GENEMARK PREDICTIONS Sequence: gi|145294016|ref|NC_009344.1| Shigella dysenteriae Sd197 plasmid pSD197_spA, complete sequence Sequence file: NC_009344.fna Sequence length: 8953 GC Content: 39.65% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 40 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 -------- -------- ---------- ----- ---- ---- 1 147 direct fr 1 0.54 .... 729 1697 direct fr 3 0.68 0.66 732 1697 direct fr 3 0.68 0.66 741 1697 direct fr 3 0.68 0.53 756 1697 direct fr 3 0.69 0.55 915 1697 direct fr 3 0.72 0.48 1176 1697 direct fr 3 0.79 0.16 1266 1697 direct fr 3 0.78 0.20 1272 1697 direct fr 3 0.78 0.19 1705 2022 direct fr 1 0.69 0.49 1900 2022 direct fr 1 0.61 0.53 2979 4112 complement fr 2 0.68 0.28 2979 4076 complement fr 2 0.70 0.45 2979 3776 complement fr 2 0.69 0.39 2979 3560 complement fr 2 0.69 0.03 2979 3311 complement fr 2 0.61 0.11 2979 3227 complement fr 2 0.72 0.12 2979 3221 complement fr 2 0.72 0.05 4112 4285 complement fr 1 0.54 0.24 4330 4476 complement fr 3 0.56 0.23 4330 4473 complement fr 3 0.56 0.30 5080 5424 complement fr 3 0.62 0.09 5080 5385 complement fr 3 0.63 0.21 5080 5370 complement fr 3 0.62 0.36 5080 5358 complement fr 3 0.61 0.45 6647 6907 direct fr 2 0.54 0.14 6722 6907 direct fr 2 0.56 0.21 8351 8686 direct fr 2 0.58 0.52 7691 8008 complement fr 1 0.54 0.08 7691 7975 complement fr 1 0.55 0.50 7691 7969 complement fr 1 0.55 0.71 7691 7963 complement fr 1 0.54 0.78 8014 8373 direct fr 1 0.60 0.89 8056 8373 direct fr 1 0.69 0.16 8062 8373 direct fr 1 0.69 0.06 8092 8373 direct fr 1 0.65 0.07 8756 8953 direct fr 2 0.55 0.21 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 1 147 direct fr 1 675 1697 direct fr 3 1663 2022 direct fr 1 2020 2256 direct fr 1 2061 2348 direct fr 3 2297 2770 direct fr 2 2979 4118 complement fr 2 4112 4351 complement fr 1 4330 4926 complement fr 3 5080 5496 complement fr 3 6176 6361 direct fr 2 6359 6907 direct fr 2 6358 6594 complement fr 3 7469 8686 direct fr 2 7691 8098 complement fr 1 8002 8373 direct fr 1 8560 8724 direct fr 1 8744 8953 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