GENEMARK PREDICTIONS Sequence: gi|161510924|ref|NC_010063.1| Staphylococcus aureus subsp. aureus USA300_TCH1516 plasmid pUSA300HOUMR, complete sequence Sequence file: NC_010063.fna Sequence length: 27041 GC Content: 30.52% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 31 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 0.85 0.47 253 1215 direct fr 1 0.85 0.34 337 1215 direct fr 1 0.85 0.05 1346 1516 direct fr 2 0.73 0.13 2071 2220 direct fr 1 0.54 0.80 2388 3080 complement fr 2 0.85 0.01 2388 2927 complement fr 2 0.89 0.34 2388 2873 complement fr 2 0.88 0.05 2388 2852 complement fr 2 0.88 0.04 3564 3698 direct fr 3 0.54 0.41 4488 5117 direct fr 3 0.67 0.86 4500 5117 direct fr 3 0.68 0.99 4749 5117 direct fr 3 0.64 0.23 4962 5117 direct fr 3 0.63 0.95 5136 5483 direct fr 3 0.55 0.55 5160 5483 direct fr 3 0.58 0.41 5337 5483 direct fr 3 0.51 0.11 5904 6554 complement fr 2 0.87 0.91 5904 6527 complement fr 2 0.90 0.41 5904 6509 complement fr 2 0.90 0.05 5904 6446 complement fr 2 0.89 0.27 6458 6847 complement fr 1 0.65 0.48 6458 6829 complement fr 1 0.67 0.95 6458 6745 complement fr 1 0.71 0.01 6458 6715 complement fr 1 0.67 0.60 6458 6670 complement fr 1 0.60 0.06 6971 7390 direct fr 2 0.59 0.13 7181 7390 direct fr 2 0.74 0.60 7235 7390 direct fr 2 0.69 0.10 7916 8410 complement fr 1 0.86 0.07 7916 8158 complement fr 1 0.76 0.37 8826 10625 direct fr 3 0.67 0.82 8868 10625 direct fr 3 0.68 0.08 8886 10625 direct fr 3 0.68 0.01 8994 10625 direct fr 3 0.71 0.12 9054 10625 direct fr 3 0.71 0.37 10615 10995 direct fr 1 0.64 0.98 10642 10995 direct fr 1 0.69 0.99 10660 10995 direct fr 1 0.73 0.90 10852 10995 direct fr 1 0.69 0.55 10897 10995 direct fr 1 0.55 0.03 11361 11837 direct fr 3 0.85 0.45 11466 11837 direct fr 3 0.81 0.32 11511 11837 direct fr 3 0.79 0.19 12507 13181 direct fr 3 0.57 0.18 13350 13715 complement fr 2 0.73 0.45 13350 13697 complement fr 2 0.73 0.09 13350 13619 complement fr 2 0.66 0.26 14197 14991 complement fr 3 0.55 0.67 14197 14982 complement fr 3 0.56 0.02 14197 14916 complement fr 3 0.56 0.53 14197 14889 complement fr 3 0.55 0.02 14197 14859 complement fr 3 0.54 0.03 15084 15614 complement fr 2 0.67 0.93 15084 15602 complement fr 2 0.69 0.85 15084 15551 complement fr 2 0.67 0.06 16387 17061 complement fr 3 0.55 0.22 17091 17294 complement fr 2 0.56 0.98 17308 18054 complement fr 3 0.50 0.71 17308 17997 complement fr 3 0.53 0.25 17308 17955 complement fr 3 0.54 0.39 17308 17952 complement fr 3 0.54 0.19 17308 17928 complement fr 3 0.54 0.48 18038 18976 complement fr 1 0.85 0.44 18038 18967 complement fr 1 0.86 0.29 18038 18814 complement fr 1 0.85 0.31 18038 18715 complement fr 1 0.83 0.03 18038 18613 complement fr 1 0.81 0.01 19083 19685 complement fr 2 0.67 0.15 19083 19679 complement fr 2 0.67 0.49 19083 19616 complement fr 2 0.65 0.02 19961 20326 complement fr 1 0.55 0.21 20396 21070 complement fr 1 0.57 0.22 21544 23010 direct fr 1 0.86 0.45 21691 23010 direct fr 1 0.89 0.14 21769 23010 direct fr 1 0.88 0.06 21775 23010 direct fr 1 0.88 0.04 23109 24008 direct fr 3 0.85 0.74 23589 24008 direct fr 3 0.83 0.47 23688 24008 direct fr 3 0.78 0.08 23721 24008 direct fr 3 0.76 0.56 24494 25102 direct fr 2 0.82 0.64 24572 25102 direct fr 2 0.89 0.06 24611 25102 direct fr 2 0.88 0.41 24656 25102 direct fr 2 0.87 0.21 25348 25680 direct fr 1 0.60 0.02 25480 25680 direct fr 1 0.68 0.02 25528 25680 direct fr 1 0.59 0.14 25543 25680 direct fr 1 0.57 0.33 25692 25877 direct fr 3 0.57 0.84 25764 25877 direct fr 3 0.61 0.04 26104 26847 complement fr 3 0.86 0.91 26104 26838 complement fr 3 0.87 0.83 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 4485 5117 direct fr 3 4757 5047 complement fr 1 5127 5483 direct fr 3 5904 6581 complement fr 2 6458 6850 complement fr 1 6923 7390 direct fr 2 7916 8839 complement fr 1 8796 10625 direct fr 3 10612 10995 direct fr 1 11244 11837 direct fr 3 12061 12312 direct fr 1 12486 13181 direct fr 3 13350 13910 complement fr 2 14197 14994 complement fr 3 15084 15638 complement fr 2 15611 15910 complement fr 1 15908 16249 complement fr 1 16387 17082 complement fr 3 17091 17315 complement fr 2 17308 18060 complement fr 3 18038 19006 complement fr 1 19083 19784 complement fr 2 19961 20371 complement fr 1 20396 21091 complement fr 1 21520 23010 direct fr 1 23094 24008 direct fr 3 23969 24112 direct fr 2 24491 25102 direct fr 2 25251 25595 complement fr 2 25336 25680 direct fr 1 25662 25877 direct fr 3 26104 26862 complement fr 3 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 2 6528 +/- 11 bp (complement) -------------------- 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