GENEMARK PREDICTIONS Sequence: gi|115345712|ref|NC_008389.1| Roseobacter denitrificans plasmid pTB4, complete sequence Sequence file: NC_008389.fna Sequence length: 5824 GC Content: 55.60% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 56 Matrix author: Borodovsky Laboratory - Georgia Tech, School of Biology, Atlanta, GA, USA Matrix order: 2 List of Open reading frames predicted as CDSs, shown with alternate starts (regions from start to stop codon w/ coding function >0.50) Left Right DNA Coding Avg Start end end Strand Frame Prob Prob -------- -------- ---------- ----- ---- ---- 3 494 direct fr 3 0.52 .... 42 494 direct fr 3 0.52 .... 1855 2859 direct fr 1 0.84 0.53 1942 2859 direct fr 1 0.88 0.40 1981 2859 direct fr 1 0.88 0.50 2095 2859 direct fr 1 0.87 0.27 3545 3667 complement fr 1 0.54 0.28 4059 4307 direct fr 3 0.50 0.63 4188 4307 direct fr 3 0.54 0.55 4139 4618 direct fr 2 0.51 0.00 4304 4618 direct fr 2 0.75 0.69 4406 4618 direct fr 2 0.65 0.17 4457 4618 direct fr 2 0.55 0.01 4664 5233 complement fr 1 0.67 0.27 4664 5134 complement fr 1 0.77 0.41 4664 5104 complement fr 1 0.77 0.52 4664 5062 complement fr 1 0.79 0.06 4664 5050 complement fr 1 0.78 0.61 5725 5826 direct fr 1 0.62 0.38 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 494 direct fr 3 192 440 complement fr 2 448 981 direct fr 1 956 1570 direct fr 2 1001 1417 complement fr 1 1843 2859 direct fr 1 2630 3529 direct fr 2 3545 4015 complement fr 1 4053 4307 direct fr 3 4136 4618 direct fr 2 4664 5239 complement fr 1 5286 5549 complement fr 2 5434 5826 direct fr 1 -------------------- ABOUT THE MATRIX USED: For details on the model building procedure see: Besemer J. and Borodovsky M. "Heuristic approach to deriving models for gene finding" NAR, 1999, Vol. 27, No. 19, pp. 3911-3920