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Command:  /bio/sw/glimmer3/bin/glimmer3 -o 50 -g 110 -t 30 ../BCTDNA Glimmer3.icm Glimmer3

Sequence file = ../BCTDNA
ICM model file = Glimmer3.icm
Excluded regions file = none
List of orfs file = none
Truncated orfs = false
Circular genome = true
Minimum gene length = 110 bp
Maximum overlap bases = 50
Input is NOT separate orfs
Threshold score = 30
Use first start codon = false
Start codons = atg,gtg,ttg
Start probs = 0.600,0.300,0.100
Stop codons = taa,tag,tga


>BCTDNA
Sequence length = 29940
GC percentage = 33.3%
Ignore independent score on orfs longer than 482

           ----- Start -----           --- Length ----  ------------- Scores -------------
 ID  Frame   of Orf  of Gene     Stop   of Orf of Gene      Raw InFrm F1 F2 F3 R1 R2 R3 NC
0001    +1    29263    29263        9      684     684     9.68    99 99  -  -  -  -  -  0 1.00
        -1      984      894      769      213     123    -9.85     0 99  -  -  0  -  -  0 1.00
0002    +1      292      298     1623     1329    1323     8.26    99 99  -  -  -  -  -  0 1.00
        +2     1592     1706     1840      246     132    -5.10     0  -  0  -  -  -  - 99 1.00
        +3     1860     1881     2003      141     120    -2.68     0  - 75  0  -  0  - 23 1.00
0003    +2     1841     1949     2098      255     147     6.59    99  - 99  -  -  0  -  0 1.00
        -2     2152     1993     1862      288     129    -3.37     0  - 44  0  -  0  - 55 1.00
        +3     2004     2040     2177      171     135    -1.77     0  -  -  0  -  -  - 99 1.00
0004    -1     2385     2349     2230      153     117     4.69    97  -  -  - 97  -  -  2 1.00
        -2     3253     3235     3095      156     138    -9.03     0  -  -  0  -  0  - 99 1.00
        +3     3087     3126     3257      168     129    -9.09     0  -  -  0  -  0  - 99 1.00
        -2     3463     3439     3320      141     117     7.18     1  -  - 98  -  1  -  0 1.00
        +1     3550     3589     3702      150     111    -0.25     0  0  - 99  -  -  -  0 1.00
        -1     4038     4026     3913      123     111   -10.13     0  -  - 99  0  -  -  0 1.00
        +1     4171     4192     4314      141     120    -8.48     0  0  - 99  -  0  0  0 1.00
0005    +3     3258     3279     4400     1140    1119    10.20    99  -  - 99  -  -  -  0 1.00
        -2     4405     4300     4181      222     117    -0.45     0  0  - 99  -  0  0  0 1.00
        -3     4481     4436     4320      159     114   -12.02     0  -  -  -  -  -  0 99 1.00
        -1     5025     4962     4798      225     162    -6.25     0  -  0  -  0  -  - 99 1.00
        +2     4790     4913     5029      237     114    -7.57     0  -  0  -  0  -  - 99 1.00
0006    +1     5038     5062     6159     1119    1095     9.92    99 99  -  -  -  -  -  0 1.00
        -3     6386     6368     6213      171     153    -1.23     0  0  - 99  -  -  0  0 1.00
        +1     6217     6295     6435      216     138    -7.86     0  0  - 99  -  -  -  0 1.00
        -2     6487     6469     6335      150     132     2.90     0  -  - 99  -  0  -  0 1.00
0007    +3     6105     6156     6620      513     462    12.86    99  -  - 99  -  -  -  0 1.00
        -2     6880     6856     6740      138     114    -9.49     0  - 99  0  -  0  -  0 1.00
        +3     7062     7062     7190      126     126    -3.41     0  - 99  0  -  0  0  0 1.00
        -2     7267     7162     7034      231     126    -8.57     0  - 99  -  -  0  0  0 1.00
        +3     7299     7299     7418      117     117    -2.08     0  - 99  0  -  -  -  0 1.00
        -2     7525     7468     7334      189     132    -0.14     0  - 99  -  -  0  -  0 1.00
        +3     7896     7920     8039      141     117    -7.88     0  - 99  0  -  0  0  0 1.00
        -3     8147     8069     7872      273     195    -0.71     0  - 99  -  -  -  0  0 1.00
        -2     8305     8293     8120      183     171   -10.93     0  - 99  -  -  0  -  0 1.00
0008    +2     6674     6686     8605     1929    1917    12.34    99  - 99  -  -  -  -  0 1.00
        -2     8986     8929     8816      168     111    -9.33     0  - 99  -  -  0  -  0 1.00
        +3     9003     9084     9200      195     114   -11.31     0  - 99  0  -  -  -  0 1.00
        -2    10417    10315    10196      219     117    -9.22     0  - 99  -  -  0  -  0 1.00
        -2    10576    10576    10418      156     156    -7.32     0  - 99  -  -  0  -  0 1.00
