GENEMARK PREDICTIONS Sequence: gi|29377895|ref|NC_004671.1| Enterococcus faecalis V583 plasmid pTEF2, complete sequence Sequence file: NC_004671.fna Sequence length: 57660 GC Content: 33.90% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: - Matrix author: - 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 -------- -------- ---------- ----- ---- ---- 100 1110 direct fr 1 0.88 0.80 196 1110 direct fr 1 0.91 0.35 226 1110 direct fr 1 0.91 0.16 316 1110 direct fr 1 0.90 0.05 1280 2437 direct fr 2 0.80 0.69 1562 2437 direct fr 2 0.78 0.21 1592 2437 direct fr 2 0.78 0.04 1679 2437 direct fr 2 0.78 0.83 2486 4075 direct fr 2 0.95 0.75 2621 4075 direct fr 2 0.96 0.00 2657 4075 direct fr 2 0.96 0.02 2756 4075 direct fr 2 0.96 0.14 4101 4565 complement fr 2 0.85 0.53 4101 4334 complement fr 2 0.72 0.01 4101 4289 complement fr 2 0.66 0.15 5822 6202 direct fr 2 0.75 0.59 5963 6202 direct fr 2 0.74 0.28 5987 6202 direct fr 2 0.72 0.10 6776 6964 direct fr 2 0.54 0.75 6812 6964 direct fr 2 0.66 0.93 6824 6964 direct fr 2 0.71 0.24 7044 9767 direct fr 3 0.97 0.26 7092 9767 direct fr 3 0.98 0.69 7227 9767 direct fr 3 0.98 0.00 7380 9767 direct fr 3 0.98 0.00 9960 13877 direct fr 3 0.97 0.85 9996 13877 direct fr 3 0.98 0.21 10047 13877 direct fr 3 0.99 0.78 10122 13877 direct fr 3 0.99 0.00 10779 13877 direct fr 3 0.98 0.11 13975 14295 direct fr 1 0.85 0.09 14071 14295 direct fr 1 0.79 0.09 14077 14295 direct fr 1 0.78 0.04 14323 15180 direct fr 1 0.85 0.36 14482 15180 direct fr 1 0.87 0.03 14728 15180 direct fr 1 0.80 0.00 15222 16121 direct fr 3 0.85 0.11 15396 16121 direct fr 3 0.89 0.14 15429 16121 direct fr 3 0.89 0.03 15468 16121 direct fr 3 0.89 0.87 16141 16575 direct fr 1 0.78 0.43 16255 16575 direct fr 1 0.83 0.00 16622 16849 direct fr 2 0.71 0.89 16691 16849 direct fr 2 0.82 0.33 16700 16849 direct fr 2 0.80 0.15 16721 16849 direct fr 2 0.77 0.10 16863 17159 direct fr 3 0.64 0.99 16881 17159 direct fr 3 0.66 0.99 17022 17159 direct fr 3 0.50 0.00 17174 17974 direct fr 2 0.85 0.90 17249 17974 direct fr 2 0.87 0.00 17309 17974 direct fr 2 0.86 0.81 17420 17974 direct fr 2 0.83 0.74 18283 20673 direct fr 1 0.95 0.51 18436 20673 direct fr 1 0.97 0.53 18484 20673 direct fr 1 0.97 0.35 18529 20673 direct fr 1 0.97 0.00 20685 23300 direct fr 3 0.94 0.96 21021 23300 direct fr 3 0.95 0.02 21111 23300 direct fr 3 0.95 0.00 21150 23300 direct fr 3 0.95 0.02 23324 23950 direct fr 2 0.91 0.57 23333 23950 direct fr 2 0.93 0.68 23393 23950 direct fr 2 0.93 0.66 23570 23950 direct fr 2 0.90 0.06 23928 24182 direct fr 3 0.71 0.92 23937 24182 direct fr 3 0.75 0.87 23982 24182 direct fr 3 0.83 0.05 24139 24774 direct fr 1 0.83 0.39 24154 24774 direct fr 1 0.84 0.74 24157 24774 direct fr 1 0.86 0.74 24166 24774 direct fr 1 0.86 0.57 24265 24774 direct fr 1 0.91 0.52 24607 24774 direct fr 1 0.74 0.00 24934 25419 direct fr 1 0.80 0.80 25003 