  -1.083  -1.141  -1.095  -0.787  -0.830  -0.780
56    L         0.831   0.819   0.736   0.858   0.846   0.748   0.792   0.770   0.608
57    T        -0.064  -0.017  -0.129   0.172   0.253   0.055  -0.155  -0.086  -0.245
58    D        -0.824  -0.841  -0.826  -0.753  -0.771  -0.727  -0.787  -0.802  -0.767
59    G        -1.376  -1.371  -1.332  -1.007  -1.025  -0.930  -1.103  -1.095  -1.031
60    Q         0.487   0.494   0.534   0.245   0.258   0.318   0.161   0.170   0.220
61    I        -0.824  -0.780  -0.823  -0.916  -0.856  -0.892  -0.787  -0.733  -0.764
62    R         0.487   0.477   0.526   0.102   0.065   0.126   0.161   0.136   0.204
63    I        -0.824  -0.780  -0.823  -0.627  -0.535  -0.633  -0.787  -0.733  -0.764
64    N        -0.064  -0.099  -0.147   0.067   0.014  -0.076  -0.155  -0.204  -0.270
65    H         1.827   1.841   1.910   2.145   2.171   2.281   2.056   2.080   2.194
66    V         0.487   0.477   0.526   0.439   0.414   0.483   0.161   0.136   0.204
67    S        -0.273  -0.228  -0.252  -0.312  -0.256  -0.268  -0.471  -0.418  -0.429
68    S         0.831   0.819   0.736   0.856   0.839   0.749   0.792   0.770   0.608
69    E         1.827   1.841   1.910   1.692   1.716   1.819   2.056   2.080   2.194
70    K         0.487   0.496   0.536   0.282   0.301   0.330   0.161   0.174   0.223
71    K         0.831   0.819   0.736   0.645   0.632   0.507   0.792   0.770   0.608
72    R         1.827   1.841   1.910   1.809   1.832   1.938   2.056   2.080   2.194
73    R         1.827   1.841   1.910   1.809   1.832   1.938   2.056   2.080   2.194
74    E        -0.064  -0.109  -0.157  -0.185  -0.252  -0.337  -0.155  -0.218  -0.285
75    L        -1.376  -1.371  -1.332  -1.313  -1.304  -1.243  -1.103  -1.095  -1.031
76    E         0.831   0.867   0.741   0.891   0.950   0.730   0.792   0.853   0.617
77    R         1.827   1.841   1.910   1.809   1.832   1.938   2.056   2.080   2.194
78    A        -1.376  -1.371  -1.332  -1.129  -1.156  -1.055  -1.103  -1.095  -1.031
79    I        -1.376  -1.371  -1.332  -1.199  -1.213  -1.127  -1.103  -1.095  -1.031
80    F         0.487   0.511   0.545   0.737   0.780   0.828   0.161   0.202   0.241
81    D         0.831   0.798   0.731   1.003   0.951   0.823   0.792   0.735   0.598
82    E        -0.824  -0.791  -0.813  -1.092  -1.050  -1.074  -0.787  -0.746  -0.753
83    L         0.487   0.477   0.526   0.226   0.207   0.279   0.161   0.136   0.204
84    V         0.831   0.798   0.731   1.065   1.023   0.927   0.792   0.735   0.598
85    A        -1.376  -1.371  -1.332  -1.298  -1.321  -1.227  -1.103  -1.095  -1.031
86    V        -0.273  -0.254  -0.246  -0.407  -0.386  -0.360  -0.471  -0.447  -0.422
87    V         0.831   0.811   0.735   1.065   1.042   0.933   0.792   0.757   0.606
88    P         1.827   1.841   1.910   2.082   2.102   2.216   2.056   2.080   2.194
89    D        -0.824  -0.866  -0.837  -0.495  -0.557  -0.502  -0.787  -0.830  -0.780
90    L         1.827   1.841   1.910   1.741   1.765   1.869   2.056   2.080   2.194
91    Q        -0.824  -0.844  -0.832  -0.769  -0.795  -0.758  -0.787  -0.806  -0.775
92    P        -0.824  -0.791  -0.813  -0.925  -0.896  -0.903  -0.787  -0.746  -0.753
93    Q        -0.824  -0.844  -0.832  -1.110  -1.149  -1.121  -0.787  -0.806  -0.775
94    E         0.831   0.798   0.731   0.759   0.718   0.619   0.792   0.735   0.598
95    S        -0.824  -0.841  -0.826  -0.734  -0.757  -0.745  -0.787  -0.802  -0.767
96    R         1.827   1.841   1.910   1.809   1.832   1.938   2.056   2.080   2.194
97    S         1.827   1.841   1.910   1.731   1.750   1.859   2.056   2.080   2.194
98    E         1.827   1.841   1.910   1.692   1.716   1.819   2.056   2.080   2.194
99    L        -0.064  -0.109  -0.157   0.025  -0.033  -0.077  -0.155  -0.218  -0.285
100   I        -0.824  -0.809  -0.812  -0.785  -0.774  -0.772  -0.787  -0.768  -0.752
101   I         0.831   0.798   0.731   0.964   0.922   0.819   0.792   0.735   0.598
