GENEMARK PREDICTIONS Sequence: gi|157149504|ref|NC_009790.1| Escherichia coli E24377A plasmid pETEC_74, complete sequence Sequence file: NC_009790.fna Sequence length: 74224 GC Content: 49.85% 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 -------- -------- ---------- ----- ---- ---- 3 287 direct fr 3 0.85 .... 30 287 direct fr 3 0.85 .... 138 287 direct fr 3 0.77 0.05 1319 1900 complement fr 1 0.79 0.15 1319 1894 complement fr 1 0.80 0.06 1319 1843 complement fr 1 0.85 0.36 1319 1813 complement fr 1 0.86 0.02 1319 1807 complement fr 1 0.86 0.10 3514 4191 direct fr 1 0.56 0.37 3544 4191 direct fr 1 0.59 0.69 3610 4191 direct fr 1 0.60 0.09 3655 4191 direct fr 1 0.60 0.00 3661 4191 direct fr 1 0.62 0.00 3706 4191 direct fr 1 0.66 0.31 3799 4191 direct fr 1 0.80 0.40 3856 4191 direct fr 1 0.81 0.71 3886 4191 direct fr 1 0.79 0.15 4191 4538 direct fr 3 0.80 0.48 4245 4538 direct fr 3 0.78 0.20 4356 4538 direct fr 3 0.66 0.47 4558 6129 direct fr 1 0.92 0.94 4633 6129 direct fr 1 0.94 0.41 4666 6129 direct fr 1 0.94 0.14 6209 6619 direct fr 2 0.64 0.00 6254 6619 direct fr 2 0.72 0.69 6341 6619 direct fr 2 0.75 0.55 6374 6619 direct fr 2 0.72 0.33 6434 6619 direct fr 2 0.68 0.59 6482 6619 direct fr 2 0.66 0.30 6577 6828 direct fr 1 0.61 0.18 6643 6828 direct fr 1 0.75 0.46 6730 6828 direct fr 1 0.64 0.01 7009 7182 complement fr 3 0.77 0.55 7009 7098 complement fr 3 0.64 0.27 7137 7502 complement fr 2 0.65 0.39 7137 7433 complement fr 2 0.72 0.29 7779 8729 complement fr 2 0.73 0.01 7779 8678 complement fr 2 0.77 0.00 7779 8633 complement fr 2 0.82 0.52 7779 8603 complement fr 2 0.84 0.95 7779 8582 complement fr 2 0.83 0.28 7779 8552 complement fr 2 0.83 0.01 8593 9912 direct fr 1 0.85 0.77 8644 9912 direct fr 1 0.86 0.15 8659 9912 direct fr 1 0.86 0.02 8665 9912 direct fr 1 0.86 0.02 9967 10401 direct fr 1 0.84 0.81 10003 10401 direct fr 1 0.86 0.38 10072 10401 direct fr 1 0.83 0.02 10075 10401 direct fr 1 0.83 0.02 10398 11117 direct fr 3 0.86 0.55 10461 11117 direct fr 3 0.89 0.15 10584 11117 direct fr 3 0.90 0.82 10647 11117 direct fr 3 0.92 0.01 10722 11117 direct fr 3 0.91 0.83 11971 12297 direct fr 1 0.80 0.16 12022 12297 direct fr 1 0.84 0.64 12294 12776 direct fr 3 0.84 0.96 12297 12776 direct fr 3 0.84 0.91 12486 12776 direct fr 3 0.81 0.18 13383 14891 direct fr 3 0.89 0.61 13533 14891 direct fr 3 0.91 0.77 13545 14891 direct fr 3 0.90 0.82 13710 14891 direct fr 3 0.93 0.22 15008 15454 direct fr 2 0.84 0.58 15026 15454 direct fr 2 0.83 0.05 15044 15454 direct fr 2 0.83 0.06 15818 16615 complement fr 1 0.92 0.99 15818 16612 complement fr 1 0.92 0.99 15818 16576 complement fr 1 0.92 0.03 16612 17784 complement fr 3 0.85 0.10 16612 17760 complement fr 3 0.87 0.55 16612 17748 complement fr 3 0.87 0.78 16612 17631 complement fr 3 0.88 0.38 16612 17610 complement fr 3 0.88 0.27 18516 19487 complement fr 2 0.83 0.16 18516 19472 complement fr 2 0.83 0.00 18516 19442 complement fr 2 0.85 0.06 18516 19418 complement fr 2 0.86 0.56 18516 19271 complement fr 2 0.87 0.03 18516 19142 complement fr 2 0.86 0.06 20027 20914 complement fr 1 0.52 0.63 20027 20911 complement fr 1 0.52 0.45 20027 20881 complement fr 1 0.53 0.46 20998 22173 complement fr 3 0.62 0.25 20998 22164 complement fr 3 