GENEMARK PREDICTIONS Sequence: gi|157149316|ref|NC_009794.1| Citrobacter koseri ATCC BAA-895 plasmid pCKO2, complete sequence Sequence file: NC_009794.fna Sequence length: 5601 GC Content: 51.28% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 51 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 -------- -------- ---------- ----- ---- ---- 3 179 direct fr 3 0.60 .... 60 179 direct fr 3 0.60 .... 63 179 direct fr 3 0.56 .... 169 513 direct fr 1 0.58 0.37 205 513 direct fr 1 0.55 0.23 262 513 direct fr 1 0.51 0.03 1919 2038 direct fr 2 0.56 0.70 1191 1700 direct fr 3 0.72 0.56 1263 1700 direct fr 3 0.72 0.06 1365 1700 direct fr 3 0.66 0.22 1377 1700 direct fr 3 0.65 0.05 3131 3526 complement fr 1 0.51 0.02 3131 3511 complement fr 1 0.51 0.00 3131 3481 complement fr 1 0.51 0.08 3131 3352 complement fr 1 0.69 0.08 3131 3277 complement fr 1 0.61 0.17 3547 4092 complement fr 3 0.55 0.70 3547 3735 complement fr 3 0.59 0.30 3547 3690 complement fr 3 0.55 0.22 4911 5018 direct fr 3 0.54 0.82 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 179 direct fr 3 73 513 direct fr 1 440 2038 direct fr 2 975 1700 direct fr 3 1698 1919 direct fr 3 2533 2811 direct fr 1 2561 2785 direct fr 2 2783 3061 direct fr 2 2883 3182 direct fr 3 3131 3574 complement fr 1 3547 4125 complement fr 3 4118 4723 complement fr 1 4797 5018 direct fr 3 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 2 3 1200 +/- 11 bp (direct) 3 2 1644 +/- 11 bp (direct) 2 3 1752 +/- 11 bp (direct) 3 2 1848 +/- 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