GENEMARK PREDICTIONS Sequence: gi|82703928|ref|NC_007617.1| Nitrosospira multiformis ATCC 25196 plasmid 3, complete sequence Sequence file: NC_007617.fna Sequence length: 14159 GC Content: 49.63% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 50 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 -------- -------- ---------- ----- ---- ---- 3 653 complement fr 2 0.65 0.19 3 386 complement fr 2 0.66 0.06 3 341 complement fr 2 0.63 0.55 3 263 complement fr 2 0.74 0.29 890 1444 direct fr 2 0.71 0.58 1061 1444 direct fr 2 0.69 0.06 1070 1444 direct fr 2 0.68 0.08 1214 1444 direct fr 2 0.57 0.08 1517 1858 complement fr 1 0.55 0.79 1833 2219 complement fr 2 0.62 0.73 1833 2162 complement fr 2 0.68 0.06 1833 2159 complement fr 2 0.67 0.05 1833 2078 complement fr 2 0.64 0.16 3427 4659 direct fr 1 0.61 0.55 3469 4659 direct fr 1 0.63 0.66 3547 4659 direct fr 1 0.61 0.02 3679 4659 direct fr 1 0.61 0.02 3892 4659 direct fr 1 0.53 0.25 5821 6252 complement fr 3 0.75 0.56 5821 6114 complement fr 3 0.78 0.27 5821 6054 complement fr 3 0.73 0.10 5821 5988 complement fr 3 0.63 0.53 6452 8053 direct fr 2 0.81 0.59 6473 8053 direct fr 2 0.81 0.40 6479 8053 direct fr 2 0.81 0.12 6521 8053 direct fr 2 0.82 0.04 6632 8053 direct fr 2 0.84 0.36 6677 8053 direct fr 2 0.83 0.37 9065 9358 complement fr 1 0.58 0.63 9505 10194 complement fr 3 0.65 0.48 9505 10182 complement fr 3 0.66 0.38 9505 9996 complement fr 3 0.67 0.49 9505 9702 complement fr 3 0.57 0.93 10374 10499 direct fr 3 0.53 0.28 10859 11356 direct fr 2 0.52 0.39 11394 11705 complement fr 2 0.72 0.36 11394 11684 complement fr 2 0.73 0.27 11394 11624 complement fr 2 0.71 0.35 11394 11600 complement fr 2 0.68 0.32 12615 12950 direct fr 3 0.72 0.26 12684 12950 direct fr 3 0.73 0.52 13880 14086 direct fr 2 0.56 0.55 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 725 complement fr 2 872 1444 direct fr 2 1517 1894 complement fr 1 1833 2228 complement fr 2 2361 3008 direct fr 3 2374 2625 complement fr 3 2995 3315 direct fr 1 3418 4659 direct fr 1 5100 5537 direct fr 3 5821 6264 complement fr 3 6380 8053 direct fr 2 8117 9067 complement fr 1 9065 9367 complement fr 1 9505 10251 complement fr 3 10206 10499 direct fr 3 10457 11356 direct fr 2 10586 10858 complement fr 1 11394 12185 complement fr 2 12576 12950 direct fr 3 12907 13674 direct fr 1 12919 13164 complement fr 3 13162 13494 complement fr 3 13715 14086 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