0.63 0.41 20998 22155 complement fr 3 0.63 0.56 20998 22116 complement fr 3 0.63 0.56 20998 21957 complement fr 3 0.62 0.33 20998 21897 complement fr 3 0.60 0.40 22697 23143 complement fr 1 0.80 0.44 22697 23125 complement fr 1 0.80 0.05 22697 23107 complement fr 1 0.79 0.05 23260 24768 complement fr 3 0.89 0.60 23260 24618 complement fr 3 0.90 0.74 23260 24606 complement fr 3 0.90 0.78 23260 24441 complement fr 3 0.92 0.25 25375 25857 complement fr 3 0.82 0.97 25375 25854 complement fr 3 0.82 0.85 25375 25665 complement fr 3 0.78 0.20 25854 26180 complement fr 2 0.79 0.21 25854 26129 complement fr 2 0.77 0.56 27397 28182 direct fr 1 0.83 0.70 27433 28182 direct fr 1 0.87 0.28 27568 28182 direct fr 1 0.95 0.02 27598 28182 direct fr 1 0.94 0.28 27601 28182 direct fr 1 0.94 0.18 28179 28370 direct fr 3 0.64 0.89 28227 28370 direct fr 3 0.57 0.11 29643 31004 direct fr 3 0.90 0.04 29664 31004 direct fr 3 0.90 0.44 29691 31004 direct fr 3 0.90 0.92 31051 31614 direct fr 1 0.83 0.75 31147 31614 direct fr 1 0.81 0.52 31177 31614 direct fr 1 0.79 0.53 31678 31779 direct fr 1 0.53 0.14 32431 32727 direct fr 1 0.58 0.02 32509 32727 direct fr 1 0.69 0.09 32578 32727 direct fr 1 0.66 0.90 32838 33659 direct fr 3 0.52 0.07 32910 33659 direct fr 3 0.56 0.06 33084 33659 direct fr 3 0.53 0.18 33219 33659 direct fr 3 0.54 0.15 33300 33659 direct fr 3 0.52 0.12 33956 34273 complement fr 1 0.53 0.80 33956 34195 complement fr 1 0.53 0.02 34347 35144 complement fr 2 0.92 0.99 34347 35141 complement fr 2 0.92 0.99 34347 35105 complement fr 2 0.92 0.03 35141 36313 complement fr 1 0.84 0.10 35141 36289 complement fr 1 0.86 0.55 35141 36277 complement fr 1 0.86 0.78 35141 36160 complement fr 1 0.88 0.38 35141 36139 complement fr 1 0.87 0.27 35141 36124 complement fr 1 0.87 0.26 38653 40191 complement fr 3 0.92 0.75 38653 40044 complement fr 3 0.92 0.41 38653 39996 complement fr 3 0.92 0.10 38653 39942 complement fr 3 0.92 0.38 40241 40588 complement fr 1 0.63 0.74 40241 40534 complement fr 1 0.56 0.10 40241 40474 complement fr 1 0.61 0.01 41065 41256 complement fr 3 0.51 0.21 41065 41178 complement fr 3 0.52 0.03 41744 42154 direct fr 2 0.63 0.00 41789 42154 direct fr 2 0.71 0.69 41876 42154 direct fr 2 0.76 0.55 41909 42154 direct fr 2 0.73 0.33 41969 42154 direct fr 2 0.69 0.36 42017 42154 direct fr 2 0.66 0.51 42112 43023 direct fr 1 0.82 0.11 42178 43023 direct fr 1 0.87 0.40 42265 43023 direct fr 1 0.87 0.01 42361 43023 direct fr 1 0.85 0.03 42397 43023 direct fr 1 0.85 0.04 43189 43461 direct fr 1 0.52 0.01 43297 43461 direct fr 1 0.68 0.33 43339 43461 direct fr 1 0.64 0.52 43360 43461 direct fr 1 0.56 0.17 43488 43883 direct fr 3 0.87 0.89 43668 43883 direct fr 3 0.80 0.29 43707 43883 direct fr 3 0.76 0.04 44240 44917 direct fr 2 0.58 0.37 44270 44917 direct fr 2 0.61 0.69 44336 44917 direct fr 2 0.61 0.09 44381 44917 direct fr 2 0.63 0.00 44387 44917 direct fr 2 0.63 0.00 44432 44917 direct fr 2 0.69 0.31 44525 44917 direct fr 2 0.83 0.40 44582 44917 direct fr 2 0.84 0.71 44612 44917 direct fr 2 0.83 0.15 44917 45264 direct fr 1 0.75 0.48 44971 45264 direct fr 1 0.72 0.20 45082 45264 direct fr 1 0.58 0.47 45172 45264 direct fr 1 0.51 0.18 45284 46855 direct fr 2 0.93 0.94 45359 46855 direct fr 2 0.94 