GENEMARK PREDICTIONS Sequence: gi|145297095|ref|NC_009343.1| Corynebacterium glutamicum R plasmid pCGR1, complete sequence Sequence file: NC_009343.fna Sequence length: 49120 GC Content: 53.93% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 54 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 -------- -------- ---------- ----- ---- ---- 673 1620 direct fr 1 0.58 0.51 790 1620 direct fr 1 0.57 0.05 805 1620 direct fr 1 0.56 0.00 853 1620 direct fr 1 0.54 0.78 1601 1894 direct fr 2 0.52 0.37 1604 1894 direct fr 2 0.52 0.23 1613 1894 direct fr 2 0.52 0.54 2391 2546 direct fr 3 0.62 0.36 2445 2546 direct fr 3 0.56 0.10 2559 3161 direct fr 3 0.77 0.86 2808 3161 direct fr 3 0.74 0.09 2814 3161 direct fr 3 0.73 0.10 2820 3161 direct fr 3 0.73 0.26 3176 3421 direct fr 2 0.51 0.82 3224 3421 direct fr 2 0.63 0.14 3233 3421 direct fr 2 0.67 0.15 3299 3421 direct fr 2 0.56 0.32 3308 3421 direct fr 2 0.56 0.34 3394 4083 direct fr 1 0.58 0.12 3418 4083 direct fr 1 0.58 0.05 3436 4083 direct fr 1 0.59 0.11 3541 4083 direct fr 1 0.65 0.79 3760 4083 direct fr 1 0.70 0.81 4175 4384 direct fr 2 0.61 0.53 4253 4384 direct fr 2 0.65 0.22 4453 4794 direct fr 1 0.51 0.07 4591 4794 direct fr 1 0.63 0.21 4663 4794 direct fr 1 0.60 0.29 4791 4979 direct fr 3 0.50 0.14 4990 5337 direct fr 1 0.67 0.47 5113 5337 direct fr 1 0.65 0.16 5125 5337 direct fr 1 0.66 0.45 5170 5337 direct fr 1 0.66 0.63 5450 5905 direct fr 2 0.59 0.00 5513 5905 direct fr 2 0.68 0.01 5558 5905 direct fr 2 0.78 0.94 5576 5905 direct fr 2 0.80 0.86 5600 5905 direct fr 2 0.82 0.28 5615 5905 direct fr 2 0.82 0.27 5624 5905 direct fr 2 0.81 0.09 5902 6207 direct fr 1 0.68 0.55 6019 6207 direct fr 1 0.71 0.07 6526 6906 direct fr 1 0.74 0.84 6601 6906 direct fr 1 0.70 0.17 6631 6906 direct fr 1 0.67 0.11 6903 7061 direct fr 3 0.60 0.90 6909 7061 direct fr 3 0.60 0.89 6912 7061 direct fr 3 0.60 0.87 6915 7061 direct fr 3 0.61 0.86 6918 7061 direct fr 3 0.61 0.80 6948 7061 direct fr 3 0.60 0.14 7192 7575 direct fr 1 0.53 0.04 7222 7575 direct fr 1 0.56 0.68 7225 7575 direct fr 1 0.58 0.41 7255 7575 direct fr 1 0.61 0.55 7288 7575 direct fr 1 0.59 0.37 7306 7575 direct fr 1 0.58 0.57 8191 9306 direct fr 1 0.61 0.38 8209 9306 direct fr 1 0.63 0.28 8287 9306 direct fr 1 0.63 0.42 8335 9306 direct fr 1 0.62 0.13 8389 9306 direct fr 1 0.61 0.01 8512 9306 direct fr 1 0.65 0.62 9708 10301 direct fr 3 0.51 0.01 9717 10301 direct fr 3 0.52 0.00 9795 10301 direct fr 3 0.59 0.97 9891 10301 direct fr 3 0.52 0.35 10298 10876 direct fr 2 0.68 0.37 10412 10876 direct fr 2 0.66 0.58 10577 10876 direct fr 2 0.55 0.57 10869 11150 direct fr 3 0.73 0.64 10902 11150 direct fr 3 0.83 0.65 11019 11150 direct fr 3 0.70 0.10 11022 11150 direct fr 3 0.70 0.12 11089 11382 complement fr 3 0.52 0.37 11615 12277 direct fr 2 0.60 0.52 11768 12277 direct fr 2 0.60 0.05 11858 12277 direct fr 2 0.66 0.05 11915 12277 direct fr 2 0.74 0.63 11954 12277 direct fr 2 0.78 0.53 12612 12758 direct fr 3 0.72 0.43 12849 13376 direct fr 3 0.59 0.80 12960 13376 direct fr 3 0.65 0.16 12963 13376 direct fr 3 0.65 0.11 13077 13376 direct fr 3 0.71 0.08 13224 13376 direct fr 3 0.63 0.40 13620 13892 direct fr 3 0.83 0.31 13644 13892 direct fr 3 0.81 0.49 13653 13892 direct fr 3 0.80 0.29 13858 15162 direct fr 1 0.58 0.94 13882 15162 direct fr 1 0.59 0.72 13903 15162 direct fr 1 0.60 0.03 13957 15162 direct fr 1 0.59 0.23 14026 15162 direct fr 1 0.59 0.55 14095 15162 direct fr 1 0.57 0.14 15288 15410 direct fr 3 