GENEMARK PREDICTIONS Sequence: gi|10957103|ref|NC_002253.1| Buchnera aphidicola str. APS (Acyrthosiphon pisum) plasmid pLeu, complete sequence Sequence file: NC_002253.fna Sequence length: 7786 GC Content: 26.71% 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 -------- -------- ---------- ----- ---- ---- 346 1197 complement fr 3 0.76 0.03 346 1104 complement fr 3 0.80 0.50 346 978 complement fr 3 0.80 0.31 346 969 complement fr 3 0.81 0.26 1514 2017 direct fr 2 0.80 0.25 1559 2017 direct fr 2 0.79 0.09 1637 2017 direct fr 2 0.85 0.72 2132 2893 direct fr 2 0.68 0.22 2141 2893 direct fr 2 0.69 0.40 2231 2893 direct fr 2 0.74 0.63 2357 2893 direct fr 2 0.71 0.45 2378 2893 direct fr 2 0.71 0.09 3032 4591 direct fr 2 0.83 0.86 3293 4591 direct fr 2 0.85 0.02 3350 4591 direct fr 2 0.85 0.74 3392 4591 direct fr 2 0.84 0.18 4652 5743 direct fr 2 0.82 0.93 4709 5743 direct fr 2 0.84 0.06 5342 5743 direct fr 2 0.84 0.24 5447 5743 direct fr 2 0.82 0.16 5733 7160 direct fr 3 0.90 0.56 5736 7160 direct fr 3 0.90 0.45 5745 7160 direct fr 3 0.91 0.37 5925 7160 direct fr 3 0.94 0.17 5976 7160 direct fr 3 0.94 0.18 5991 7160 direct fr 3 0.94 0.01 7163 7786 direct fr 2 0.80 0.93 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 346 1260 complement fr 3 1436 2017 direct fr 2 2129 2893 direct fr 2 2386 2574 complement fr 3 3014 4591 direct fr 2 4625 5743 direct fr 2 4663 5085 complement fr 3 5727 7160 direct fr 3 7154 7786 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