diff test-data/refseq63m/ncRNA/OL.cm @ 0:39b6485e2d34 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
author iuc
date Fri, 27 Mar 2020 17:53:04 -0400
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/refseq63m/ncRNA/OL.cm	Fri Mar 27 17:53:04 2020 -0400
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+INFERNAL1/a [1.1.2 | July 2016]
+NAME     OL
+STATES   103
+NODES    26
+CLEN     33
+W        72
+ALPH     RNA
+RF       no
+CONS     yes
+MAP      yes
+DATE     Thu May 24 22:04:50 2018
+COM      [1] /work/berntm/progz/infernal-1.1.2/src//cmbuild -F metazoa/cleaned/OL.cm metazoa/cleaned/OL.stk
+COM      [2] /work/berntm/progz/infernal-1.1.2/src//cmcalibrate --cpu 8 metazoa/cleaned/OL.cm
+PBEGIN   0.05
+PEND     0.05
+WBETA    1e-07
+QDBBETA1 1e-07
+QDBBETA2 1e-15
+N2OMEGA  1.52588e-05
+N3OMEGA  1.52588e-05
+ELSELF   -0.08926734
+NSEQ     821
+EFFN     821.000000
+CKSUM    625725364
+NULL     0.000  0.000  0.000  0.000 
+EFP7GF   -7.6753 0.73996
+ECMLC    0.66646    -5.32898     3.74545     1600000      507768  0.002363
+ECMGC    0.42409   -13.50951     1.11839     1600000      197811  0.002022
+ECMLI    0.64950    -4.93781     4.20090     1600000      453896  0.002644
+ECMGI    0.44313   -12.13032     1.75670     1600000      188195  0.002125
+CM
+                                             [ ROOT    0 ]      -      - - - - -
+     S     0    -1 0     1     6     1     1    72   118 -15.595 -15.535  -0.396  -2.336  -4.839  -7.136 
+    IL     1     1 2     1     6     1     5    73   120  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR     2     2 3     2     5     1     6    73   120  -2.408  -0.496  -5.920  -4.087  -5.193          0.000  0.000  0.000  0.000 
+                                             [ MATP    1 ]      1     44 U A - -
+    MP     3     2 3     7     6     2     8    72   118  -3.583 -15.139  -0.133 -13.915 -14.195  -7.885 -12.245 -12.523 -11.563 -1.433 -9.914 -11.708  0.213 -10.829 -11.666 -8.732 -11.787 -10.921  3.816 -12.080 -1.656 -4.074 
+    ML     4     2 3     7     6     1     7    70   117  -4.633 -14.486  -0.348  -2.527 -14.336 -11.866 -9.074 -5.575 -9.989  1.991 
+    MR     5     2 3     7     6     1     6    69   115 -12.205 -10.934  -3.866 -10.912  -0.107  -9.125  1.937 -5.921 -2.872 -5.708 
+     D     6     2 3     7     6     0     3    67   114 -12.605 -11.303  -7.100  -7.782  -7.800  -0.025 
+    IL     7     7 5     7     6     1     9    71   118  -8.577  -0.191  -3.065 -10.495 -11.272 -10.932  0.000  0.000  0.000  0.000 
+    IR     8     8 6     8     5     1     9    71   117  -7.534  -0.012 -11.045  -9.212 -10.318          0.000  0.000  0.000  0.000 
+                                             [ MATP    2 ]      3     42 C G - -
+    MP     9     8 6    13     6     2     9    70   116 -15.480 -15.419  -0.000 -14.196 -14.475 -14.870 -12.518 -12.793 -11.840 -1.303 -3.500 -11.987  3.560 -4.553 -11.942 -8.991 -12.064 -11.181  1.854 -12.355 -7.895 -4.460 
+    ML    10     8 6    13     6     1     5    68   115 -11.630 -11.976  -0.220  -2.846 -11.826  -9.356 -4.488  0.595 -5.435  1.276 
+    MR    11     8 6    13     6     1     5    67   114 -12.115 -10.844  -6.753 -10.823  -0.018  -9.036 -5.602 -7.321  1.986 -6.353 
+     D    12     8 6    13     6     0     3    67   114 -13.102 -11.800  -0.082  -8.279  -8.297  -4.372 
+    IL    13    13 5    13     6     1     4    69   116  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR    14    14 6    14     5     1     4    69   115  -2.408  -0.496  -5.920  -4.087  -5.193          0.000  0.000  0.000  0.000 
+                                             [ MATP    3 ]      4     41 U A - -
+    MP    15    14 6    19     6     2     8    68   114 -15.541 -15.480  -0.003  -9.131 -14.536 -14.931 -12.590 -12.872 -11.908 -9.109 -10.258 -12.052  2.130 -11.173 -12.011 -9.080 -12.131 -11.276  3.504 -12.424 -1.897 -10.813 
+    ML    16    14 6    19     6     1     4    66   113  -8.904  -9.250  -0.144  -3.659  -9.100  -6.629 -1.201  0.668 -2.036  0.792 