        -1    10851    10728    10573      276     153     1.00     0  - 99  -  0  -  -  0 1.00
0009    +2     8606     8624    11128     2520    2502    12.77    99  - 99  -  -  -  -  0 1.00
        -3    11399    11345    11202      195     141    -9.23     0  -  - 99  -  -  0  0 1.00
        -2    11584    11536    11393      189     141    -3.32     0  -  - 99  -  0  -  0 1.00
0010    +3    11118    11133    12122     1002     987    11.55    99  -  - 99  -  -  -  0 1.00
        +1    11974    11974    12132      156     156    -4.16     0  0  -  -  - 54  - 45 1.00
0011    -2    12142    12130    11918      222     210     2.27    92  -  -  -  - 92  -  7 1.00
        -3    12149    12143    12009      138     132    -5.42     0  -  -  -  - 56  0 43 1.00
        -2    12469    12355    12164      303     189    -7.16     0  -  - 20  -  0  - 79 1.00
0012    +3    12123    12273    12473      348     198    10.08    99  -  - 99  -  0  -  0 1.00
        -3    12494    12470    12306      186     162    -4.46     0  -  - 99  -  0  0  0 1.00
        +3    12477    12507    12665      186     156    -5.68     0  -  -  0  -  -  - 99 1.00
        -3    13169    13166    12969      198     195     2.54     0 99  -  -  -  -  0  0 1.00
0013    +1    12670    12715    13452      780     735    11.22    99 99  -  -  -  -  -  0 1.00
        -1    13470    13449    13291      177     156    -7.69     0 99  -  -  0  -  -  0 1.00
0014    +3    13656    13722    13841      183     117     4.01    92  -  - 92  -  -  -  7 1.00
        -3    13889    13871    13737      150     132    -1.62     1  -  -  -  -  -  1 98 1.00
        +1    13762    13774    13920      156     144    -3.79     0  0  -  -  -  -  - 99 1.00
        +2    13928    13949    14077      147     126     3.00     0  0  0  - 99  -  -  0 1.00
        +1    13921    13963    14091      168     126   -10.74     0  0  -  - 99  -  -  0 1.00
        +3    14103    14142    14333      228     189    -3.47     0  -  -  0 99  -  -  0 1.00
        -3    14603    14594    14436      165     156    -3.77     0  -  -  - 99  -  0  0 1.00
0015    -1    14847    14805    13804     1041     999     5.49    99  -  -  - 99  -  -  0 1.00
        -2    15682    15676    15527      153     147    -1.39     0  -  -  0  -  0 99  0 1.00
0016    +3    15210    15219    15749      537     528   -12.48     0  0  -  0  -  - 99  0 1.00
0017    -3    15791    15776    15216      573     558    11.35    99  -  -  -  -  - 99  0 1.00
        +2    17198    17207    17338      138     129    -3.68     0  -  0 99  0  -  -  0 1.00
        -1    17370    17271    17155      213     114     3.30     0  -  - 99  0  -  -  0 1.00
0018    +3    15849    15948    17462     1611    1512     9.36    99  -  - 99  -  -  -  0 1.00
        -2    17677    17623    17480      195     141    -1.26     1  -  - 34  -  1  - 64 1.00
0019    +3    17463    17484    18377      912     891     6.43    99  -  - 99  -  -  -  0 1.00
        -3    18620    18554    18435      183     117    -5.09     0  0  -  - 99  -  0  0 1.00
        -3    19040    18995    18882      156     111    -2.90     0  -  -  - 99  -  0  0 1.00
        +3    18978    19014    19127      147     111     1.67     0  -  -  0 99  -  -  0 1.00
        -3    19235    19211    19041      192     168     1.29     0  -  -  - 99  -  0  0 1.00
        -2    19357    19357    19208      147     147    -3.27     0  -  -  0 99  0  -  0 1.00
        +3    19188    19269    19394      204     123    -2.25     0  -  -  0 98  -  -  1 1.00
0020    -1    19449    19407    18319     1128    1086     7.49    99  -  -  - 99  -  -  0 1.00
        -2    19873    19843    19715      156     126    -8.77     0  -  -  0  -  0  - 99 1.00
        +3    19719    19740    19898      177     156    -7.39     0  -  -  0  -  -  - 99 1.00
        -2    20185    20110    19973      210     135    -0.77     0  -  - 98  -  0  -  1 1.00
0021    +3    19977    19980    20195      216     213     3.39    99  -  - 99  -  -  -  0 1.00
        -1    20445    20418    20302      141     114    -3.04     0  -  0  -  0 99  -  0 1.00
        +2    20261    20309    20449      186     138    -4.98     0  -  0  -  0 99  -  0 1.00
        +1    20404    20413    20604      198     189    -5.81     0  0  -  -  - 99  -  0 1.00
        +3    20469    20583    20759      288     174     2.71     0  -  -  0  - 99  -  0 1.00
0022    -2    20824    20749    20186      636     561     9.10    99  -  -  -  - 99  -  0 1.00
