This file is indexed.

/usr/include/libphylo/adrianCodon.dat.q is in rate4site 3.0.0-5.

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The actual contents of the file can be viewed below.

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"   634                                                                                                                                                                                                                                                                                                                                                                         "
" 25105   560                                                                                                                                                                                                                                                                                                                                                                   "
"  1209 37271   620                                                                                                                                                                                                                                                                                                                                                             "
"  1353   344   196   494                                                                                                                                                                                                                                                                                                                                                       "
"   112  2048   176    34 21460                                                                                                                                                                                                                                                                                                                                                 "
"     0   140  1656   380 71026 41523                                                                                                                                                                                                                                                                                                                                           "
"   238   255    56  2967 35040 33972 43340                                                                                                                                                                                                                                                                                                                                     "
"  8628   295   812   370  1546    65     0    23                                                                                                                                                                                                                                                                                                                               "
"   328  7142   272   370   715  4680  1286   876   707                                                                                                                                                                                                                                                                                                                         "
"  1192   289  7588   303   103   124  1929    82 52300   924                                                                                                                                                                                                                                                                                                                   "
"   509     0   304 10057   836     0   806  6124  1328 45060  1132                                                                                                                                                                                                                                                                                                             "
"   607    43    47   105  5067     0     0     0   863    56   221   189                                                                                                                                                                                                                                                                                                       "
"     0   301    43     0     0  2141   279     0     0   475    32     0 27331                                                                                                                                                                                                                                                                                                 "
"   167    88   393   141  1487   366  3364   545   193   140   538   162  5087  1030                                                                                                                                                                                                                                                                                           "
"    34     0    42   421     0     0   346  3233     0     0    61   718 31469 35230  1626                                                                                                                                                                                                                                                                                     "
"  2841   308    69   647   711    76     0   346  1297   278   124   413   193    49   200     0                                                                                                                                                                                                                                                                               "
"   195  2491   229   114    57   356    73    12   114   945   197     0     8    74    42     9  2449                                                                                                                                                                                                                                                                         "
"   286   295  1514   350   199   128   640    63    66   257   565   175    42    15   241    41 31892  2201                                                                                                                                                                                                                                                                   "
"   352    19   175  3379   195    32     0   441   246    85   129  1259   106     0   126   176  4155 62775  2262                                                                                                                                                                                                                                                             "
"   190    36    58   114  2112     0     0     0     0    51    81   158   201     0   114    51  2926   203   490   116                                                                                                                                                                                                                                                       "