+    MR    17    14 6    19     6     1     5    66   113 -12.115 -10.844  -6.753 -10.823  -0.018  -9.036  1.989 -6.982 -6.320 -6.494 
+     D    18    14 6    19     6     0     0    62   109  -9.049  -7.747  -3.544  -4.226  -4.244  -0.319 
+    IL    19    19 5    19     6     1     4    67   114  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR    20    20 6    20     5     1     4    67   113  -2.408  -0.496  -5.920  -4.087  -5.193          0.000  0.000  0.000  0.000 
+                                             [ MATP    4 ]      5     40 C G - -
+    MP    21    20 6    25     6     2     6    66   112 -15.545 -15.484  -0.020  -7.019  -7.465 -14.936 -12.592 -12.867 -11.911 -1.689 -10.263 -12.057  3.715 -5.251 -12.014 -9.077 -2.847 -11.259  1.253 -12.428 -7.966 -10.816 
+    ML    22    20 6    25     6     1     4    64   111  -7.830  -8.176  -0.321  -2.585  -8.026  -5.556 -1.212  1.444 -2.012 -0.736 
+    MR    23    20 6    25     6     1     4    65   112 -12.115  -0.098  -4.419 -10.823  -5.956  -9.036 -5.602 -7.321  1.986 -6.353 
+     D    24    20 6    25     6     0     0    61   107  -9.049  -7.747  -3.544  -4.226  -4.244  -0.319 
+    IL    25    25 5    25     6     1     3    65   112  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR    26    26 6    26     5     1     4    65   111  -6.565  -0.024 -10.076  -8.244  -9.350          0.000  0.000  0.000  0.000 
+                                             [ MATP    5 ]      6     38 C G - -
+    MP    27    26 6    31     6     2     4    64   110 -15.577 -15.516  -0.094 -14.293 -14.572  -3.992 -12.622 -12.886 -11.943 -0.842 -2.658 -12.092  3.932 -11.211 -12.045 -9.101 -12.167 -11.259 -7.030 -12.462 -8.001 -10.848 
+    ML    28    26 6    31     6     1     4    63   109  -9.546  -9.893  -0.090  -4.301  -9.742  -7.272 -4.066  1.922 -4.743 -3.142 
+    MR    29    26 6    31     6     1     1    61   107  -9.715  -8.444  -4.353  -8.422  -3.556  -0.219  1.905 -3.837 -3.340 -3.523 
+     D    30    26 6    31     6     0     0    60   106  -9.049  -7.747  -3.544  -4.226  -4.244  -0.319 
+    IL    31    31 5    31     6     1     3    63   110  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR    32    32 6    32     5     1     3    63   109  -2.408  -0.496  -5.920  -4.087  -5.193          0.000  0.000  0.000  0.000 
+                                             [ MATP    6 ]      7     37 C G - -
+    MP    33    32 6    37     6     2     5    62   108 -15.495 -15.434  -0.008 -14.211  -7.899  -9.378 -12.544 -12.825 -11.861 -9.062 -3.712 -12.005  3.912 -11.127 -11.965 -1.171 -12.085 -11.228 -1.253 -12.378 -7.914 -10.767 
+    ML    34    32 6    37     6     1     1    60   107  -6.250  -6.596  -1.310  -1.005  -6.446  -3.975  0.368 -0.385 -0.191  0.094 
+    MR    35    32 6    37     6     1     1    59   106  -6.988  -5.717  -1.625  -5.695  -0.829  -3.908  0.368 -0.385 -0.191  0.094 
+     D    36    32 6    37     6     0     0    59   106 -15.742 -14.440  -0.218 -10.919 -10.937  -2.844 
+    IL    37    37 5    37     6     1     2    61   108  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR    38    38 6    38     5     1     2    61   107  -2.408  -0.496  -5.920  -4.087  -5.193          0.000  0.000  0.000  0.000 
+                                             [ MATP    7 ]      8     36 G C - -
+    MP    39    38 6    43     6     2     6    60   106 -15.575 -15.514  -0.002 -14.291  -9.706 -14.965 -13.539 -2.880 -16.018 -0.547 -15.142 -3.709 -1.263 -15.409 -11.501  3.876 -11.690 -8.069 -9.798 -11.753 -11.883 -15.209 
+    ML    40    38 6    43     6     1     1    58   105  -6.250  -6.596  -1.310  -1.005  -6.446  -3.975  0.368 -0.385 -0.191  0.094 
+    MR    41    38 6    43     6     1     2    57   104  -9.312  -8.041  -3.950  -8.020  -0.132  -6.233 -2.437 -3.769  1.860 -3.150 
+     D    42    38 6    43     6     0     0    56   102 -13.109 -11.808  -2.132  -8.287  -8.304  -0.386 