0.53 0.18 15309 15410 direct fr 3 0.55 0.44 15410 15679 direct fr 2 0.69 0.73 15521 15679 direct fr 2 0.67 0.65 15572 15679 direct fr 2 0.56 0.17 15575 15679 direct fr 2 0.56 0.10 15924 17462 direct fr 3 0.70 0.13 15933 17462 direct fr 3 0.71 0.04 15945 17462 direct fr 3 0.71 0.05 15984 17462 direct fr 3 0.72 0.77 15993 17462 direct fr 3 0.72 0.63 16098 17462 direct fr 3 0.75 0.04 16173 17462 direct fr 3 0.77 0.34 16206 17462 direct fr 3 0.78 0.72 16233 17462 direct fr 3 0.77 0.80 17467 18573 direct fr 1 0.63 0.39 17509 18573 direct fr 1 0.66 0.48 17644 18573 direct fr 1 0.62 0.11 17716 18573 direct fr 1 0.58 0.31 18560 18943 complement fr 1 0.58 0.18 18560 18901 complement fr 1 0.63 0.17 18560 18790 complement fr 1 0.53 0.50 19118 19630 complement fr 1 0.62 0.25 19118 19528 complement fr 1 0.58 0.51 19118 19513 complement fr 1 0.58 0.10 19118 19423 complement fr 1 0.72 0.68 19118 19420 complement fr 1 0.72 0.73 19764 20153 complement fr 2 0.61 0.02 19764 20090 complement fr 2 0.72 0.25 19764 20057 complement fr 2 0.78 0.79 19764 19982 complement fr 2 0.74 0.48 19764 19865 complement fr 2 0.54 0.32 20160 20849 complement fr 2 0.60 0.46 20160 20843 complement fr 2 0.61 0.47 20160 20840 complement fr 2 0.61 0.37 20160 20789 complement fr 2 0.62 0.03 20160 20735 complement fr 2 0.66 0.10 20911 21642 direct fr 1 0.69 0.47 21049 21642 direct fr 1 0.81 0.65 21361 21642 direct fr 1 0.68 0.13 21451 21642 direct fr 1 0.55 0.04 21653 22564 direct fr 2 0.61 0.15 21722 22564 direct fr 2 0.65 0.27 21875 22564 direct fr 2 0.69 0.64 21887 22564 direct fr 2 0.69 0.72 22640 23059 direct fr 2 0.58 0.68 22646 23059 direct fr 2 0.57 0.45 22685 23059 direct fr 2 0.54 0.17 22993 23412 direct fr 1 0.53 0.00 23047 23412 direct fr 1 0.60 0.86 23056 23412 direct fr 1 0.61 0.56 23152 23412 direct fr 1 0.59 0.07 23161 23412 direct fr 1 0.59 0.13 23182 23412 direct fr 1 0.61 0.38 23191 23412 direct fr 1 0.60 0.13 23224 23412 direct fr 1 0.65 0.17 23393 23746 direct fr 2 0.64 0.83 23396 23746 direct fr 2 0.64 0.89 23405 23746 direct fr 2 0.66 0.81 23471 23746 direct fr 2 0.65 0.04 23522 23746 direct fr 2 0.61 0.43 23585 23746 direct fr 2 0.60 0.13 24323 24706 direct fr 2 0.59 0.74 24801 25166 direct fr 3 0.72 0.49 24867 25166 direct fr 3 0.82 0.39 24897 25166 direct fr 3 0.81 0.38 24900 25166 direct fr 3 0.81 0.26 25508 26494 direct fr 2 0.54 0.75 26143 31533 direct fr 1 0.77 0.08 26179 31533 direct fr 1 0.77 0.47 26197 31533 direct fr 1 0.77 0.48 26251 31533 direct fr 1 0.77 0.22 32360 34588 direct fr 2 0.68 0.67 32384 34588 direct fr 2 0.69 0.50 32513 34588 direct fr 2 0.68 0.50 32525 34588 direct fr 2 0.68 0.39 32540 34588 direct fr 2 0.68 0.62 32558 34588 direct fr 2 0.68 0.60 32570 34588 direct fr 2 0.68 0.37 34661 36103 direct fr 2 0.53 0.81 34664 36103 direct fr 2 0.53 0.64 34670 36103 direct fr 2 0.54 0.62 34697 36103 direct fr 2 0.53 0.27 34787 36103 direct fr 2 0.51 0.82 36103 36438 direct fr 1 0.70 0.87 36217 36438 direct fr 1 0.64 0.31 36439 36918 direct fr 1 0.67 0.09 36514 36918 direct fr 1 0.77 0.76 36646 36918 direct fr 1 0.71 0.45 36673 36918 direct fr 1 0.69 0.17 36909 37364 direct fr 3 0.70 0.90 36963 37364 direct fr 3 0.72 0.04 37050 37364 direct fr 3 0.69 0.13 37149 37364 direct fr 3 0.70 0.48 37301 38581 direct fr 2 0.58 0.51 37340 38581 direct fr 2 0.60 0.42 37361 38581 direct fr 2 0.60 0.19 37436 38581 direct fr 2 0.60 0.64 37469 38581 direct fr 2 0.59 0.26 38855 39415 direct fr 2 0.53 0.76 39134 39415 direct fr 2 