GENEMARK PREDICTIONS Sequence: gi|108793532|ref|NC_008120.1| Yersinia pestis Antiqua plasmid pMT, complete sequence Sequence file: NC_008120.fna Sequence length: 96471 GC Content: 50.24% 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 -------- -------- ---------- ----- ---- ---- 89 1111 direct fr 2 0.77 .... 110 1111 direct fr 2 0.78 0.28 140 1111 direct fr 2 0.80 0.20 368 1111 direct fr 2 0.82 0.07 458 1111 direct fr 2 0.80 0.47 1108 1890 direct fr 1 0.77 0.72 1111 1890 direct fr 1 0.77 0.64 1114 1890 direct fr 1 0.77 0.48 1138 1890 direct fr 1 0.79 0.28 1228 1890 direct fr 1 0.82 0.81 1291 1890 direct fr 1 0.80 0.34 1303 1890 direct fr 1 0.79 0.11 2024 2632 complement fr 1 0.78 0.36 2024 2620 complement fr 1 0.79 0.80 2024 2593 complement fr 1 0.81 0.09 2024 2380 complement fr 1 0.80 0.18 2024 2230 complement fr 1 0.66 0.01 2934 5870 complement fr 2 0.56 0.05 2934 5822 complement fr 2 0.57 0.04 2934 5747 complement fr 2 0.57 0.77 2934 5720 complement fr 2 0.57 0.17 2934 5546 complement fr 2 0.54 0.00 5903 6535 complement fr 1 0.63 0.73 5903 6520 complement fr 1 0.65 0.52 5903 6481 complement fr 1 0.68 0.01 5903 6427 complement fr 1 0.73 0.02 5903 6049 complement fr 1 0.57 0.22 5903 6043 complement fr 1 0.54 0.19 6538 11169 complement fr 3 0.93 0.97 6538 11052 complement fr 3 0.93 0.03 6538 11004 complement fr 3 0.93 0.03 6538 10887 complement fr 3 0.93 0.02 11191 11778 complement fr 3 0.64 0.15 11191 11760 complement fr 3 0.67 0.06 11191 11742 complement fr 3 0.68 0.25 11191 11706 complement fr 3 0.68 0.65 11191 11643 complement fr 3 0.64 0.01 11191 11631 complement fr 3 0.63 0.01 11766 12563 complement fr 2 0.83 0.32 11766 12524 complement fr 2 0.84 0.90 11766 12464 complement fr 2 0.82 0.06 11766 12434 complement fr 2 0.82 0.21 12556 13287 complement fr 3 0.84 0.78 12556 13254 complement fr 3 0.88 0.24 12556 13188 complement fr 3 0.88 0.36 12556 13131 complement fr 3 0.87 0.16 13344 13679 complement fr 2 0.81 0.49 13344 13628 complement fr 2 0.79 0.29 13344 13616 complement fr 2 0.78 0.06 13721 15244 complement fr 1 0.94 0.85 13721 15157 complement fr 1 0.94 0.03 13721 15094 complement fr 1 0.94 0.01 15254 18298 complement fr 1 0.97 0.92 15254 18064 complement fr 1 0.97 0.01 15254 17842 complement fr 1 0.97 0.05 15254 17833 complement fr 1 0.97 0.01 18306 18575 complement fr 2 0.78 0.15 18306 18539 complement fr 2 0.75 0.58 18306 18530 complement fr 2 0.75 0.81 18656 18973 complement fr 1 0.76 0.94 18656 18889 complement fr 1 0.85 0.04 18656 18856 complement fr 1 0.82 0.23 18656 18832 complement fr 1 0.80 0.10 19033 19779 complement fr 3 0.87 0.21 19033 19734 complement fr 3 0.91 0.60 19033 19572 complement fr 3 0.89 0.01 19033 19560 complement fr 3 0.89 0.05 19854 20237 complement fr 2 0.78 0.97 19854 20210 complement fr 2 0.79 0.42 19854 20159 complement fr 2 0.76 0.10 19854 20147 complement fr 2 0.75 0.46 20239 20712 complement fr 3 0.75 0.68 20239 20619 complement fr 3 0.76 0.58 20239 20577 complement fr 3 0.72 0.00 20239 20424 complement fr 3 0.50 0.01 20703 21152 complement fr 2 0.62 0.57 20703 21047 complement fr 2 0.80 0.34 20703 20846 complement fr 2 0.61 0.03 21145 21978 complement fr 3 0.91 0.97 21145 21825 complement fr 3 0.94 0.09 21145 21807 complement fr 3 0.94 0.04 21145 21741 complement fr 3 0.93 0.02 21978 22424 complement fr 