+    IL    43    43 5    43     6     1     2    59   106  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR    44    44 6    44     5     1     2    59   105  -2.408  -0.496  -5.920  -4.087  -5.193          0.000  0.000  0.000  0.000 
+                                             [ MATP    8 ]      9     35 C G - -
+    MP    45    44 6    49     6     2     5    58   104 -15.577 -15.516  -0.000 -14.293 -14.572 -14.967 -2.269 -12.601 -11.828 -8.740 -2.143 -12.029  3.628 -11.118 -1.730 -3.568 -12.066 -10.782  1.131 -3.838 -0.865 -10.697 
+    ML    46    44 6    49     6     1     1    56   103  -6.250  -6.596  -1.310  -1.005  -6.446  -3.975  0.368 -0.385 -0.191  0.094 
+    MR    47    44 6    49     6     1     1    56   102  -9.618  -8.347  -4.256  -8.325  -0.106  -6.539  1.894 -3.688 -3.202 -3.363 
+     D    48    44 6    49     6     0     0    55   101 -12.746 -11.444  -7.241  -7.923  -0.109  -4.016 
+    IL    49    49 5    49     6     1     1    57   104  -2.579  -2.842  -0.760  -4.497  -5.274  -4.934  0.000  0.000  0.000  0.000 
+    IR    50    50 6    50     5     1     1    57   104  -2.408  -0.496  -5.920  -4.087  -5.193          0.000  0.000  0.000  0.000 
+                                             [ MATP    9 ]     10     34 C G - -
+    MP    51    50 6    55     4     2     3    56   102 -14.797 -15.004  -0.000 -13.418                 -2.867 -12.643 -11.845 -8.793 -1.750 -12.038  3.499 -11.131 -4.100 -1.028 -12.080 -10.849  1.877 -12.329 -4.831 -10.718 
+    ML    52    50 6    55     4     1     1    55   102  -3.758  -3.940  -0.507  -2.670                  0.368 -0.385 -0.191  0.094 
+    MR    53    50 6    55     4     1     1    55   101  -8.844  -7.873  -0.062  -4.801                  1.968 -5.412 -4.845 -5.100 
+     D    54    50 6    55     4     0     0    53    99  -4.568  -4.250  -2.265  -0.520                 
+    IL    55    55 5    55     4     1     1    56   103  -1.686  -2.369  -1.117  -4.855                  0.000  0.000  0.000  0.000 
+    IR    56    56 6    56     3     1     1    55   102  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   10 ]     11      - U - - -
+    ML    57    56 6    59     3     1     1    54   100 -15.726  -0.373  -2.136                         -1.307 -2.678  0.350  1.114 
+     D    58    56 6    59     3     0     0    51    98  -6.174  -1.687  -0.566                         
+    IL    59    59 3    59     3     1     1    55   102  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   11 ]     12      - U - - -
+    ML    60    59 3    62     3     1     1    53   100 -15.353  -0.032  -5.525                         -0.392 -0.265 -2.013  1.110 
+     D    61    59 3    62     3     0     0    49    96 -15.012 -10.525  -0.001                         
+    IL    62    62 3    62     3     1     1    54   101  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   12 ]     13      - u - - -
+    ML    63    62 3    65     3     1     1    52    99 -15.322  -0.008  -7.467                         -0.652 -0.158 -0.456  0.798 
+     D    64    62 3    65     3     0     0    49    96 -15.114  -5.848  -0.025                         
+    IL    65    65 3    65     3     1     1    53   100  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   13 ]     14      - a - - -
+    ML    66    65 3    68     3     1     1    51    98 -15.321  -0.006  -7.890                          0.584 -0.904 -0.279  0.193 
+     D    67    65 3    68     3     0     0    49    96 -15.115  -7.055  -0.011                         
+    IL    68    68 3    68     3     1     1    52    99  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   14 ]     15      - a - - -
+    ML    69    68 3    71     3     1     1    50    97  -1.246  -3.711  -0.994                          0.397 -1.359  0.325  0.057 
+     D    70    68 3    71     3     0     0    49    96  -1.122  -2.517  -1.451                         
+    IL    71    71 3    71     3     1     1    51    98  -0.568  -1.660  -6.772                          0.000  0.000  0.000  0.000 
+                                             [ MATL   15 ]     24      - a - - -
