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Smo9 Genscan maize predictions

    GENSCANW output for sequence smo9

     

    Explanation Gn.Ex : gene number, exon number (for reference)
    Type  : Init = Initial exon (ATG to 5' splice site)
            Intr = Internal exon (3' splice site to 5' splice site)
            Term = Terminal exon (3' splice site to stop codon)
            Sngl = Single-exon gene (ATG to stop)
            Prom = Promoter (TATA box / initation site)
            PlyA = poly-A signal (consensus: AATAAA)
    S     : DNA strand (+ = input strand; - = opposite strand)
    Begin : beginning of exon or signal (numbered on input strand)
    End   : end point of exon or signal (numbered on input strand)
    Len   : length of exon or signal (bp)
    Fr    : reading frame (a forward strand codon ending at x has frame x mod 3)
    Ph    : net phase of exon (exon length modulo 3)
    I/Ac  : initiation signal or 3' splice site score (tenth bit units)
    Do/T  : 5' splice site or termination signal score (tenth bit units)
    CodRg : coding region score (tenth bit units)
    P     : probability of exon (sum over all parses containing exon)
    Tscr  : exon score (depends on length, I/Ac, Do/T and CodRg scores)
    
    

    Comments
    The SCORE of a predicted feature (e.g., exon or splice site) is a log-odds measure of the quality of the feature based on local sequence properties. For example, a predicted 5' splice site with score > 100 is strong; 50-100 is moderate; 0-50 is weak; and below 0 is poor (more than likely not a real donor site).
    The PROBABILITY of a predicted exon is the estimated probability under GENSCAN's model of genomic sequence structure that the exon is correct. This probability depends in general on global as well as local sequence properties, e.g., it depends on how well the exon fits with neighboring exons. It has been shown that predicted exons with higher probabilities are more likely to be correct than those with lower probabilities.

     

    
    GENSCAN 1.0	Date run: 10-Oct-108	Time: 22:37:45
    
    Sequence scaffold_89 : 125001 bp : 47.23% C+G : Isochore 1 ( 0 - 100 C+G%)
    
    Parameter matrix: Maize.smat
    
    Predicted genes/exons:
    
    
    Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
    ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
    
     1.00 Prom -    270    231   40                               5.02
    
     2.10 PlyA -    401    396    6                               2.27
     2.09 Term -    696    648   49  2  1   64   45    64 0.187  -0.96
     2.08 Intr -   2608   2326  283  2  1  100  -21   137 0.352   4.32
     2.07 Intr -   4513   4418   96  2  0   76   80    14 0.669   2.10
     2.06 Intr -   4641   4565   77  2  2   73   58    24 0.785  -0.33
     2.05 Intr -   4743   4703   41  0  2   78   92    -1 0.833  -1.29
     2.04 Intr -   4994   4851  144  2  0   -4   94    84 0.303   3.29
     2.03 Intr -   5159   5049  111  2  0   93   75    26 0.386   5.19
     2.02 Intr -   5614   5517   98  2  2   55   90    73 0.340   6.66
     2.01 Init -   7223   7211   13  2  1  106   -7    23 0.295  -2.70
     2.00 Prom -   7377   7338   40                              -4.53
    
     3.00 Prom +   7704   7743   40                              -7.14
     3.01 Init +   8225   8547  323  1  2   54   22   298 0.478  20.79
     3.02 Term +   8761  10297 1537  1  1   72   45   217 0.378  17.22
     3.03 PlyA +  10659  10664    6                               2.27
    
     4.10 PlyA -  12025  12020    6                              -0.73
     4.09 Term -  14782  14627  156  1  0   63   45   106 0.208   4.94
     4.08 Intr -  15711  15403  309  0  0   67   60   102 0.118   5.80
     4.07 Intr -  16133  16095   39  2  0  111   95   -14 0.630   2.40
     4.06 Intr -  18586  18481  106  0  1   82   77   -13 0.460  -0.00
     4.05 Intr -  19033  18876  158  1  2   62   79    85 0.983   6.90
     4.04 Intr -  19650  19495  156  0  0  100  -12   189 0.529  13.39
     4.03 Intr -  19788  19684  105  0  0  116   16    76 0.862   6.38
     4.02 Intr -  20517  20450   68  1  2   68   89    50 0.993   4.28
     4.01 Init -  21216  20763  454  0  1   74  100   297 0.786  30.49
     4.00 Prom -  24422  24383   40                              -0.98
    
     5.03 PlyA -  24668  24663    6                               0.77
     5.02 Term -  26292  26221   72  0  0   34   46    96 0.542   0.61
     5.01 Init -  26868  26653  216  0  0  117   97   291 0.971  35.13
     5.00 Prom -  26959  26920   40                              -5.39
    
