GENEMARK PREDICTIONS Sequence: gi|16119200|ref|NC_003140.1| Staphylococcus aureus subsp. aureus N315 plasmid pN315, complete sequence Sequence file: NC_003140.fna Sequence length: 24653 GC Content: 28.70% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 30 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 -------- -------- ---------- ----- ---- ---- 232 1215 direct fr 1 0.83 0.51 253 1215 direct fr 1 0.83 0.35 337 1215 direct fr 1 0.83 0.04 1346 1516 direct fr 2 0.73 0.13 2071 2220 direct fr 1 0.53 0.79 2388 3080 complement fr 2 0.84 0.01 2388 2927 complement fr 2 0.89 0.37 2388 2873 complement fr 2 0.88 0.05 2388 2852 complement fr 2 0.87 0.04 3564 3698 direct fr 3 0.55 0.45 4489 5118 direct fr 1 0.69 0.89 4501 5118 direct fr 1 0.70 0.99 4750 5118 direct fr 1 0.64 0.22 4963 5118 direct fr 1 0.62 0.95 5137 5484 direct fr 1 0.57 0.58 5161 5484 direct fr 1 0.61 0.41 5338 5484 direct fr 1 0.53 0.13 5905 6876 complement fr 3 0.89 0.47 5905 6858 complement fr 3 0.90 0.95 5905 6774 complement fr 3 0.92 0.01 5905 6744 complement fr 3 0.92 0.57 5905 6699 complement fr 3 0.91 0.05 7000 7419 direct fr 1 0.62 0.12 7210 7419 direct fr 1 0.76 0.61 7264 7419 direct fr 1 0.69 0.09 7945 8439 complement fr 3 0.85 0.06 7945 8187 complement fr 3 0.76 0.38 8855 10654 direct fr 2 0.67 0.82 8897 10654 direct fr 2 0.68 0.09 8915 10654 direct fr 2 0.68 0.00 9023 10654 direct fr 2 0.71 0.13 9083 10654 direct fr 2 0.71 0.41 9374 10654 direct fr 2 0.74 0.50 10644 11024 direct fr 3 0.64 0.99 10671 11024 direct fr 3 0.71 0.99 10689 11024 direct fr 3 0.73 0.93 10881 11024 direct fr 3 0.69 0.55 10926 11024 direct fr 3 0.55 0.03 11390 11881 direct fr 2 0.86 0.45 11495 11881 direct fr 2 0.83 0.25 11573 11881 direct fr 2 0.79 0.24 11757 13295 direct fr 3 0.79 0.06 11763 13295 direct fr 3 0.80 0.07 11799 13295 direct fr 3 0.81 0.20 11853 13295 direct fr 3 0.84 0.56 12126 13295 direct fr 3 0.83 0.07 12237 13295 direct fr 3 0.83 0.18 13288 14046 direct fr 1 0.85 0.52 13513 14046 direct fr 1 0.90 0.15 13609 14046 direct fr 1 0.88 0.44 13711 14046 direct fr 1 0.86 0.08 14254 14421 direct fr 1 0.62 0.63 14421 15710 direct fr 3 0.72 0.09 14466 15710 direct fr 3 0.74 0.89 14604 15710 direct fr 3 0.73 0.10 14670 15710 direct fr 3 0.71 0.22 15728 16123 direct fr 2 0.77 0.03 15782 16123 direct fr 2 0.78 0.97 15881 16123 direct fr 2 0.74 0.01 16503 16796 direct fr 3 0.72 0.14 16871 18805 direct fr 2 0.55 0.15 17027 18805 direct fr 2 0.56 0.64 17348 18805 direct fr 2 0.52 0.00 17573 18805 direct fr 2 0.59 0.04 17594 18805 direct fr 2 0.60 0.08 17717 18805 direct fr 2 0.65 0.02 17741 18805 direct fr 2 0.66 0.26 17744 18805 direct fr 2 0.66 0.19 18809 19120 direct fr 2 0.57 0.08 19132 19758 direct fr 1 0.81 0.92 19456 19758 direct fr 1 0.84 0.08 19996 20373 direct fr 1 0.61 0.34 20026 20373 direct fr 1 0.65 0.86 20361 20639 direct fr 3 0.82 0.11 20382 20639 direct fr 3 0.81 0.17 20706 21206 direct fr 3 0.90 0.65 20829 21206 direct fr 3 0.87 0.08 20928 21206 direct fr 3 0.83 0.29 21570 22430 direct fr 3 0.74 0.94 21603 22430 direct fr 3 0.75 0.04 21660 22430 direct fr 3 0.74 0.33 21786 22430 direct fr 3 0.71 0.15 22517 22756 direct fr 2 0.63 0.99 22664 22756 direct fr 2 0.52 0.24 23303 23500 direct fr 2 0.53 0.94 23315 23500 direct fr 2 0.56 0.96 23716 24459 complement fr 3 0.86 0.92 23716 24450 complement fr 3 0.87 0.84 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 157 1215 direct fr 1 1187 1516 direct fr 2 1723 2112 complement fr 3 1766 1975 direct fr 2 2026 2220 direct fr 1 2388 3110 complement fr 2 3501 3698 direct fr 3 4486 5118 direct fr 1 4758 5048 complement fr 2 5128 5484 direct fr 1 5905 6879 complement fr 3 6952 7419 direct fr 1 7945 8868 complement fr 3 8825 10654 direct fr 2 10641 11024 direct fr 3 11273 11881 direct fr 2 11736 13295 direct fr 3 13273 14046 direct fr 1 14086 14421 direct fr 1 14412 15710 direct fr 3 15632 16123 direct fr 2 16476 16796 direct fr 3 16820 18805 direct fr 2 17954 18124 complement fr 1 18803 19120 direct fr 2 19123 19758 direct fr 1 19987 20373 direct fr 1 20286 20639 direct fr 3 20637 21206 direct fr 3 21495 22430 direct fr 3 22493 22756 direct fr 2 23288 23500 direct fr 2 23716 24474 complement fr 3 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 3 20280 +/- 11 bp (direct) -------------------- 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