0.41 45392 46855 direct fr 2 0.94 0.14 47113 47406 complement fr 3 0.79 0.22 47113 47331 complement fr 3 0.72 0.01 47113 47322 complement fr 3 0.71 0.04 47535 47810 complement fr 2 0.52 0.00 47535 47762 complement fr 2 0.61 0.88 47535 47759 complement fr 2 0.61 0.66 48269 48409 direct fr 2 0.61 0.32 51913 53406 direct fr 1 0.51 0.09 51922 53406 direct fr 1 0.51 0.04 52033 53406 direct fr 1 0.54 0.01 52069 53406 direct fr 1 0.56 0.15 52087 53406 direct fr 1 0.56 0.13 52093 53406 direct fr 1 0.57 0.14 52228 53406 direct fr 1 0.60 0.06 52348 53406 direct fr 1 0.63 0.45 52474 53406 direct fr 1 0.61 0.35 52534 53406 direct fr 1 0.60 0.34 55821 56462 complement fr 2 0.69 0.37 55821 56399 complement fr 2 0.71 0.41 55821 56294 complement fr 2 0.65 0.01 55821 56099 complement fr 2 0.63 0.06 55821 56078 complement fr 2 0.66 0.71 55821 56063 complement fr 2 0.68 0.70 55821 56054 complement fr 2 0.68 0.28 55821 55940 complement fr 2 0.52 0.30 56792 57505 complement fr 1 0.75 0.57 56792 57478 complement fr 1 0.79 0.92 56792 57472 complement fr 1 0.79 0.95 56792 57430 complement fr 1 0.79 0.06 56792 57388 complement fr 1 0.78 0.30 56792 57337 complement fr 1 0.76 0.00 57506 57832 complement fr 1 0.72 0.16 57506 57811 complement fr 1 0.78 0.44 57506 57760 complement fr 1 0.82 0.43 57506 57718 complement fr 1 0.78 0.41 57506 57715 complement fr 1 0.78 0.27 57813 58061 complement fr 2 0.54 0.01 57813 58043 complement fr 2 0.59 0.09 57813 58031 complement fr 2 0.62 0.62 57813 57938 complement fr 2 0.64 0.50 58476 58733 direct fr 3 0.69 0.95 58491 58733 direct fr 3 0.75 0.87 58569 58733 direct fr 3 0.72 0.78 58605 58733 direct fr 3 0.65 0.27 58733 59263 direct fr 2 0.82 0.41 58772 59263 direct fr 2 0.87 0.97 58781 59263 direct fr 2 0.89 0.52 58817 59263 direct fr 2 0.88 0.09 58841 59263 direct fr 2 0.88 0.68 62718 63098 direct fr 3 0.65 0.23 62745 63098 direct fr 3 0.66 0.93 62748 63098 direct fr 3 0.66 0.87 62751 63098 direct fr 3 0.66 0.89 63467 63652 complement fr 1 0.60 0.03 63467 63622 complement fr 1 0.52 0.70 63830 64507 direct fr 2 0.64 0.27 63947 64507 direct fr 2 0.59 0.38 64040 64507 direct fr 2 0.51 0.08 64360 64980 direct fr 1 0.75 0.99 64372 64980 direct fr 1 0.76 1.00 64375 64980 direct fr 1 0.76 1.00 64558 64980 direct fr 1 0.70 0.09 64940 65209 complement fr 1 0.63 0.51 64940 65092 complement fr 1 0.55 0.01 65257 66795 complement fr 3 0.92 0.75 65257 66648 complement fr 3 0.92 0.41 65257 66600 complement fr 3 0.92 0.10 65257 66546 complement fr 3 0.92 0.38 66845 67192 complement fr 1 0.63 0.74 66845 67138 complement fr 1 0.56 0.10 66845 67078 complement fr 1 0.61 0.01 67898 68257 direct fr 2 0.68 0.02 67967 68257 direct fr 2 0.81 0.69 67982 68257 direct fr 2 0.83 0.72 68042 68257 direct fr 2 0.80 0.03 68051 68257 direct fr 2 0.80 0.06 68259 68564 direct fr 3 0.69 0.10 68358 68564 direct fr 3 0.72 0.08 68364 68564 direct fr 3 0.72 0.01 68418 68564 direct fr 3 0.64 0.47 68584 69147 direct fr 1 0.75 0.12 68689 69147 direct fr 1 0.82 0.24 68737 69147 direct fr 1 0.81 0.22 68797 69147 direct fr 1 0.80 0.42 69194 69430 direct fr 2 0.51 0.24 69281 69430 direct fr 2 0.55 0.09 69332 69430 direct fr 2 0.53 0.83 69514 71505 direct fr 1 0.94 0.34 69529 71505 direct fr 1 0.94 0.33 69625 71505 direct