     6.04 PlyA -  26988  26983    6                              -3.99
     6.03 Term -  27210  27012  199  2  1   66   35   285 0.971  21.34
     6.02 Intr -  27606  27266  341  0  2   25   53   356 0.999  24.26
     6.01 Init -  27725  27657   69  2  0   95   39    60 0.993   5.51
     6.00 Prom -  27775  27736   40                               0.82
    
     7.03 PlyA -  28500  28495    6                               0.77
     7.02 Term -  30275  30125  151  1  1   14   35   186 0.587   6.46
     7.01 Init -  30510  30341  170  0  2   33   97    83 0.993   5.97
     7.00 Prom -  30974  30935   40                              -4.04
    
     8.04 PlyA -  31002  30997    6                               0.77
     8.03 Term -  31736  31586  151  1  1  109   35    27 0.811   0.06
     8.02 Intr -  32699  32529  171  1  0   37  106   125 0.179  11.43
     8.01 Init -  36370  36306   65  1  2   53   99   -11 0.177  -1.09
     8.00 Prom -  37349  37310   40                               4.52
    
     9.03 PlyA -  38524  38519    6                               2.27
     9.02 Term -  39018  39011    8  1  2   97   45     0 0.476  -3.05
     9.01 Init -  39844  39454  391  1  1   -1   26   287 0.563  15.14
     9.00 Prom -  41370  41331   40                              -1.67
    
    10.04 PlyA -  41459  41454    6                               0.77
    10.03 Term -  42167  42142   26  0  2   38   45    64 0.465  -2.08
    10.02 Intr -  42631  42550   82  1  1   65   85    54 0.433   4.65
    10.01 Init -  44179  44096   84  1  0   59   75    90 0.604   8.38
    10.00 Prom -  44780  44741   40                              -3.95
    
    11.04 PlyA -  44963  44958    6                               2.27
    11.03 Term -  46850  46648  203  0  2   18   46   116 0.827   1.44
    11.02 Intr -  47580  46972  609  1  0   45   36   395 0.626  28.18
    11.01 Init -  48461  48392   70  2  1   39   74    79 0.465   5.47
    11.00 Prom -  49850  49811   40                              -0.28
    
    12.06 PlyA -  50921  50916    6                               2.27
    12.05 Term -  51038  50937  102  2  0   28   46   109 0.986   1.86
    12.04 Intr -  51152  51096   57  2  0   87  103    73 0.631  10.27
    12.03 Intr -  51294  51233   62  1  2   15   46    -8 0.358 -11.33
    12.02 Intr -  51426  51351   76  0  1   77  101    98 0.371  11.69
    12.01 Init -  53160  53026  135  0  0   86   49    84 0.988   7.50
    12.00 Prom -  53563  53524   40                              -1.18
    
    13.06 PlyA -  53872  53867    6                              -2.22
    13.05 Term -  54551  54140  412  1  1   46   45   423 0.999  33.25
    13.04 Intr -  54795  54614  182  0  2   58   98   179 0.892  17.80
    13.03 Intr -  55243  55145   99  1  0  124   98    77 0.999  15.35
    13.02 Intr -  55417  55301  117  1  0   64  110     8 0.546   4.11
    13.01 Init -  55585  55469  117  1  0   42   36    58 0.790  -0.86
    13.00 Prom -  55700  55661   40                               0.12
    
    14.05 PlyA -  55929  55924    6                               0.77
    14.04 Term -  56346  55968  379  2  1  106   45   155 0.471  11.80
    14.03 Intr -  56530  56409  122  1  2   54   67    87 0.994   5.37
    14.02 Intr -  57135  57071   65  1  2   84   87    13 0.957   1.77
    14.01 Init -  57884  57224  661  2  1  107  103   433 0.046  48.32
    14.00 Prom -  58596  58557   40                              -6.65
    
    15.06 PlyA -  58625  58620    6                               0.77
    15.05 Term -  58779  58645  135  0  0  109   45    91 0.039   8.00
    15.04 Intr -  60949  60752  198  1  0   53   94   274 0.816  27.38
    15.03 Intr -  61063  60979   85  0  1   52   20    28 0.013  -5.12
    15.02 Intr -  62046  61925  122  0  2   13   23   183 0.009   6.47
    15.01 Init -  63051  62677  375  0  0   97   34   313 0.473  28.22
    15.00 Prom -  64465  64426   40                               2.12
    
    16.06 PlyA -  64880  64875    6                               2.27
    16.05 Term -  64961  64890   72  2  0   66   46    27 0.306  -3.09
    16.04 Intr -  65391  65154  238  2  1   99   45    13 0.289  -0.71
    16.03 Intr -  65773  65464  310  2  1   48  113   180 0.749  15.87
    16.02 Intr -  66142  66091   52  1  1   58  110   -13 0.612  -1.16
    16.01 Init -  67644  67276  369  0  0  109   69   416 0.793  43.25
    16.00 Prom -  70447  70408   40                              -0.38
    