"    37   204    30    71     0  1701   355   109    35   444     1     0    27   114    56    21   205  1284   335    79 21842                                                                                                                                                                                                                                                 "
"    81    99   218    95   183     0  4067    30    94   182    10    76   164    61   192     0   617   512  2569   361 57041 44793                                                                                                                                                                                                                                           "
"    54    30    30   239   134   158     0  2062    10    30    35   370   101     0    70   141   263     0   183  1574 32490 33996 32457                                                                                                                                                                                                                                     "
"  1891     0   623    93     0   147   671     0 46674   151 12628     0    11     0     0   134  8237   543     0   277   818    47     0     0                                                                                                                                                                                                                               "
"   701   549  1184     0     0   246   241    87  5836  1540 12311     0     6    41    48     0   452  5598   739     0    16   841   253     0 40388                                                                                                                                                                                                                         "
"   854   120  2602    57    54    69   359     0 13337    47 37725    91     0    31   105     0     0   660  5014   399   118     0  2656     0 82443 40802                                                                                                                                                                                                                   "
"   695     0   735   893    81    28     0   661 12916     0  6008  2384    89    35    60    56  1344     0   484  9142     0     0     0  1483 85032 87710 53112                                                                                                                                                                                                             "
"   208    39     0    46   600     0     0     0    19     0     0    55  7884     0  1512   386  2427   200    95     0  3069     0     0     0  2011     0    15     0                                                                                                                                                                                                       "
"    35   133     6     0     0   387    59     0     0   142    42     0   365  3634   769   272    79   813   191   114     0  1470     0    70    95  1012     0     0 17551                                                                                                                                                                                                 "
"     0    15    74     0    97    91   378    52    27    44    46     8   876   732  2298   588   106    83   604    90   286     0  1947     0     0    70   707     0 33878 14863                                                                                                                                                                                           "
"    63     0    14   229     8     0   114   484    67    48     0   147   280   278   720  3849   349     0   160  1407     0     0     0  1951     0     3    43  1427 22703 32337 15002                                                                                                                                                                                     "
"  1304   155     0   389   408    75     0    79   444   170     0   236   197    11    45     0  2595    59   234   256   149    35    74    60    51     0     0   143   109    12     0    27                                                                                                                                                                               "
"   120  2602    73    69     0   258   160   112    46   821    22    78     0    43    18     0   158   647   151    46    14   149    84    17     1   119    23     2     0    42     7    20  2320                                                                                                                                                                         "
"     0   168   893   221   158    73   415   109     0   180   336   209    35     1   131    44   138   148  1538   143   107    83   168    39     1    91   217     0     0    26    55    14 23280  3052                                                                                                                                                                   "
"   117     9    91  3406   173     5     0   311    55    62    40  1017    39     0    16    75   274     0   113   787    57    14    76    93     0    16    26   138    10     0     1    44  3660 28072  2533                                                                                                                                                             "
"   450    59   100   310  7741     0     0     0   225   220   182   557  1008     0   588   153   639    41   127   145  2469    39   211   190   150     0    48    78   625     0    97    61  1324    82   245   122                                                                                                                                                       "
"    28   466    94    52     0  6013    75     0    50  1265   106     0     0   452   240     0    47   248   183     0    14  2010   303   164    55   277     0    61     0   333    64    62    86   670   189     0 17008                                                                                                                                                 "
"   130   336   356   168     0   401 16072     0   103   537   357   370   656   161   817     0   379    93   512   228     0   428 10166     0     0   195   789     0     0    83   543    33     0   379  1907    42 47381 29661                                                                                                                                           "
"    89    80    65   525     0     0     0  7268    98   211     0  1307    86    67   226   484   125    11   108   230    58   130     0  2312     0     0   130   252    29    17    64   381   133     0   145   799 30850 26704 28871                                                                                                                                     "
"   285    65    23   253   446    24   106     6  2230   278     0   315   177     0    65    33   468    34    17    54   163    23    55    33   366     0     0     0   145    26     0    28  1661   180     0   104  2231    92     0   278                                                                                                                               "
"    28  1227    58   189    12   521   129   103    53  5470     0     0    37    87    33    21    31   344    83    26    64   236   268    30     0   941   162     1     0    80    13    28     0  1655   105     0     0  2186   744   149 19297                                                                                                                         "
"    27   356   299   139   176     0   843   160     0   684  3262   829    29    45   241     0   110    65   309    60    76   115   522    18     0     0  1073     0     0     2    82     0     0    67  1559   183   750   315  5134    73 44365 23295                                                                                                                   "