        +1    20752    20773    20913      159     138    -3.20     0  0  0  -  -  -  - 99 1.00
        -1    21078    21039    20839      237     198     4.53     0  - 99  -  0  -  -  0 1.00
        +3    21063    21069    21215      150     144    -2.93     0  - 99  0  -  -  -  0 1.00
0023    +2    20765    20810    21706      939     894    11.73    99  - 99  -  -  -  -  0 1.00
        -2    22108    22051    21911      195     138    -4.96     0  - 99  -  -  0  -  0 1.00
        +3    21918    21945    22112      192     165    -9.58     0  - 99  0  -  0  -  0 1.00
        +3    22113    22116    22241      126     123    -1.18     0  - 99  0  0  -  0  0 1.00
        -3    22277    22187    22017      258     168     3.69     0  - 99  -  -  -  0  0 1.00
        -1    22320    22194    22078      240     114     8.28     0  - 99  -  0  -  0  0 1.00
0024    +2    21845    21851    22354      507     501    10.64    99  - 99  -  -  -  -  0 1.00
        -2    22465    22462    22238      225     222    -1.02     1  -  -  -  -  1  - 98 1.00
        +1    22402    22420    22557      153     135     0.60     0  0  - 99  -  -  -  0 1.00
        -2    22720    22681    22544      174     135     5.32     0  -  - 99  -  0  -  0 1.00
        +1    22657    22663    22779      120     114    -5.87     0  0  - 99  -  -  0  0 1.00
0025    +3    22332    22359    23102      768     741    14.02    99  -  - 99  -  -  -  0 1.00
        -3    23501    23432    23268      231     162    -6.68     0  -  - 99  -  -  0  0 1.00
0026    +3    23112    23118    23726      612     606    11.58    99  -  - 99  -  -  -  0 1.00
        +1    23920    23920    24036      114     114    -9.23     0  0  -  -  -  -  - 99 1.00
0027    -2    24673    24670    24545      126     123     9.42    38  0  - 61  - 38  -  0 1.00
        +1    24496    24586    24726      228     138    -4.39     0  0  - 99  -  -  -  0 1.00
        -1    25095    25089    24964      129     123   -11.50     0  -  - 99  0  -  -  0 1.00
        -3    25343    25304    25182      159     120   -19.97     0  -  - 99  -  -  0  0 1.00
        +2    25208    25331    25447      237     114   -11.98     0  -  0 99  -  -  -  0 1.00
0028    +3    24150    24216    25898     1746    1680    11.26    99  -  - 99  -  -  -  0 1.00
        -2    26158    26125    25967      189     156    -6.07     0  -  -  -  -  0  - 99 1.00
0029    +3    26055    26103    26219      162     114     2.53    65  -  - 65  -  -  - 34 1.00
        -3    26309    26249    26130      177     117    -1.20     3  -  -  -  -  -  3 96 1.00
        -1    26370    26328    26209      159     117    -2.70     0  -  -  -  0  -  - 99 1.00
0030    -2    26698    26593    26474      222     117     4.01    91  -  -  0  - 91  -  8 1.00
        -1    26703    26697    26554      147     141    -3.06     0  -  -  -  0  6  - 93 1.00
        +2    26672    26684    26893      219     207    -1.12     1  -  1  -  -  -  - 98 1.00
        +2    26945    26954    27070      123     114     6.59     0  -  0  - 99  -  -  0 1.00
0031    -1    27117    27090    26728      387     360    10.98    99  -  -  - 99  -  -  0 1.00
        +1    27904    27952    28095      189     141    -0.69     4  4  -  -  -  -  - 95 1.00
0032    +2    28001    28025    28144      141     117     1.77    53  - 53  -  -  -  - 46 1.00
0033    -1    28272    28203    28078      192     123     1.32    35  -  -  - 35  -  - 64 1.00
        +1    28240    28240    28365      123     123    -9.11     0  0  - 99  -  0  -  0 1.00
0034    -2    28390    28276    28151      237     123     6.20    93  -  -  5  - 93  -  0 1.00
        -3    28544    28502    28380      162     120    -5.88     0  -  - 99  -  -  0  0 1.00
        +1    28387    28417    28551      162     132    -3.22     0  0  - 71  -  -  - 28 1.00
        +1    28591    28663    28794      201     129    -6.01     0  0  - 99  -  -  0  0 1.00
        -3    28988    28940    28809      177     129    -9.43     0  -  - 99  -  0  0  0 1.00
        -2    29005    28885    28763      240     120     4.66     0  -  - 99  -  0  -  0 1.00
0035    +3    28155    28188    29198     1041    1008     7.00    99  -  - 99  -  -  -  0 1.00
        +1    28987    29119    29247      258     126    -7.99     0  0  -  -  -  -  - 99 1.00
        -3    29579    29561    29427      150     132     3.22     0 99  -  -  -  -  0  0 1.00
        -2    29866    29836    29699      165     135     0.42     0 99  -  0  -  0  0  0 1.00