    17.00 Prom +  71807  71846   40                               2.12
    17.01 Init +  74676  74754   79  2  1   85   77    43 0.906   6.84
    17.02 Intr +  74959  75156  198  2  0   14   91    69 0.782   2.45
    17.03 Intr +  75547  75661  115  2  1  109   67   -57 0.237  -3.36
    17.04 Term +  76524  76554   31  0  1  118   45    22 0.476   0.68
    17.05 PlyA +  77516  77521    6                               2.27
    
    18.00 Prom +  77855  77894   40                              -0.88
    18.01 Init +  78209  79060  852  1  0   53   89   774 0.764  76.00
    18.02 Term +  79423  79905  483  0  0   48   46  1011 0.970  92.81
    18.03 PlyA +  80724  80729    6                               0.77
    
    19.03 PlyA -  81497  81492    6                               2.27
    19.02 Term -  81826  81823    4  0  1   93   46     0 0.443  -5.03
    19.01 Init -  84618  81941 2678  0  2   67   46  2659 0.951 263.43
    19.00 Prom -  84679  84640   40                              -9.40
    
    20.00 Prom +  84730  84769   40                              -9.29
    20.01 Init +  85041  85245  205  2  1   57   -3   156 0.659   5.89
    20.02 Intr +  85368  85489  122  1  2   85    6    60 0.339   0.59
    20.03 Intr +  85687  85854  168  0  0   85  106    69 0.392  11.69
    20.04 Term +  85946  86323  378  1  0   80   35   160 0.746   9.23
    20.05 PlyA +  86602  86607    6                              -2.62
    
    21.03 PlyA -  87043  87038    6                               2.27
    21.02 Term -  88227  88205   23  1  2   91   46    44 0.907   1.38
    21.01 Init -  88560  88509   52  0  1   44   78    39 0.904   2.38
    21.00 Prom -  89535  89496   40                               4.02
    
    22.00 Prom +  91427  91466   40                               1.12
    22.01 Init +  92123  92510  388  1  1   90   38   107 0.434   6.89
    22.02 Intr +  92997  93087   91  1  1    4   74    95 0.367   1.44
    22.03 Intr +  95637  95740  104  0  2   63   84    29 0.148   2.59
    22.04 Intr +  95796  95896  101  1  2   51   55   124 0.974   7.98
    22.05 Intr +  95952  96160  209  2  2   20   58   210 0.850  12.47
    22.06 Intr +  96223  96350  128  1  2   84   64    45 0.631   4.93
    22.07 Term +  96437  96459   23  0  2   89   45   -29 0.554  -6.22
    22.08 PlyA +  96979  96984    6                               2.27
    
    23.00 Prom +  97548  97587   40                              -1.28
    23.01 Init +  98655  99065  411  2  0   93  115   255 0.911  29.92
    23.02 Term + 101569 101667   99  0  0   30   46    93 0.278   0.29
    23.03 PlyA + 102653 102658    6                               2.27
    
    24.03 PlyA - 102795 102790    6                               0.77
    24.02 Term - 103205 103188   18  2  0   86   45    -2 0.035  -4.00
    24.01 Init - 108065 107289  777  2  0  103   -3   480 0.982  41.99
    24.00 Prom - 108158 108119   40                              -2.77
    
    25.03 PlyA - 108188 108183    6                               2.27
    25.02 Term - 109813 109579  235  0  1 -106   45   695 0.316  45.27
    25.01 Init - 110038 109836  203  1  2   97  -66   215 0.285   8.81
    25.00 Prom - 110699 110660   40                               1.02
    
    26.00 Prom + 111218 111257   40                               0.42
    26.01 Init + 111659 111979  321  1  0   66   30   119 0.466   5.57
    26.02 Term + 112460 113170  711  1  0   28   45   399 0.568  29.63
    26.03 PlyA + 113465 113470    6                               0.77
    
    27.00 Prom + 114066 114105   40                              -2.77
    27.01 Init + 114286 114319   34  0  1  132   69    26 0.777   6.10
    27.02 Term + 114567 114727  161  1  2   79   45   149 0.876  11.04
    27.03 PlyA + 115495 115500    6                               0.77
    
    28.00 Prom + 115795 115834   40                              -5.20
    28.01 Init + 116099 116167   69  1  0   73   77    64 0.952   7.62
    28.02 Intr + 116394 116468   75  2  0    6   28   238 0.005  11.91
    28.03 Intr + 117833 117863   31  1  1   69   36    16 0.004  -5.47
    28.04 Intr + 119902 120092  191  2  2   45   76   152 0.869  12.29
    28.05 Term + 122731 122799   69  0  0   75   46   138 0.757   8.93
    28.06 PlyA + 124710 124715    6                               2.27
    
    
    
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