102   Y         0.487   0.477   0.526   0.468   0.433   0.494   0.161   0.136   0.204
103   L        -1.376  -1.371  -1.332  -1.171  -1.151  -1.098  -1.103  -1.095  -1.031
104   K         1.827   1.841   1.910   1.592   1.617   1.717   2.056   2.080   2.194
105   S         0.487   0.504   0.536   0.312   0.330   0.390   0.161   0.188   0.224
106   L        -0.824  -0.841  -0.826  -0.691  -0.723  -0.711  -0.787  -0.802  -0.767
107   S        -1.376  -1.371  -1.332  -1.051  -1.035  -0.976  -1.103  -1.095  -1.031
108   Y         0.831   0.798   0.731   1.232   1.195   1.107   0.792   0.735   0.598
109   L         0.831   0.811   0.735   0.781   0.755   0.634   0.792   0.757   0.606
110   S        -1.376  -1.371  -1.332  -1.588  -1.586  -1.523  -1.103  -1.095  -1.031
111   W        -0.064  -0.115  -0.165   0.350   0.276   0.184  -0.155  -0.226  -0.296
112   L         1.827   1.841   1.910   1.741   1.765   1.869   2.056   2.080   2.194
113   Y        -0.064  -0.115  -0.165   0.157   0.071  -0.052  -0.155  -0.226  -0.296
114   E         0.487   0.478   0.525   0.268   0.254   0.334   0.161   0.139   0.201
115   R        -0.824  -0.819  -0.827  -0.994  -0.975  -1.020  -0.787  -0.779  -0.769
116   N         0.831   0.798   0.731   1.033   0.991   0.898   0.792   0.735   0.598
117   E        -0.824  -0.784  -0.814  -1.029  -0.970  -1.007  -0.787  -0.738  -0.755
118   K        -0.273  -0.279  -0.250  -0.612  -0.614  -0.555  -0.471  -0.476  -0.427
119   L         1.827   1.841   1.910   1.741   1.765   1.869   2.056   2.080   2.194
120   R        -0.064  -0.115  -0.165  -0.118  -0.204  -0.304  -0.155  -0.226  -0.296
121   K        -0.824  -0.791  -0.813  -0.730  -0.681  -0.724  -0.787  -0.746  -0.753
122   Q        -0.824  -0.835  -0.823  -0.976  -1.004  -0.992  -0.787  -0.796  -0.764
123   I        -0.273  -0.274  -0.255  -0.150  -0.136  -0.124  -0.471  -0.469  -0.432
124   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   Q        -0.273  -0.278  -0.251  -0.217  -0.222  -0.181  -0.471  -0.473  -0.427
142   E         0.831   0.811   0.735   0.745   0.720   0.604   0.792   0.757   0.606
143   Q        -0.273  -0.253  -0.248  -0.630  -0.598  -0.579  -0.471  -0.446  -0.424
144   N        -0.824  -0.819  -0.827  -0.492  -0.488  -0.474  -0.787  -0.779  -0.769
145   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   D        -0.824  -0.780  -0.823  -0.858  -0.770  -0.873  -0.787  -0.733  -0.764
150   L        -0.824  -0.844  -0.832  -0.929  -0.947  -0.933  -0.787  -0.806  -0.775
151   V        -0.824  -0.816  -0.824  -0.517  -0.493  -0.503  -0.787  -0.775  -0.765
152   P         1.827   1.841   1.910   2.082   2.102   2.216   2.056   2.080   2.194
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   K        -0.824  -0.809  -0.812  -0.842  -0.824  -0.800  -0.787  -0.768  -0.752
160   E         0.831   0.819   0.736   0.796   0.784   0.680   0.792   0.770   0.608
161   L         0.831   0.798   0.731   0.703   0.649   0.511   0.792   0.735   0.598
162   I        -0.273  -0.274  -0.255  -0.159  -0.149  -0.105  -0.471  -0.469  -0.432
163   W        -0.824  -0.866  -0.837  -0.597  -0.683  -0.653  -0.787  -0.830  -0.780
164   E        -0.273  -0.228  -0.252  -0.691  -0.638  -0.651  -0.471  -0.418  -0.429
165   L        -0.824  -0.866  -0.837  -0.929  -0.997  -0.949  -0.787  -0.830  -0.780
166   G        -0.359  -0.354  -0.303  -0.133  -0.123  -0.040  -0.576  -0.567  -0.493
167   D         0.560   0.549   0.576   0.446   0.412   0.432   0.301   0.277   0.302
168   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   Q        -0.824  -0.784  -0.814  -1.087  -1.013  -1.084  -0.787  -0.738  -0.755
172   S        -0.273  -0.279  -0.247  -0.349  -0.371  -0.318  -0.471  -0.475  -0.423
173   G        -0.824  -0.844  -0.832  -0.623  -0.660  -0.630  -0.787  -0.806  -0.775
174   Q        -1.376  -1.371  -1.332  -1.147  -1.152  -1.074  -1.103  -1.095  -1.031
* 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/P13902
Output conservation file - output/P13902
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