25419 direct fr 1 0.88 0.19 25090 25419 direct fr 1 0.86 0.42 25135 25419 direct fr 1 0.84 0.29 25416 27248 direct fr 3 0.89 0.32 25419 27248 direct fr 3 0.89 0.34 25476 27248 direct fr 3 0.91 0.67 25629 27248 direct fr 3 0.91 0.28 25662 27248 direct fr 3 0.92 0.58 25668 27248 direct fr 3 0.92 0.53 27298 29457 direct fr 1 0.93 1.00 27304 29457 direct fr 1 0.94 1.00 27328 29457 direct fr 1 0.95 0.73 27358 29457 direct fr 1 0.95 0.00 27511 29457 direct fr 1 0.96 0.18 29490 29762 direct fr 3 0.93 0.89 29604 29762 direct fr 3 0.89 0.26 30008 30364 direct fr 2 0.72 0.29 30230 30364 direct fr 2 0.66 0.10 30365 32050 direct fr 2 0.91 0.43 30368 32050 direct fr 2 0.91 0.38 30503 32050 direct fr 2 0.94 0.32 30524 32050 direct fr 2 0.94 0.44 30554 32050 direct fr 2 0.94 0.01 32254 32433 direct fr 1 0.75 0.92 32950 34293 complement fr 3 0.81 0.58 32950 34287 complement fr 3 0.81 0.50 32950 33903 complement fr 3 0.91 0.15 32950 33663 complement fr 3 0.88 0.29 32950 33585 complement fr 3 0.87 0.15 34284 35060 complement fr 2 0.87 0.65 34284 34724 complement fr 2 0.88 0.02 34284 34646 complement fr 2 0.86 0.22 34284 34520 complement fr 2 0.79 0.27 35203 35751 complement fr 3 0.72 0.98 35203 35577 complement fr 3 0.67 0.37 35203 35475 complement fr 3 0.79 0.75 35775 35966 complement fr 2 0.72 0.39 35775 35948 complement fr 2 0.81 0.85 35775 35840 complement fr 2 0.81 0.05 35951 36136 complement fr 1 0.62 0.96 36142 36591 complement fr 3 0.76 0.58 36142 36363 complement fr 3 0.73 0.50 36142 36288 complement fr 3 0.61 0.07 37179 37409 complement fr 2 0.64 0.99 37179 37361 complement fr 2 0.69 0.01 37566 37958 direct fr 3 0.85 0.02 37572 37958 direct fr 3 0.85 0.03 37590 37958 direct fr 3 0.84 0.20 38024 38476 direct fr 2 0.81 0.87 38036 38476 direct fr 2 0.83 0.80 38177 38476 direct fr 2 0.90 0.02 38243 38476 direct fr 2 0.88 0.01 38297 38476 direct fr 2 0.84 0.17 38654 39232 direct fr 2 0.83 0.81 38843 39232 direct fr 2 0.87 0.10 39053 39232 direct fr 2 0.74 0.41 39062 39232 direct fr 2 0.73 0.12 39868 41328 direct fr 1 0.61 0.89 39892 41328 direct fr 1 0.62 0.84 39928 41328 direct fr 1 0.62 0.00 39937 41328 direct fr 1 0.62 0.11 40090 41328 direct fr 1 0.59 0.16 42132 43472 direct fr 3 0.73 0.91 42639 43472 direct fr 3 0.63 0.02 42906 43472 direct fr 3 0.62 0.89 43023 43472 direct fr 3 0.62 0.16 43146 43472 direct fr 3 0.78 0.60 43158 43472 direct fr 3 0.80 0.09 43469 45571 direct fr 2 0.63 0.52 43490 45571 direct fr 2 0.64 0.62 43532 45571 direct fr 2 0.65 0.01 43598 45571 direct fr 2 0.65 0.01 43622 45571 direct fr 2 0.64 0.01 43709 45571 direct fr 2 0.63 0.83 46844 48016 complement fr 1 0.80 0.65 46844 47905 complement fr 1 0.80 0.29 46844 47743 complement fr 1 0.76 0.16 46844 47707 complement fr 1 0.75 0.12 48079 48453 direct fr 1 0.66 0.11 48259 48453 direct fr 1 0.81 0.80 48454 48858 direct fr 1 0.71 0.82 48463 48858 direct fr 1 0.72 0.49 