2 0.73 0.00 21978 22412 complement fr 2 0.75 0.00 21978 22277 complement fr 2 0.96 0.75 21978 22169 complement fr 2 0.95 0.04 21978 22163 complement fr 2 0.95 0.02 22456 23118 complement fr 3 0.80 0.78 22456 23103 complement fr 3 0.81 0.37 22456 23061 complement fr 3 0.84 0.19 22456 22923 complement fr 3 0.88 0.15 22456 22887 complement fr 3 0.87 0.27 23193 24068 complement fr 2 0.91 0.90 23193 24011 complement fr 2 0.93 0.01 23193 23960 complement fr 2 0.93 0.26 23193 23891 complement fr 2 0.92 0.02 24095 24928 complement fr 1 0.91 0.98 24095 24913 complement fr 1 0.92 0.99 24095 24907 complement fr 1 0.93 0.99 24095 24889 complement fr 1 0.94 0.26 24095 24748 complement fr 1 0.93 0.00 24951 26540 complement fr 2 0.86 0.17 24951 26525 complement fr 2 0.86 0.56 24951 26492 complement fr 2 0.88 0.27 24951 26315 complement fr 2 0.87 0.00 24951 26189 complement fr 2 0.87 0.86 26559 27815 complement fr 2 0.89 0.66 26559 27767 complement fr 2 0.91 0.01 26559 27731 complement fr 2 0.93 0.03 26559 27620 complement fr 2 0.94 0.20 26559 27542 complement fr 2 0.93 0.01 26559 27533 complement fr 2 0.93 0.01 27818 28459 complement fr 1 0.92 0.92 27818 28279 complement fr 1 0.92 0.42 27818 28270 complement fr 1 0.91 0.33 27818 28267 complement fr 1 0.91 0.11 28655 28921 complement fr 1 0.78 0.93 28655 28828 complement fr 1 0.84 0.22 28655 28798 complement fr 1 0.81 0.01 28655 28774 complement fr 1 0.77 0.03 28931 29830 complement fr 1 0.96 1.00 28931 29821 complement fr 1 0.96 1.00 28931 29752 complement fr 1 0.96 0.01 29827 30081 complement fr 3 0.69 0.92 29827 29949 complement fr 3 0.54 0.27 30074 30772 complement fr 1 0.83 0.00 30074 30712 complement fr 1 0.91 0.57 30074 30673 complement fr 1 0.93 0.46 30074 30661 complement fr 1 0.93 0.24 30074 30577 complement fr 1 0.92 0.00 30709 31410 complement fr 3 0.85 0.13 30709 31377 complement fr 3 0.89 0.88 30709 31320 complement fr 3 0.88 0.10 30709 31164 complement fr 3 0.86 0.04 31377 32075 complement fr 2 0.86 0.50 31377 32057 complement fr 2 0.88 0.97 31377 32051 complement fr 2 0.89 0.93 31377 32030 complement fr 2 0.91 0.68 31377 31853 complement fr 2 0.88 0.58 31377 31817 complement fr 2 0.87 0.49 32140 33699 direct fr 1 0.83 0.35 32200 33699 direct fr 1 0.84 0.12 32221 33699 direct fr 1 0.84 0.08 32236 33699 direct fr 1 0.84 0.04 33702 33980 direct fr 3 0.82 0.35 33843 33980 direct fr 3 0.97 0.02 33849 33980 direct fr 3 0.97 0.01 33912 33980 direct fr 3 0.95 0.19 34040 34462 direct fr 2 0.65 0.06 34109 34462 direct fr 2 0.78 0.53 34184 34462 direct fr 2 0.88 0.30 34190 34462 direct fr 2 0.88 0.41 34205 34462 direct fr 2 0.88 0.05 34431 34994 direct fr 3 0.67 0.05 34467 34994 direct fr 3 0.71 0.83 34533 34994 direct fr 3 0.69 0.04 34548 34994 direct fr 3 0.68 0.00 35317 35967 direct fr 1 0.81 0.91 35464 35967 direct fr 1 0.84 0.14 35602 35967 direct fr 1 0.80 0.02 35686 35967 direct fr 1 0.77 0.30 37056 37625 complement fr 2 0.83 0.76 37056 37607 complement fr 2 0.86 0.96 37056 37586 complement fr 2 0.88 0.35 37056 37511 complement fr 2 0.85 0.02 37056 37400 complement fr 2 0.82 0.07 37638 38384 complement fr 2 0.52 0.14 37638 38348 complement fr 2 0.55 0.02 37638 38339 complement fr 2 0.55 0.04 37638 38336 complement fr 2 0.55 0.04 37638 38207 complement fr 2 0.59 0.14 37638 38192 complement fr 2 0.60 0.20 37638 