User:James Estevez/Notebook/Spring 2011: Bdellovibrio Independent Study/2011/01/30/Bdellovibrio strain W glimmer3.detail

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Command:  glimmer3 /home/james/Data/bdcost/b_strain_w/bdw.contigs.seq /home/james/Data/bdcost/bd100.icm bdw

Sequence file = /home/james/Data/bdcost/b_strain_w/bdw.contigs.seq
Number of sequences = 561
ICM model file = /home/james/Data/bdcost/bd100.icm
Excluded regions file = none
List of orfs file = none
Input is NOT separate orfs
Independent (non-coding) scores are used
Circular genome = true
Truncated orfs = false
Minimum gene length = 100 bp
Maximum overlap bases = 30
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
GC percentage = 49.7%
Ignore score on orfs longer than 725


>bdw.fasta.screen.Contig1
Sequence length = 1001

           ----- Start -----           --- Length ----  ------------- Scores -------------
 ID  Frame   of Orf  of Gene     Stop   of Orf of Gene      Raw InFrm F1 F2 F3 R1 R2 R3 NC
        +1      957      100      387      429     285    -7.17     0  0  -  -  0  -  - 99
        -2      481      451      332      147     117   -23.76     0  -  -  0  0  0  - 99
        +1      412      514      624      210     108   -15.35     0  0  -  0  -  -  0 99
        +3      264      501      662      396     159   -16.85     0  -  -  0  -  -  0 99
        -3      662      617      363      297     252   -18.34     0  -  -  0  -  -  0 99
        -1      924      654      541      381     111   -14.50     0  -  -  0  0  -  0 99
        +3      663      681      956      291     273   -10.71     0  -  -  0  -  -  - 99
        -2      985      976      851      132     123   -14.39     0  0  -  -  -  0  - 99
        -2      362      113      986      375     126   -17.61     0  -  -  0  0  0  0 99
        -3      528      120      957      570     162   -18.76     0  -  -  0  0  -  0 99
        -1      163       88      925      237     162   -16.78     0  -  -  -  0  -  - 99


>bdw.fasta.screen.Contig2
Sequence length = 2651

           ----- Start -----           --- Length ----  ------------- Scores -------------
 ID  Frame   of Orf  of Gene     Stop   of Orf of Gene      Raw InFrm F1 F2 F3 R1 R2 R3 NC
        +2     2497     2506       19      171     162   -21.87     0  -  0  -  -  0  - 99
        +3     2648       78      221      222     141    -8.99     0  -  -  0  0  -  - 99
        +3      330      441      572      240     129   -17.43     0  -  -  0  0  -  - 99
        +2      494      509      637      141     126   -11.66     0  -  0  -  0  -  - 99
        -3      986      923      801      183     120   -11.84     0  -  -  -  0  -  0 99
        +1      868      871      990      120     117   -18.35     0  0  -  -  0  -  0 99
        +1     1003     1048     1236      231     186   -20.39     0  0  -  -  0  -  - 99
        +2     1166     1223     1366      198     141   -19.64     0  -  0  -  0  0  - 99
        -3     1748     1742     1617      129     123   -11.47     0  -  -  -  0  -  0 99
        +2     1646     1814     1954      306     138   -14.14     0  -  0  -  0  -  - 99
        -3     2024     2003     1899      123     102    -6.68     0  0  -  0  0  -  0 99
        +3     2046     2055     2168      120     111    -6.20     0  0  -  0  0  -  - 99
        +1     2059     2062     2184      123     120   -22.11     0  0  -  -  0  -  - 99
        +2     2180     2228     2371      189     141   -22.98     0  -  0  -  0  -  - 99
        +1     2317     2368     2496      177     126   -34.11     0  0  -  -  0  -  - 99
        +2     2510     2543     2647      135     102   -10.31     0  0  0  -  0  -  - 99
0001    -1       37        7       40     2646    2616   -15.52     0  -  -  -  0  -  - 99

Full report at: b_strain_w.detail