0.73 0.77 39179 39415 direct fr 2 0.72 0.14 39655 39924 complement fr 3 0.68 0.16 39655 39831 complement fr 3 0.62 0.09 42738 43193 complement fr 2 0.58 0.10 42738 43154 complement fr 2 0.63 0.35 42738 43088 complement fr 2 0.64 0.56 42738 43040 complement fr 2 0.60 0.15 42738 42977 complement fr 2 0.64 0.17 42738 42938 complement fr 2 0.66 0.57 43541 44164 direct fr 2 0.63 0.22 43646 44164 direct fr 2 0.73 0.67 43766 44164 direct fr 2 0.67 0.03 43814 44164 direct fr 2 0.64 0.66 44167 45024 direct fr 1 0.80 0.75 44200 45024 direct fr 1 0.81 0.72 44227 45024 direct fr 1 0.81 0.07 44260 45024 direct fr 1 0.80 0.23 45569 45955 direct fr 2 0.54 0.27 45596 45955 direct fr 2 0.56 0.16 45650 45955 direct fr 2 0.54 0.58 45698 45955 direct fr 2 0.52 0.09 46020 46502 direct fr 3 0.52 0.01 46077 46502 direct fr 3 0.59 0.07 46275 46502 direct fr 3 0.79 0.22 46296 46502 direct fr 3 0.78 0.18 46371 46502 direct fr 3 0.68 0.82 46503 47426 direct fr 3 0.52 0.24 46563 47426 direct fr 3 0.55 0.42 46626 47426 direct fr 3 0.53 0.39 46659 47426 direct fr 3 0.51 0.16 47419 47802 direct fr 1 0.62 0.29 47452 47802 direct fr 1 0.68 0.77 47494 47802 direct fr 1 0.70 0.15 47539 47802 direct fr 1 0.67 0.57 47575 47802 direct fr 1 0.63 0.11 47786 49063 direct fr 2 0.84 0.53 47795 49063 direct fr 2 0.84 0.32 47852 49063 direct fr 2 0.84 0.49 47861 49063 direct fr 2 0.84 0.68 47864 49063 direct fr 2 0.84 0.66 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 2 391 direct fr 2 89 733 complement fr 1 389 673 direct fr 2 658 1620 direct fr 1 1484 1894 direct fr 2 1831 2211 direct fr 1 2202 2546 direct fr 3 2544 3161 direct fr 3 3170 3421 direct fr 2 3283 4083 direct fr 1 3872 4384 direct fr 2 4324 4794 direct fr 1 4713 4979 direct fr 3 4843 5337 direct fr 1 5372 5905 direct fr 2 5875 6207 direct fr 1 6171 6533 direct fr 3 6346 6906 direct fr 1 6810 7061 direct fr 3 7174 7575 direct fr 1 7506 7790 direct fr 3 7759 8130 direct fr 1 8158 9306 direct fr 1 9549 10301 direct fr 3 10187 10876 direct fr 2 10845 11150 direct fr 3 11089 11403 complement fr 3 11138 12277 direct fr 2 12279 12758 direct fr 3 12825 13376 direct fr 3 12861 13235 complement fr 2 13443 13892 direct fr 3 13840 15162 direct fr 1 15168 15410 direct fr 3 15275 15679 direct fr 2 15885 17462 direct fr 3 17449 18573 direct fr 1 18560 19093 complement fr 1 19118 19690 complement fr 1 19328 19783 direct fr 2 19764 20162 complement fr 2 20160 20879 complement fr 2 20301 20798 direct fr 3 20896 21642 direct fr 1 21650 22564 direct fr 2 22562 23059 direct fr 2 22978 23412 direct fr 1 23360 23746 direct fr 2 23569 24174 direct fr 1 24164 24706 direct fr 2 24789 25166 direct fr 3 25043 25498 direct fr 2 25496 26494 direct fr 2 26065 31533 direct fr 1 26820 27329 complement fr 2 31506 32366 direct fr 3 32333 34588 direct fr 2 34613 36103 direct fr 2 35780 36067 complement fr 1 36013 36438 direct fr 1 36436 36918 direct fr 1 36870 37364 direct fr 3 37292 38581 direct fr 2 38849 39415 direct fr 2 39655 39963 complement fr 3 40043 40249 complement fr 1 40262 41482 complement fr 1 42738 43202 complement fr 2 43230 43619 complement fr 2 43529 44164 direct fr 2 44107 45024 direct fr 1 45022 45666 direct fr 1 45335 45955 direct fr 2 45993 46502 direct fr 3 46422 46793 complement fr 2 46500 47426 direct fr 3 46791 47402 complement fr 2 47401 47802 direct fr 1 47735 49063 direct fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 2 1 26124 +/- 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