fr 1 0.94 0.23 71532 71915 direct fr 3 0.79 0.23 71538 71915 direct fr 3 0.79 0.40 71598 71915 direct fr 3 0.80 0.05 73642 74226 direct fr 1 0.85 0.47 73654 74226 direct fr 1 0.86 0.10 73705 74226 direct fr 1 0.95 0.86 73756 74226 direct fr 1 0.95 0.04 73768 74226 direct fr 1 0.94 0.01 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 287 direct fr 3 605 853 complement fr 1 945 1169 direct fr 3 1319 1921 complement fr 1 1632 1985 complement fr 2 2146 3345 direct fr 1 3475 4191 direct fr 1 3563 3784 complement fr 1 4131 4538 direct fr 3 4546 6129 direct fr 1 6206 6619 direct fr 2 6556 6828 direct fr 1 7009 7275 complement fr 3 7137 7529 complement fr 2 7779 8759 complement fr 2 8560 9912 direct fr 1 9913 10401 direct fr 1 10359 11117 direct fr 3 11540 11803 direct fr 2 11917 12297 direct fr 1 12228 12776 direct fr 3 12703 13104 complement fr 3 13359 14891 direct fr 3 14810 14953 direct fr 2 14951 15454 direct fr 2 15818 16627 complement fr 1 16612 17814 complement fr 3 18277 18579 complement fr 3 18516 19619 complement fr 2 20027 21004 complement fr 1 20998 22179 complement fr 3 22630 22815 complement fr 3 22697 23200 complement fr 1 23260 24792 complement fr 3 25047 25448 direct fr 3 25375 25923 complement fr 3 25854 26234 complement fr 2 26143 26700 direct fr 1 27262 27597 complement fr 3 27379 28182 direct fr 1 28107 28370 direct fr 3 28349 29119 complement fr 1 28516 28845 complement fr 3 28916 29137 direct fr 2 29379 29651 complement fr 2 29592 31004 direct fr 3 30976 31614 direct fr 1 31595 32134 complement fr 1 31615 31779 direct fr 1 31762 32142 complement fr 3 32186 32407 direct fr 2 32395 32727 direct fr 1 32787 33659 direct fr 3 33956 34294 complement fr 1 34347 35156 complement fr 2 35141 36343 complement fr 1 38617 38979 direct fr 1 38653 40254 complement fr 3 40241 40675 complement fr 1 40349 40579 direct fr 2 40585 40992 complement fr 3 41065 41289 complement fr 3 41741 42154 direct fr 2 42091 43023 direct fr 1 43177 43461 direct fr 1 43416 43883 direct fr 3 44201 44917 direct fr 2 44857 45264 direct fr 1 45272 46855 direct fr 2 46837 47043 direct fr 1 47113 47481 complement fr 3 47535 47822 complement fr 2 48128 48409 direct fr 2 49204 53406 direct fr 1 55821 56477 complement fr 2 56605 56808 direct fr 1 56792 57508 complement fr 1 57506 57850 complement fr 1 57813 58085 complement fr 2 58434 58733 direct fr 3 58724 59263 direct fr 2 59504 60349 direct fr 2 60343 61440 direct fr 1 61424 62395 direct fr 2 62454 63098 direct fr 3 63025 63405 direct fr 1 63467 63715 complement fr 1 63788 64507 direct fr 2 64333 64980 direct fr 1 64940 65263 complement fr 1 65257 66858 complement fr 3 66845 67279 complement fr 1 66953 67183 direct fr 2 67189 67596 complement fr 3 67880 68257 direct fr 2 68241 68564 direct fr 3 68557 69147 direct fr 1 69064 69324 complement fr 3 69131 69430 direct fr 2 69343 71505 direct fr 1 71397 71915 direct fr 3 72077 72391 direct fr 2 72802 72951 complement fr 3 73639 74226 direct fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 1 16692 +/- 11 bp (complement) 1 3 22752 +/- 11 bp (complement) 3 1 28668 +/- 11 bp (complement) 1 2 35220 +/- 11 bp (complement) 2 1 64356 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Mon Sep 17 10:25:27 2007