38051 complement fr 2 0.62 0.14 37638 37979 complement fr 2 0.55 0.12 37638 37805 complement fr 2 0.67 0.13 37818 37922 direct fr 3 0.51 0.42 37821 37922 direct fr 3 0.51 0.10 38374 40290 complement fr 3 0.93 0.76 38374 40257 complement fr 3 0.95 0.97 38374 40212 complement fr 3 0.95 0.01 38374 40143 complement fr 3 0.95 0.44 40520 41605 complement fr 1 0.89 0.00 40520 41587 complement fr 1 0.91 0.00 40520 41473 complement fr 1 0.94 0.01 40520 41449 complement fr 1 0.93 0.00 40520 41443 complement fr 1 0.93 0.00 42206 43042 direct fr 2 0.61 0.25 42212 43042 direct fr 2 0.61 0.27 42320 43042 direct fr 2 0.60 0.08 42335 43042 direct fr 2 0.59 0.02 42347 43042 direct fr 2 0.58 0.00 43402 44046 complement fr 3 0.61 0.64 43402 43851 complement fr 3 0.60 0.53 43402 43671 complement fr 3 0.59 0.08 43402 43662 complement fr 3 0.62 0.01 43402 43626 complement fr 3 0.63 0.96 43402 43593 complement fr 3 0.60 0.14 44791 45855 direct fr 1 0.79 0.82 44914 45855 direct fr 1 0.80 0.10 44974 45855 direct fr 1 0.80 0.99 44983 45855 direct fr 1 0.79 0.99 46424 46636 complement fr 1 0.63 0.93 46424 46624 complement fr 1 0.66 0.99 46424 46558 complement fr 1 0.58 0.35 46636 46971 complement fr 3 0.85 0.98 46636 46896 complement fr 3 0.81 0.74 46636 46890 complement fr 3 0.81 0.68 47531 47899 complement fr 1 0.87 0.73 47531 47827 complement fr 1 0.84 0.01 47531 47773 complement fr 1 0.81 0.18 48005 49027 direct fr 2 0.77 0.69 48026 49027 direct fr 2 0.78 0.28 48056 49027 direct fr 2 0.80 0.20 48284 49027 direct fr 2 0.82 0.07 48374 49027 direct fr 2 0.80 0.47 49138 49800 direct fr 1 0.83 0.89 49201 49800 direct fr 1 0.81 0.34 49213 49800 direct fr 1 0.81 0.11 50403 51233 complement fr 2 0.88 0.25 50403 51212 complement fr 2 0.91 0.69 50403 51188 complement fr 2 0.93 0.84 50403 51164 complement fr 2 0.93 0.24 50403 51032 complement fr 2 0.92 0.61 51237 51419 complement fr 2 0.54 0.36 51237 51404 complement fr 2 0.56 0.08 51237 51401 complement fr 2 0.56 0.08 51528 52604 complement fr 2 0.95 0.98 51528 52391 complement fr 2 0.95 0.92 51528 52316 complement fr 2 0.95 0.64 52607 52873 complement fr 1 0.76 0.89 52607 52831 complement fr 1 0.86 0.16 52607 52789 complement fr 1 0.83 0.07 52607 52786 complement fr 1 0.82 0.13 52873 53868 complement fr 3 0.86 0.01 52873 53817 complement fr 3 0.90 0.47 52873 53802 complement fr 3 0.91 0.73 52873 53742 complement fr 3 0.93 0.22 52873 53715 complement fr 3 0.92 0.02 52873 53670 complement fr 3 0.92 0.16 53878 54957 complement fr 3 0.91 0.13 53878 54906 complement fr 3 0.94 0.62 53878 54765 complement fr 3 0.93 0.02 53878 54744 complement fr 3 0.93 0.12 55026 55499 complement fr 2 0.81 0.01 55026 55457 complement fr 2 0.87 0.99 55026 55430 complement fr 2 0.86 0.11 55026 55364 complement fr 2 0.83 0.11 56002 56565 direct fr 1 0.74 0.58 56263 56565 direct fr 1 0.67 0.16 56272 56565 direct fr 1 0.66 0.05 56293 56565 direct fr 1 0.63 0.08 56595 57038 complement fr 2 0.85 1.00 56595 57020 complement fr 2 0.86 1.00 56595 56942 complement fr 2 0.83 0.04 56595 56732 complement fr 2 0.59 0.01 57035 60559 complement fr 1 0.94 0.85 57035 60547 complement fr 1 0.94 0.47 57035 60493 complement fr 1 0.95 0.46 57035 60442 complement fr 1 0.95 0.55 57035 60427 complement fr 1 0.95 0.05 60740 61975 complement fr 1 0.90 0.96 60740 61876 complement fr 1 