GENEMARK PREDICTIONS Sequence: gi|110666922|ref|NC_008226.1| Clostridium difficile 630 plasmid pCD630, complete sequence Sequence file: NC_008226.fna Sequence length: 7881 GC Content: 27.90% 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 -------- -------- ---------- ----- ---- ---- 1 99 complement fr 3 0.60 0.72 257 550 complement fr 1 0.65 0.12 257 433 complement fr 1 0.65 0.07 550 765 complement fr 3 0.61 0.90 1017 2348 complement fr 2 0.90 0.95 1017 2312 complement fr 2 0.90 0.04 1017 2273 complement fr 2 0.90 0.01 2903 3295 complement fr 1 0.76 0.56 2903 3091 complement fr 1 0.66 0.18 2903 3076 complement fr 1 0.68 0.07 2903 3010 complement fr 1 0.55 0.19 3495 6104 complement fr 2 0.76 0.93 3495 5660 complement fr 2 0.76 0.04 3495 5603 complement fr 2 0.76 0.19 3495 5474 complement fr 2 0.75 0.03 6366 6857 complement fr 2 0.61 0.02 6366 6686 complement fr 2 0.81 0.40 6366 6566 complement fr 2 0.72 0.12 6366 6521 complement fr 2 0.64 0.15 7052 7597 direct fr 2 0.81 0.70 7361 7597 direct fr 2 0.82 0.20 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 257 568 complement fr 1 550 783 complement fr 3 1017 2393 complement fr 2 2903 3385 complement fr 1 3495 6128 complement fr 2 6366 6926 complement fr 2 6779 6979 direct fr 2 7025 7597 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