GENEMARK PREDICTIONS Sequence: gi|157149612|ref|NC_009796.1| Campylobacter concisus 13826 plasmid pCCON16, complete sequence Sequence file: NC_009796.fna Sequence length: 16457 GC Content: 33.46% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 33 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 -------- -------- ---------- ----- ---- ---- 349 1308 direct fr 1 0.79 0.64 421 1308 direct fr 1 0.81 0.21 676 1308 direct fr 1 0.76 0.05 742 1308 direct fr 1 0.77 0.12 1123 1308 direct fr 1 0.52 0.03 1126 1308 direct fr 1 0.52 0.08 1408 1827 direct fr 1 0.84 0.91 1531 1827 direct fr 1 0.83 0.15 1549 1827 direct fr 1 0.81 0.01 1558 1827 direct fr 1 0.81 0.00 1881 3023 direct fr 3 0.80 0.05 2106 3023 direct fr 3 0.91 0.06 2181 3023 direct fr 3 0.90 0.05 2223 3023 direct fr 3 0.91 0.88 3098 3697 direct fr 2 0.65 0.23 3116 3697 direct fr 2 0.66 0.84 3134 3697 direct fr 2 0.69 0.43 3239 3697 direct fr 2 0.63 0.05 3242 3697 direct fr 2 0.62 0.05 3697 3984 direct fr 1 0.59 0.87 3841 3984 direct fr 1 0.55 0.61 4010 4567 direct fr 2 0.75 0.91 4049 4567 direct fr 2 0.81 0.62 4124 4567 direct fr 2 0.81 0.23 4280 4567 direct fr 2 0.76 0.57 4334 4567 direct fr 2 0.73 0.37 4621 5820 direct fr 1 0.74 0.08 4864 5820 direct fr 1 0.77 0.37 5026 5820 direct fr 1 0.81 0.10 5110 5820 direct fr 1 0.86 0.03 5218 5820 direct fr 1 0.88 0.66 6048 6278 direct fr 3 0.79 0.77 6126 6278 direct fr 3 0.75 0.31 6281 6727 direct fr 2 0.75 0.46 6290 6727 direct fr 2 0.77 0.51 7024 8130 complement fr 3 0.82 0.10 7024 8028 complement fr 3 0.85 0.08 7024 8004 complement fr 3 0.85 0.88 7024 7896 complement fr 3 0.86 0.04 7024 7839 complement fr 3 0.87 0.91 8190 8627 complement fr 2 0.81 0.51 8190 8321 complement fr 2 0.53 0.03 9186 9686 direct fr 3 0.75 0.87 9324 9686 direct fr 3 0.76 0.20 9435 9686 direct fr 3 0.64 0.01 9742 10530 direct fr 1 0.81 0.20 9814 10530 direct fr 1 0.83 0.27 9853 10530 direct fr 1 0.81 0.09 10054 10530 direct fr 1 0.89 0.18 10540 11097 complement fr 3 0.84 0.67 10540 10926 complement fr 3 0.78 0.08 10540 10893 complement fr 3 0.76 0.03 11118 11741 complement fr 2 0.64 0.04 11118 11672 complement fr 2 0.64 0.35 11118 11573 complement fr 2 0.59 0.07 11118 11567 complement fr 2 0.58 0.13 12027 12800 complement fr 2 0.87 0.40 12027 12755 complement fr 2 0.91 0.32 12027 12665 complement fr 2 0.90 0.08 12027 12434 complement fr 2 0.85 0.64 12828 13463 complement fr 2 0.82 0.10 12828 13331 complement fr 2 0.84 0.04 12828 13220 complement fr 2 0.80 0.13 12828 13187 complement fr 2 0.78 0.01 14592 16457 direct fr 3 0.65 0.75 14760 16457 direct fr 3 0.65 0.45 14853 16457 direct fr 3 0.63 0.15 14943 16457 direct fr 3 0.60 0.03 15673 15828 direct fr 1 0.62 0.33 15697 15828 direct fr 1 0.56 0.36 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 316 1308 direct fr 1 1363 1827 direct fr 1 1875 3023 direct fr 3 3083 3697 direct fr 2 3253 3480 complement fr 3 3691 3984 direct fr 1 4007 4567 direct fr 2 4534 5820 direct fr 1 5979 6278 direct fr 3 6272 6727 direct fr 2 6752 7006 complement fr 1 7024 8136 complement fr 3 8190 8681 complement fr 2 8757 9077 complement fr 2 9162 9686 direct fr 3 9691 10530 direct fr 1 10540 11139 complement fr 3 11118 11984 complement fr 2 12027 12806 complement fr 2 12828 13499 complement fr 2 13649 13966 complement fr 1 14089 14298 direct fr 1 14267 14602 direct fr 2 14586 16457 direct fr 3 15271 15828 direct fr 1 15826 16380 direct fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 1 16056 +/- 11 bp (direct) 3 1 16128 +/- 11 bp (direct) 3 1 16320 +/- 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