GENEMARK PREDICTIONS Sequence: gi|157149399|ref|NC_009787.1| Escherichia coli E24377A plasmid pETEC_35, complete sequence Sequence file: NC_009787.fna Sequence length: 34367 GC Content: 51.62% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 52 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 4718 complement fr 2 0.80 0.20 3 4628 complement fr 2 0.81 0.80 3 4574 complement fr 2 0.81 0.04 3 4565 complement fr 2 0.81 0.03 4718 6949 complement fr 1 0.66 0.47 4718 6901 complement fr 1 0.66 0.21 4718 6889 complement fr 1 0.66 0.18 4718 6847 complement fr 1 0.65 0.22 7093 7830 complement fr 3 0.67 0.28 7093 7809 complement fr 3 0.69 0.03 7093 7803 complement fr 3 0.69 0.02 7093 7776 complement fr 3 0.72 0.08 7093 7755 complement fr 3 0.73 0.70 7093 7722 complement fr 3 0.75 0.29 7093 7710 complement fr 3 0.75 0.06 7093 7632 complement fr 3 0.73 0.34 7998 8573 complement fr 2 0.50 0.78 7998 8534 complement fr 2 0.53 0.03 8583 11465 complement fr 2 0.66 0.83 8583 11402 complement fr 2 0.66 0.29 8583 11357 complement fr 2 0.66 0.18 8583 11345 complement fr 2 0.66 0.02 11467 13071 complement fr 3 0.58 0.01 11467 13008 complement fr 3 0.60 0.09 11467 12975 complement fr 3 0.61 0.00 11467 12972 complement fr 3 0.62 0.00 11467 12924 complement fr 3 0.64 0.23 11467 12834 complement fr 3 0.66 0.33 11467 12747 complement fr 3 0.67 0.16 11467 12726 complement fr 3 0.66 0.17 11467 12525 complement fr 3 0.68 0.63 12884 13753 complement fr 1 0.64 0.16 12884 13732 complement fr 1 0.64 0.19 12884 13705 complement fr 1 0.63 0.40 14257 14397 complement fr 3 0.52 0.73 15035 15226 complement fr 1 0.54 0.36 15035 15178 complement fr 1 0.56 0.30 15035 15154 complement fr 1 0.51 0.59 15223 15645 complement fr 3 0.68 0.33 15223 15597 complement fr 3 0.71 0.20 15223 15570 complement fr 3 0.72 0.23 15223 15567 complement fr 3 0.72 0.25 15223 15549 complement fr 3 0.72 0.50 15692 16117 complement fr 1 0.53 0.19 15692 16015 complement fr 1 0.62 0.54 15692 15994 complement fr 1 0.60 0.19 15692 15991 complement fr 1 0.60 0.15 17344 17778 complement fr 3 0.64 0.07 17344 17712 complement fr 3 0.65 0.65 17344 17664 complement fr 3 0.61 0.05 20408 20836 complement fr 1 0.59 0.09 20408 20830 complement fr 1 0.60 0.02 20408 20770 complement fr 1 0.66 0.38 20408 20719 complement fr 1 0.66 0.66 20408 20710 complement fr 1 0.65 0.31 20408 20707 complement fr 1 0.65 0.20 20833 21750 complement fr 3 0.51 0.03 20833 21333 complement fr 3 0.50 0.51 24197 25201 complement fr 1 0.61 0.35 24197 24958 complement fr 1 0.58 0.70 24197 24919 complement fr 1 0.56 0.05 24197 24514 complement fr 1 0.70 0.88 25630 25914 complement fr 3 0.60 0.67 25630 25908 complement fr 3 0.62 0.46 25630 25863 complement fr 3 0.66 0.33 25630 25851 complement fr 3 0.65 0.59 25630 25830 complement fr 3 0.63 0.12 26436 26861 complement fr 2 0.50 0.08 29051 29920 complement fr 1 0.51 0.38 29051 29908 complement fr 1 0.52 0.22 29051 29857 complement fr 1 0.54 0.21 29051 29806 complement fr 1 0.53 0.34 29051 29794 complement fr 1 0.52 0.02 29051 29758 complement fr 1 0.53 0.01 29051 29722 complement fr 1 0.56 0.19 29051 29713 complement fr 1 0.56 0.12 29051 29431 complement fr 1 0.58 0.03 30200 30460 complement fr 1 0.52 0.02 30200 30439 complement fr 1 0.57 0.06 30200 30409 complement fr 1 0.62 0.66 30200 30391 complement fr 1 0.62 0.58 30200 30370 complement fr 1 0.62 0.20 30976 31101 direct fr 1 0.50 0.25 32479 33210 complement fr 3 0.61 0.33 32479 33186 complement fr 3 0.63 0.18 32479 33129 complement fr 3 0.61 0.66 32479 33126 complement fr 3 0.61 0.53 32479 33117 complement fr 3 0.61 0.29 33207 33440 complement fr 2 0.54 0.15 33207 33419 complement fr 2 0.54 0.76 33791 34366 complement fr 1 0.71 .... 33791 34270 complement fr 1 0.69 0.04 33791 34267 complement fr 1 0.69 0.04 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 4739 complement fr 2 3309 4022 direct fr 3 4116 4538 direct fr 3 4718 6988 complement fr 1 5120 5650 direct fr 2 5966 6751 direct fr 2 7093 7839 complement fr 3 7658 7996 direct fr 2 7998 8585 complement fr 2 8583 11474 complement fr 2 9413 9598 complement fr 1 11467 13098 complement fr 3 11792 12196 direct fr 2 12884 13804 complement fr 1 14130 14345 complement fr 2 14257 14478 complement fr 3 15035 15298 complement fr 1 15223 15690 complement fr 3 15689 16228 direct fr 2 15692 16138 complement fr 1 16083 16616 complement fr 2 16239 16418 direct fr 3 16412 17143 direct fr 2 16529 17305 complement fr 1 17299 17802 direct fr 1 17344 17880 complement fr 3 17681 18172 direct fr 2 18014 18715 complement fr 1 18281 18832 direct fr 2 19081 20034 complement fr 3 19285 19653 direct fr 1 19809 20192 complement fr 2 20408 20884 complement fr 1 20833 21816 complement fr 3 21241 21489 direct fr 1 21827 22003 direct fr 2 22004 22471 direct fr 2 22556 23650 complement fr 1 24197 25213 complement fr 1 25355 25657 complement fr 1 25630 25923 complement fr 3 25985 26275 complement fr 1 26436 26921 complement fr 2 27297 28130 direct fr 3 28422 28733 direct fr 3 29051 29923 complement fr 1 29534 30148 direct fr 2 30200 30472 complement fr 1 30391 30594 direct fr 1 30865 31101 direct fr 1 30904 31923 complement fr 3 31896 32288 complement fr 2 32479 33273 complement fr 3 33207 33854 complement fr 2 33791 34366 complement fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 2 1 9540 +/- 11 bp (complement) -------------------- 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