GENEMARK PREDICTIONS Sequence: gi|32470581|ref|NC_005007.1| Staphylococcus epidermidis ATCC 12228 plasmid pSE-12228-02, complete sequence Sequence file: NC_005007.fna Sequence length: 4679 GC Content: 31.78% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 32 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 -------- -------- ---------- ----- ---- ---- 3 236 direct fr 3 0.50 .... 9 236 direct fr 3 0.50 .... 57 236 direct fr 3 0.50 .... 598 909 direct fr 1 0.52 0.69 628 909 direct fr 1 0.58 0.04 930 1490 complement fr 2 0.70 0.16 930 1481 complement fr 2 0.71 0.07 930 1430 complement fr 2 0.75 0.44 930 1256 complement fr 2 0.66 0.30 930 1250 complement fr 2 0.66 0.45 1769 2689 direct fr 2 0.82 0.38 1865 2689 direct fr 2 0.91 0.52 1901 2689 direct fr 2 0.94 0.65 1955 2689 direct fr 2 0.94 0.13 2081 2689 direct fr 2 0.93 0.11 3197 3580 direct fr 2 0.64 0.75 3218 3580 direct fr 2 0.68 0.24 3290 3580 direct fr 2 0.77 0.21 3341 3580 direct fr 2 0.78 0.58 3347 3580 direct fr 2 0.78 0.62 3562 4413 direct fr 1 0.82 0.32 3733 4413 direct fr 1 0.86 0.05 3874 4413 direct fr 1 0.83 0.54 4006 4413 direct fr 1 0.79 0.47 4253 4681 direct fr 2 0.54 0.01 4271 4681 direct fr 2 0.55 0.05 4322 4681 direct fr 2 0.66 0.26 4439 4681 direct fr 2 0.89 0.31 4580 4681 direct fr 2 1.00 0.06 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 236 direct fr 3 316 597 direct fr 1 595 909 direct fr 1 930 1502 complement fr 2 1742 2689 direct fr 2 2687 2926 direct fr 2 3194 3580 direct fr 2 3556 4413 direct fr 1 4247 4681 direct fr 2 -------------------- 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