+    ML    72    71 3    74     3     1     2    18    36 -14.781  -0.000 -13.435                          0.982 -0.947  0.452 -2.862 
+     D    73    71 3    74     3     0     0    16    35 -16.088  -2.164  -0.364                         
+    IL    74    74 3    74     3     1     1    26    44  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   16 ]     25      - a - - -
+    ML    75    74 3    77     3     1     2    17    35 -15.051  -0.000 -13.706                          0.767 -0.865  0.494 -1.556 
+     D    76    74 3    77     3     0     0    16    34 -15.725  -0.688  -1.399                         
+    IL    77    77 3    77     3     1     1    25    43  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   17 ]     26      - a - - -
+    ML    78    77 3    80     3     1     2    16    34 -15.506  -0.000 -14.160                          0.861 -1.151  0.221 -0.815 
+     D    79    77 3    80     3     0     0    15    33 -14.327  -1.588  -0.583                         
+    IL    80    80 3    80     3     1     1    24    42  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   18 ]     27      - A - - -
+    ML    81    80 3    83     3     1     1    14    33 -15.583  -0.001 -10.423                          1.101 -0.867  0.039 -1.842 
+     D    82    80 3    83     3     0     0    14    32 -13.746  -9.259  -0.002                         
+    IL    83    83 3    83     3     1     1    23    41  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   19 ]     28      - A - - -
+    ML    84    83 3    86     3     1     1    13    32 -15.582  -0.000 -14.236                          1.042 -1.605  0.359 -1.600 
+     D    85    83 3    86     3     0     0    13    31 -13.756  -0.473  -1.839                         
+    IL    86    86 3    86     3     1     1    22    40  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   20 ]     29      - A - - -
+    ML    87    86 3    89     3     1     1    12    31 -15.687  -0.003  -9.134                          1.429 -2.778 -0.188 -1.816 
+     D    88    86 3    89     3     0     0    13    31 -11.925  -7.438  -0.009                         
+    IL    89    89 3    89     3     1     1    21    39  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   21 ]     30      - A - - -
+    ML    90    89 3    92     3     1     1    11    29 -15.685  -0.000 -14.339                          1.405 -3.084  0.132 -2.849 
+     D    91    89 3    92     3     0     0    12    30 -12.013  -0.017  -6.405                         
+    IL    92    92 3    92     3     1     1    20    38  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   22 ]     31      - A - - -
+    ML    93    92 3    95     3     1     1     9    28 -15.726  -0.000 -14.380                          1.335 -2.040 -0.305 -1.232 
+     D    94    92 3    95     3     0     0    15    33  -6.174  -1.687  -0.566                         
+    IL    95    95 3    95     3     1     1    19    37  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   23 ]     32      - A - - -
+    ML    96    95 3    98     3     1     1     8    26 -15.726  -0.000 -14.380                          1.617 -3.723 -0.742 -1.953 
+     D    97    95 3    98     3     0     0    13    32  -6.174  -1.687  -0.566                         
+    IL    98    98 3    98     3     1     1    18    36  -1.442  -0.798  -4.142                          0.000  0.000  0.000  0.000 
+                                             [ MATL   24 ]     33      - A - - -
+    ML    99    98 3   101     2     1     1     1     1       *   0.000                                  1.849 -4.292 -2.088 -3.166 
+     D   100    98 3   101     2     0     0     0     0       *   0.000                                 
+    IL   101   101 3   101     2     1     1    13    28  -1.823  -0.479                                  0.000  0.000  0.000  0.000 
+                                             [ END    25 ]      -      - - - - -
+     E   102   101 3    -1     0     0     0     0     0                                                 