0.95 0.97 60740 61831 complement fr 1 0.94 0.02 60740 61822 complement fr 1 0.94 0.00 62072 63958 complement fr 1 0.87 0.17 62072 63898 complement fr 1 0.89 0.27 62072 63835 complement fr 1 0.89 0.37 62072 63820 complement fr 1 0.88 0.13 63997 64779 complement fr 3 0.77 0.69 63997 64776 complement fr 3 0.78 0.57 63997 64773 complement fr 3 0.78 0.32 63997 64749 complement fr 3 0.80 0.28 63997 64659 complement fr 3 0.81 0.83 63997 64596 complement fr 3 0.79 0.15 63997 64584 complement fr 3 0.79 0.22 64776 65798 complement fr 2 0.75 0.73 64776 65777 complement fr 2 0.77 0.46 64776 65747 complement fr 2 0.78 0.22 64776 65519 complement fr 2 0.80 0.12 64776 65429 complement fr 2 0.78 0.38 65825 66397 complement fr 1 0.73 0.98 65825 66385 complement fr 1 0.75 0.89 65825 66373 complement fr 1 0.74 0.32 65825 66322 complement fr 1 0.71 0.07 66987 67373 direct fr 3 0.83 0.97 67203 67373 direct fr 3 0.76 0.24 67209 67373 direct fr 3 0.76 0.12 67368 67712 complement fr 2 0.51 0.28 67368 67574 complement fr 2 0.58 0.09 67368 67559 complement fr 2 0.64 0.31 67368 67529 complement fr 2 0.59 0.76 69232 69420 complement fr 3 0.51 0.19 69232 69360 complement fr 3 0.54 0.09 74709 75917 direct fr 3 0.89 1.00 74793 75917 direct fr 3 0.90 0.04 75015 75917 direct fr 3 0.89 0.29 75051 75917 direct fr 3 0.88 0.09 76386 77408 direct fr 3 0.71 0.91 76425 77408 direct fr 3 0.72 0.09 76539 77408 direct fr 3 0.70 0.33 76608 77408 direct fr 3 0.72 0.16 76638 77408 direct fr 3 0.71 0.48 77607 77924 complement fr 2 0.66 0.44 77607 77894 complement fr 2 0.64 0.33 77607 77816 complement fr 2 0.50 0.01 82538 82828 direct fr 2 0.54 0.30 82553 82828 direct fr 2 0.57 0.00 82637 82828 direct fr 2 0.58 0.77 82851 83831 complement fr 2 0.79 0.16 82851 83792 complement fr 2 0.82 0.01 82851 83708 complement fr 2 0.88 0.19 82851 83600 complement fr 2 0.88 0.03 82851 83579 complement fr 2 0.88 0.81 82851 83555 complement fr 2 0.88 0.05 83858 84478 complement fr 1 0.58 0.51 83858 84340 complement fr 1 0.60 0.18 83858 84322 complement fr 1 0.58 0.11 83858 84271 complement fr 1 0.59 0.00 85004 85231 complement fr 1 0.63 0.84 85004 85207 complement fr 1 0.70 0.86 86010 86738 direct fr 3 0.53 0.07 86067 86738 direct fr 3 0.50 0.38 86415 86738 direct fr 3 0.53 0.82 86735 87706 direct fr 2 0.67 0.05 86795 87706 direct fr 2 0.70 0.79 86843 87706 direct fr 2 0.70 0.04 86870 87706 direct fr 2 0.71 0.66 86936 87706 direct fr 2 0.70 0.03 88142 89482 direct fr 2 0.51 0.02 88157 89482 direct fr 2 0.51 0.07 88163 89482 direct fr 2 0.51 0.33 88244 89482 direct fr 2 0.54 0.29 88397 89482 direct fr 2 0.54 0.24 88400 89482 direct fr 2 0.54 0.15 88406 89482 direct fr 2 0.54 0.13 89644 89889 complement fr 3 0.61 0.06 89644 89844 complement fr 3 0.67 0.82 89644 89832 complement fr 3 0.66 0.75 89644 89760 complement fr 3 0.56 0.50 90345 91022 direct fr 3 0.62 0.01 90381 91022 direct fr 3 0.65 0.60 90516 91022 direct fr 3 0.71 0.70 90525 91022 direct fr 3 0.71 0.48 90546 91022 direct fr 3 0.69 0.12 91022 91243 direct fr 2 0.64 0.96 91058 91243 direct fr 2 0.70 0.08 91079 91243 direct fr 2 0.68 0.05 91109 91243 direct fr 2 0.60 0.43 91182 91673 direct fr 3 0.71 0.00 91224 91673 direct fr 3 0.77 0.03 91254 91673 direct fr 3 0.83 0.21 91368 91673 direct fr 3 0.89 0.02 91416 91673 direct fr 3 0.87 0.25 91455 91673 direct fr 