"    92   205    66  1727    96   190     0   728     0    13     0  7147     0     0    47    96     0     0    89   555    60    34     0   335   244     0     0  1432    18     0    18   105    59     0    63  2203   356     0     0  2632 28434 37047 23095                                                                                                             "
"   318    54    33   115  3527    41    76     0   518   181     0    64 23970     0  1303   260   576    75    64    47   821   131     0     0   179     0     0     0  4505    11    14   274   764    39    80    51  6746     0     0    30  1310     0   179     0                                                                                                       "
"    27   179    23    44     3  2249     0   308    11   354    78    34   330 12669   395   164    61   157    53    32    75   413   144     0     0   108    75    38   251  3338    87    38    51   294    54     0     0  4666     0     0     0   797     0     0 22326                                                                                                 "
"    20    26   113    25   429   137  2071   322     0    22   220    58  3262  1931  2537  1548    21    38   128    48   121    44   321    57     0    41   121    25    34    50  1723     0    34     0   336    11  1230   167  5933    77     0     0   790    43 45141 19340                                                                                           "
"    76    42     6   207   135   150   294  2554    64   143     0   486   810   110   539 13791   171     2    57   142     0     0   134   537     0    31     5   200     0    58    22  3459   129     0     7   388     0     0     0  5346     0    31     0  1160 31707 35610 22203                                                                                     "
"    18   407    23     0     0    68    19    36    42   165     0     0     2    88    44     2   117  3381   122     0     0    99    45     6     0   290    36     0     0   266    30    38    18   159    13     0     1    58   142    23     0    80     5     0     3   144    35     0                                                                               "
"    33     0    23   658    24    44   108   126     0    20    64   327    60    14    66   133   254   286    87  4548    15     0     8    90   141     9     0   754   142     1    81   288    33     0    33   255    39    24     0   112    18     0    29   130    37    14    20   166 53555                                                                         "
"   277   164   108   290  6514   235   482  1018   165   446     8  1100   435    12   319     0   838   111   227   157  5890     0   507     0   340     0    64     3   320     0     0     0   245    73    90   109  6631   419     0   627   412    59   338   125   825   102   176   201    47    59                                                                   "
"    51   577    50    66   169  4821  1421   355    54  2047    24   106   112    72    80    62   188   439   166    46     0  5279     0     0     0   368   104    23     0   445    72     0    30   239    87     0   264  4869   738   374   122   466   103    38     4   415    40   126   541    37 22923                                                             "
"   110    82   145   163  1203     0 14459   754    24  1451   151   763   183    30   477    38     0   233   599     0   273     0 12183     0   111   219   802     0   707     0     0     0   110   158   176    42   520   675 20335     0     0   499  1107   178     0     0   564     0   146     0 76141 40261                                                       "
"   112   181    54   602  1180   581     0  5578   112   651    68  1954     0    31   157   150   297    90   115   657     0   135     0  5714     0     0     0   679     0     0    41   578    87     3    74   288   631   521   937  5109   167   107    21   611   147    31    96   454     0   834 31553 32600 44414                                                 "
"    31   241    33     0    45   319     0    86    16  1649    42   219    33   130    46     2   125   576    73    12     0   102    64    24   110  1890   226     0     0   317    18    43     0    51    24     0    56   410   279    66     0   774    82     0    50   219    33   124  1297     0   172  1595   327    77                                           "
"    20    14    49    22    39    18    92     0    48    39   549    56    30    14    95    20    79    42   201   130    28     0   142     1   270    84  1199    29    74    19   105    19    10     3    27     6    35    31    67     0     8    14   446     0    13     9    56    41   166   229   174    47   576    33   341                                     "
"    43     8    28   397   156    20   280   403   108   352    75  2043    29    21    59   187   145    43    89   989    22     0    91   211   106     0   104  2711   123    20    35   305    27    19     7    86   180    46   200   423    72    80    88  1072   108    58   112   224     0  2135   495     0   187  2090 61046   387                               "
"   123     9     9   101   615     6   102   140   180    69   106     0  6752   231  1116   418   193     9   104   167   205    38    23    15     0    83     4   103 54777  7485  8703  8464    67    34    41     0   611    88     0    90    49     0    18    92  6666   153     0   364   159   265  4644    80     0   186    96    51   168                         "
"    12    70     0     0    23   155    11    48     3    70     0     0    70   742   186    61    38   346    27    46    25   170     6     0     0   117    17    14   220  2693   284     0     5    27     8     0     0   162   124    20     3    48    23     0    28   957    87     0  3979   750    23   924     0     0   574   154    61  1268                   "
"    59    45    80    75   192    81   637   163    28     0    74    99  1733    57  3345   832   131    42   198    55   181     6   226   149    53     0    94   204 14044  5603 27723  9664    97     0    37    34   172    50  1000   141     1    32   254     0   523    72  2117   491   102    84  1377   107  5207   276   111   744   201 47609   814             "
"     9    17    12    85    47    14   107   170    21    21    26   101   326    48   262   910    73    74    23   359     0     0    55   201    17     0    20   146   234     0   387  2714    16     0     5    30    82     2    39   186    30    18     5    66   172    13   125   928   625  4904   160     0   206   991   125   212   787  1638 32469  1494       "
" 0.0282483 0.0206292 0.0319075 0.0182494 0.0168831 0.0159757 0.0058938 0.0144022 0.0135116 0.0190724 0.0118542 0.0136325 0.0093705 0.0199714 0.0218874 0.0174818 "
" 0.0136792 0.0143825 0.0337043 0.0116006 0.0177685 0.0150006 0.0058835 0.0176118 0.0061893 0.0087184 0.0084944 0.0054224 0.0080368 0.0173529 0.0373569 0.0150280 "
" 0.0311168 0.0246045 0.0388972 0.0251865 0.0179100 0.0212765 0.0059683 0.0199671 0.0184506 0.0176209 0.0132786 0.0115579 0.0083782 0.0137699 0.0265260 0.0136025 "
" 0.0159995 0.0132055 0.0133496 0.0159777 0.0043280 0.0171276 0.0119089 0.0124708 0.0109899 0.0085271 0.0195872 0.0141357 0.0190797 "
" AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT "
" CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT "
" GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT "
" TAC TAT TCA TCC TCG TCT TGC TGG TGT TTA TTC TTG TTT "
" S_ij = S_ji and PI_i based on the empirical codon matrix: "
" A Schneider, GM Cannarozzi and GH Gonnet. Empirical codon "
" substitution matrix. BMC Bioinformatics 6:134. 2005. "