+//
+HMMER3/f [3.1b3 | July 2016]
+NAME  OL
+LENG  33
+MAXL  84
+ALPH  RNA
+RF    no
+MM    no
+CONS  yes
+CS    yes
+MAP   yes
+DATE  Thu May 24 22:04:50 2018
+COM   [1] /work/berntm/progz/infernal-1.1.2/src//cmbuild -F metazoa/cleaned/OL.cm metazoa/cleaned/OL.stk
+NSEQ  821
+EFFN  700.883545
+CKSUM 625725364
+STATS LOCAL MSV       -7.1802  0.73996
+STATS LOCAL VITERBI   -7.9876  0.73996
+STATS LOCAL FORWARD   -2.8371  0.73996
+HMM          A        C        G        U   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.23799  1.41836  1.19633  1.79805
+          1.38629  1.38629  1.38629  1.38629
+          0.04341  9.01578  3.16146  1.46634  0.26236  0.00000        *
+      1   3.98762  2.83246  8.23308  0.08086      1 U - - <
+          1.38629  1.38629  1.38629  1.38629
+          0.08188  2.58830  5.66312  0.00337  5.69387  2.92683  0.05505
+      2   3.69044  0.31201  7.67463  1.41635      3 C - - <
+          1.38629  1.38629  1.38629  1.38629
+          0.00025  8.97153  8.97153  1.46634  0.26236  1.42962  0.27365
+      3   7.14182  1.29378  7.50843  0.32237      4 U - - <
+          1.38629  1.38629  1.38629  1.38629
+          0.00025  8.98227  8.98227  1.46634  0.26236  5.61422  0.00365
+      4   3.92855  0.19611  4.70887  1.90121      5 C - - <
+          1.38629  1.38629  1.38629  1.38629
+          0.00591  8.98227  5.15540  1.46634  0.26236  0.00732  4.92108
+      5   3.35849  0.03691  8.16798  6.75413      6 C - - <
+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
+          0.00593  8.94554  5.15267  1.46634  0.26236  0.14574  1.99793
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+          0.00141  9.00140  6.65597  1.46634  0.26236  1.73433  0.19421
+      8   4.32160  0.23982  3.71857  1.73905      9 C - - <
+          1.38629  1.38629  1.38629  1.38629
+          0.00025  9.00274  9.00274  1.46634  0.26236  4.69761  0.00916
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+          1.38629  1.38629  1.38629  1.38629
+          0.00025  9.00274  9.00274  1.46634  0.26236  0.01840  4.00446
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+          0.25833  9.01578  1.48043  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
+          0.00025  8.98736  8.98736  1.46634  0.26236  0.00859  4.76092
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+          0.00024  9.01578  9.01578  1.46634  0.26236  1.09861  0.40547
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+          0.00024  9.01578  9.01578  1.46634  0.26236  1.09861  0.40547
+     25   1.31170  3.49244  0.35695  7.81404     34 G - - >
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+          0.00820  9.01578  4.82284  1.46634  0.26236  1.09861  0.40547
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+          0.00273  9.00783  5.95033  1.46634  0.26236  4.22270  0.01477
+     27   7.92571  0.07602  3.51183  3.14664     36 C - - >
+          1.38629  1.38629  1.38629  1.38629
+          0.06155  9.00534  2.82061  1.46634  0.26236  1.96893  0.15037
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+          0.00828  8.94554  4.81436  1.46634  0.26236  0.00357  5.63733
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+          0.03444  3.44062  6.31266  0.00762  4.88064  0.03162  3.46965
+     30   1.93438  8.38419  0.18067  3.88520     40 G - - >
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+          0.00473  9.01410  5.38327  1.46634  0.26236  0.12663  2.12914
+     31   0.33086  8.31034  1.26898  8.01221     41 A - - >
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+          0.04141  9.01131  3.20789  1.46634  0.26236  3.68247  0.02548
+     32   1.49713  8.32172  0.29297  3.50844     42 G - - >
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+          0.27396  2.70446  1.75604  0.00380  5.57559  2.60448  0.07682
+     33   0.12383  7.74949  2.40777  3.64879     44 A - - >
+          1.38629  1.38629  1.38629  1.38629
+          0.00015  8.78458        *  1.46634  0.26236  0.00000        *
+//