48866 49360 direct fr 2 0.78 0.51 49378 49629 direct fr 1 0.63 0.24 49405 49629 direct fr 1 0.72 0.99 49483 49629 direct fr 1 0.67 0.00 49507 49629 direct fr 1 0.62 0.07 49837 50172 direct fr 1 0.74 0.96 49882 50172 direct fr 1 0.83 0.04 49906 50172 direct fr 1 0.83 0.04 49909 50172 direct fr 1 0.82 0.03 50325 50930 direct fr 3 0.88 0.97 50358 50930 direct fr 3 0.93 0.29 50463 50930 direct fr 3 0.91 0.00 50466 50930 direct fr 3 0.91 0.00 50985 52877 direct fr 3 0.70 0.92 51111 52877 direct fr 3 0.71 0.07 51177 52877 direct fr 3 0.71 0.03 51222 52877 direct fr 3 0.72 0.18 51270 52877 direct fr 3 0.74 0.01 51642 52877 direct fr 3 0.77 0.25 51879 52877 direct fr 3 0.77 0.88 53404 54720 direct fr 1 0.86 0.17 53515 54720 direct fr 1 0.90 0.16 53527 54720 direct fr 1 0.90 0.14 53557 54720 direct fr 1 0.89 0.02 54683 55231 direct fr 2 0.86 0.92 54695 55231 direct fr 2 0.88 0.89 54725 55231 direct fr 2 0.94 0.90 54935 55231 direct fr 2 0.92 0.75 55010 55231 direct fr 2 0.89 0.46 56369 57151 direct fr 2 0.82 0.32 56486 57151 direct fr 2 0.89 0.71 56951 57151 direct fr 2 0.75 0.32 57144 57500 direct fr 3 0.72 0.61 57270 57500 direct fr 3 0.80 0.02 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 76 1110 direct fr 1 1202 2437 direct fr 2 2071 2292 complement fr 3 2456 4075 direct fr 2 4101 5111 complement fr 2 5756 6202 direct fr 2 6761 6964 direct fr 2 7008 9767 direct fr 3 9954 13877 direct fr 3 13879 14295 direct fr 1 14293 15180 direct fr 1 15210 16121 direct fr 3 16126 16575 direct fr 1 16604 16849 direct fr 2 16830 17159 direct fr 3 17153 17974 direct fr 2 17961 18329 direct fr 3 18265 20673 direct fr 1 20649 23300 direct fr 3 23234 23950 direct fr 2 23901 24182 direct fr 3 24136 24774 direct fr 1 24916 25419 direct fr 1 25340 25627 direct fr 2 25374 27248 direct fr 3 27277 29457 direct fr 1 29412 29762 direct fr 3 29987 30364 direct fr 2 30362 32050 direct fr 2 32035 32433 direct fr 1 32950 34305 complement fr 3 34284 35081 complement fr 2 35203 35805 complement fr 3 35775 35969 complement fr 2 35951 36163 complement fr 1 36142 36606 complement fr 3 37179 37424 complement fr 2 37443 37958 direct fr 3 38021 38476 direct fr 2 38484 38642 direct fr 3 38648 39232 direct fr 2 39312 39644 direct fr 3 39847 41328 direct fr 1 41847 42116 direct fr 3 42117 43472 direct fr 3 43463 45571 direct fr 2 45559 46860 direct fr 1 46844 48049 complement fr 1 47535 47729 direct fr 3 48064 48453 direct fr 1 48451 48858 direct fr 1 48848 49360 direct fr 2 49372 49629 direct fr 1 49828 50172 direct fr 1 50295 50930 direct fr 3 50976 52877 direct fr 3 53380 54720 direct fr 1 54677 55231 direct fr 2 55792 56115 direct fr 1 56345 57151 direct fr 2 57141 57500 direct fr 3 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 1 27276 +/- 11 bp (direct) 2 3 35760 +/- 11 bp (complement) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 16:03:09 2007