GENEMARK PREDICTIONS Sequence: gi|121583590|ref|NC_008771.1| Verminephrobacter eiseniae EF01-2 plasmid pVEIS01, complete sequence Sequence file: NC_008771.fna Sequence length: 31194 GC Content: 58.61% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 59 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 -------- -------- ---------- ----- ---- ---- 121 1227 direct fr 1 0.82 0.92 130 1227 direct fr 1 0.82 0.82 241 1227 direct fr 1 0.85 0.10 283 1227 direct fr 1 0.85 0.76 286 1227 direct fr 1 0.85 0.49 1222 2355 complement fr 3 0.69 0.62 1222 2307 complement fr 3 0.73 0.21 1222 2223 complement fr 3 0.75 0.55 1222 2181 complement fr 3 0.78 0.24 1222 2157 complement fr 3 0.78 0.26 2501 2677 complement fr 1 0.53 0.30 2501 2635 complement fr 1 0.54 0.58 2501 2617 complement fr 1 0.51 0.47 2689 3975 complement fr 3 0.79 0.36 2689 3942 complement fr 3 0.81 0.05 2689 3912 complement fr 3 0.82 0.50 2689 3828 complement fr 3 0.85 0.64 2689 3750 complement fr 3 0.85 0.03 3988 6264 complement fr 3 0.90 0.83 3988 6231 complement fr 3 0.90 0.67 3988 6213 complement fr 3 0.90 0.19 6261 7304 complement fr 2 0.75 0.30 6261 7277 complement fr 2 0.77 0.30 6261 7238 complement fr 2 0.78 0.64 6261 7226 complement fr 2 0.78 0.43 6261 7196 complement fr 2 0.77 0.19 7282 8634 complement fr 3 0.77 0.49 7282 8607 complement fr 3 0.78 0.64 7282 8529 complement fr 3 0.79 0.52 7282 8502 complement fr 3 0.78 0.33 7282 8496 complement fr 3 0.78 0.39 8631 9428 complement fr 2 0.72 0.50 8631 9407 complement fr 2 0.74 0.15 8631 9335 complement fr 2 0.76 0.25 8631 9332 complement fr 2 0.76 0.18 8631 9323 complement fr 2 0.75 0.19 9425 10141 complement fr 1 0.76 0.38 9425 9997 complement fr 1 0.79 0.06 9425 9994 complement fr 1 0.79 0.03 9425 9973 complement fr 1 0.79 0.47 9425 9868 complement fr 1 0.82 0.59 10145 11128 complement fr 1 0.69 0.43 10145 11077 complement fr 1 0.72 0.02 10145 10972 complement fr 1 0.73 0.02 10145 10912 complement fr 1 0.72 0.66 10145 10855 complement fr 1 0.71 0.07 10145 10702 complement fr 1 0.71 0.77 11420 12163 complement fr 1 0.70 0.00 11420 12091 complement fr 1 0.77 0.49 11420 12085 complement fr 1 0.77 0.26 11420 11995 complement fr 1 0.80 0.43 11420 11854 complement fr 1 0.75 0.12 11420 11698 complement fr 1 0.68 0.67 12088 14571 complement fr 3 0.75 0.02 12088 14502 complement fr 3 0.77 0.80 12088 14421 complement fr 3 0.77 0.55 12088 14400 complement fr 3 0.77 0.51 12088 14361 complement fr 3 0.76 0.22 14465 14848 complement fr 1 0.65 0.43 14465 14788 complement fr 1 0.70 0.31 14465 14767 complement fr 1 0.69 0.45 14465 14749 complement fr 1 0.68 0.22 14853 15161 complement fr 2 0.66 0.68 14853 15119 complement fr 2 0.74 0.07 14853 15107 complement fr 2 0.73 0.18 15680 16054 complement fr 1 0.65 0.94 15680 16042 complement fr 1 0.67 0.82 15680 15958 complement fr 1 0.60 0.19 15680 15940 complement fr 1 0.61 0.20 16119 16262 complement fr 2 0.51 0.22 16119 16250 complement fr 2 0.53 0.14 16316 16480 complement fr 1 0.52 0.25 16316 16462 complement fr 1 0.54 0.16 16469 16888 direct fr 2 0.72 0.20 16526 16888 direct fr 2 0.70 0.38 16952 17431 complement fr 1 0.52 0.01 16952 17395 complement fr 1 0.56 0.02 16952 17269 complement fr 1 0.75 0.61 16952 17176 complement fr 1 0.71 0.07 16952 17110 complement fr 1 0.60 0.11 17244 17561 complement fr 2 0.63 0.80 17244 17534 complement fr 2 0.68 0.57 17244 17501 complement fr 2 0.69 0.37 17244 17399 complement fr 2 0.56 0.26 17588 17914 complement fr 1 0.54 0.09 17588 17842 complement fr 1 0.64 0.38 17588 17809 complement fr 1 0.64 0.55 17588 17797 complement fr 1 0.62 0.30 17690 18193 direct fr 2 0.52 0.57 17804 18193 direct fr 2 0.64 0.06 17927 18193 direct fr 2 0.73 0.33 17969 18193 direct fr 2 0.68 0.26 17981 18193 direct fr 2 0.66 0.10 18393 19073 complement fr 2 0.60 0.01 18393 19022 complement fr 2 0.64 0.07 18393 18968 complement fr 2 0.66 0.75 18393 18950 complement fr 2 0.66 0.33 18393 18920 complement fr 2 0.64 0.15 19603 19884 direct fr 1 0.61 0.67 19735 19884 direct fr 1 0.64 0.40 20084 20818 direct fr 2 0.65 0.36 20198 20818 direct fr 2 0.77 0.25 20213 20818 direct fr 2 0.78 0.47 20264 20818 direct fr 2 0.82 0.85 20285 20818 direct fr 2 0.82 0.46 20315 20818 direct fr 2 0.81 0.01 20815 21681 direct fr 1 0.69 0.71 20929 21681 direct fr 1 0.71 0.13 21007 21681 direct fr 1 0.71 0.16 21073 21681 direct fr 1 0.69 0.11 22397 22705 direct fr 2 0.53 0.19 22987 23502 direct fr 1 0.51 0.22 23074 23502 direct fr 1 0.56 0.61 23182 23502 direct fr 1 0.59 0.38 23260 23502 direct fr 1 0.68 0.49 23326 23502 direct fr 1 0.65 0.12 23502 23768 direct fr 3 0.68 0.71 23598 23768 direct fr 3 0.68 0.46 23747 23959 direct fr 2 0.51 0.43 23768 23959 direct fr 2 0.57 0.13 23956 24339 direct fr 1 0.63 0.16 23962 24339 direct fr 1 0.63 0.12 23998 24339 direct fr 1 0.68 0.40 24076 24339 direct fr 1 0.69 0.16 24169 24339 direct fr 1 0.59 0.34 24397 24918 direct fr 1 0.72 0.69 24511 24918 direct fr 1 0.69 0.58 24844 24918 direct fr 1 0.52 0.65 24994 25251 direct fr 1 0.79 0.14 25015 25251 direct fr 1 0.77 0.10 25033 25251 direct fr 1 0.74 0.04 25283 25561 direct fr 2 0.68 0.66 25527 25838 direct fr 3 0.63 0.21 25545 25838 direct fr 3 0.65 0.22 25581 25838 direct fr 3 0.70 0.43 25623 25838 direct fr 3 0.68 0.27 25835 26035 direct fr 2 0.53 0.73 25853 26035 direct fr 2 0.60 0.81 25892 26035 direct fr 2 0.59 0.10 26013 26834 direct fr 3 0.79 0.94 26022 26834 direct fr 3 0.80 0.80 26052 26834 direct fr 3 0.82 0.88 26118 26834 direct fr 3 0.84 0.03 26157 26834 direct fr 3 0.85 0.39 26301 26834 direct fr 3 0.86 0.15 26313 26834 direct fr 3 0.87 0.03 26325 26834 direct fr 3 0.88 0.10 26385 26834 direct fr 3 0.89 0.33 28118 28297 direct fr 2 0.51 0.72 28163 28297 direct fr 2 0.64 0.07 28169 28297 direct fr 2 0.61 0.09 28196 28297 direct fr 2 0.54 0.58 28282 28494 direct fr 1 0.54 0.83 28294 28494 direct fr 1 0.57 0.71 28642 29070 complement fr 3 0.53 0.83 28642 28971 complement fr 3 0.52 0.14 29071 29823 complement fr 3 0.71 0.05 29071 29754 complement fr 3 0.77 0.17 29071 29613 complement fr 3 0.87 0.11 29071 29571 complement fr 3 0.88 0.31 29071 29559 complement fr 3 0.88 0.35 30466 31047 direct fr 1 0.71 0.66 30469 31047 direct fr 1 0.72 0.49 30484 31047 direct fr 1 0.74 0.55 30493 31047 direct fr 1 0.74 0.35 30577 31047 direct fr 1 0.69 0.05 31064 31195 direct fr 2 0.93 0.71 31106 31195 direct fr 2 0.98 .... List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 79 1227 direct fr 1 1222 2361 complement fr 3 2108 2692 direct fr 2 2352 2573 complement fr 2 2501 2731 complement fr 1 2689 3990 complement fr 3 3430 4476 direct fr 1 3988 6306 complement fr 3 6261 7316 complement fr 2 7282 8649 complement fr 3 7861 8358 direct fr 1 8631 9431 complement fr 2 9425 10147 complement fr 1 10145 11158 complement fr 1 11133 11486 complement fr 2 11420 12169 complement fr 1 11962 13239 direct fr 1 12088 14598 complement fr 3 14465 14968 complement fr 1 14853 15176 complement fr 2 15164 15673 complement fr 1 15680 16087 complement fr 1 16119 16322 complement fr 2 16316 16576 complement fr 1 16328 16888 direct fr 2 16645 17004 direct fr 1 16952 17500 complement fr 1 17244 17573 complement fr 2 17513 18193 direct fr 2 17588 18292 complement fr 1 18393 19325 complement fr 2 19189 19392 direct fr 1 19585 19884 direct fr 1 19878 20087 direct fr 3 20018 20818 direct fr 2 20785 21681 direct fr 1 22367 22705 direct fr 2 22617 22802 direct fr 3 22849 23502 direct fr 1 23463 23768 direct fr 3 23675 23959 direct fr 2 23773 24339 direct fr 1 24337 24918 direct fr 1 24655 24855 complement fr 3 24916 25251 direct fr 1 25160 25561 direct fr 2 25317 25838 direct fr 3 25811 26035 direct fr 2 26010 26834 direct fr 3 27075 27281 direct fr 3 27355 28212 direct fr 1 27364 28059 complement fr 3 28103 28297 direct fr 2 28210 28494 direct fr 1 28642 29073 complement fr 3 29071 29835 complement fr 3 29836 30213 complement fr 3 30430 31047 direct fr 1 30983 31195 direct fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 3 14520 +/- 11 bp (complement) 2 1 16788 +/- 11 bp (direct) 2 1 17304 +/- 11 bp (complement) 2 3 22632 +/- 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