3 0.84 0.04 91727 92506 direct fr 2 0.71 0.94 91757 92506 direct fr 2 0.73 0.34 91760 92506 direct fr 2 0.73 0.18 91943 92506 direct fr 2 0.80 0.06 92108 92506 direct fr 2 0.81 0.02 92905 93411 direct fr 1 0.79 0.40 92938 93411 direct fr 1 0.79 0.19 93070 93411 direct fr 1 0.86 0.19 93280 93411 direct fr 1 0.67 0.00 94124 94354 direct fr 2 0.79 0.95 94205 94354 direct fr 2 0.86 0.24 94265 94354 direct fr 2 0.77 0.36 94427 96436 direct fr 2 0.92 0.74 94577 96436 direct fr 2 0.93 0.04 94598 96436 direct fr 2 0.93 0.34 94691 96436 direct fr 2 0.92 0.57 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 41 1111 direct fr 2 1030 1890 direct fr 1 2024 2662 complement fr 1 2934 5873 complement fr 2 5903 6547 complement fr 1 6538 11190 complement fr 3 11191 11784 complement fr 3 11766 12599 complement fr 2 12556 13329 complement fr 3 13344 13727 complement fr 2 13721 15256 complement fr 1 15254 18331 complement fr 1 18306 18671 complement fr 2 18656 18979 complement fr 1 19033 19809 complement fr 3 19854 20279 complement fr 2 20239 20814 complement fr 3 20703 21164 complement fr 2 21145 21984 complement fr 3 21978 22427 complement fr 2 22456 23130 complement fr 3 23193 24074 complement fr 2 24095 24946 complement fr 1 24951 26561 complement fr 2 26559 27833 complement fr 2 27818 28513 complement fr 1 28655 28933 complement fr 1 28931 29911 complement fr 1 28940 31081 direct fr 2 29827 30093 complement fr 3 30074 30844 complement fr 1 30709 31443 complement fr 3 31377 32093 complement fr 2 32080 33699 direct fr 1 33690 33980 direct fr 3 34013 34462 direct fr 2 34350 34994 direct fr 3 35269 35967 direct fr 1 36389 36907 complement fr 1 37056 37640 complement fr 2 37638 38438 complement fr 2 37749 37922 direct fr 3 37987 38607 direct fr 1 38374 40425 complement fr 3 40520 41626 complement fr 1 41730 41942 direct fr 3 42122 43042 direct fr 2 43309 43947 direct fr 1 43402 44058 complement fr 3 44773 45855 direct fr 1 44898 45290 complement fr 2 45453 45596 complement fr 2 46424 46657 complement fr 1 46636 47034 complement fr 3 46968 47162 complement fr 2 47188 47490 complement fr 3 47209 47439 direct fr 1 47531 47995 complement fr 1 47957 49027 direct fr 2 49051 49800 direct fr 1 49878 50252 complement fr 2 50403 51239 complement fr 2 51237 51494 complement fr 2 51528 52655 complement fr 2 52607 52888 complement fr 1 52873 53880 complement fr 3 53878 55011 complement fr 3 55026 55523 complement fr 2 55990 56565 direct fr 1 56595 57044 complement fr 2 57035 60568 complement fr 1 59729 60214 direct fr 2 60534 60767 complement fr 2 60740 62029 complement fr 1 62072 63961 complement fr 1 63997 64857 complement fr 3 64631 64846 complement fr 1 64776 65846 complement fr 2 65825 66433 complement fr 1 66945 67373 direct fr 3 67368 67805 complement fr 2 67735 68586 complement fr 3 68276 68575 direct fr 2 69232 69750 complement fr 3 69825 72350 complement fr 2 72351 73181 complement fr 2 74673 75917 direct fr 3 76338 77408 direct fr 3 77607 77969 complement fr 2 78095 78247 direct fr 2 78760 79239 direct fr 1 78935 79117 direct fr 2 79484 81253 complement fr 1 81325 81819 complement fr 3 82502 82828 direct fr 2 82851 83867 complement fr 2 83858 84484 complement fr 1 84678 85031 complement fr 2 85004 85258 complement fr 1 85434 86738 direct fr 3 86711 87706 direct fr 2 88082 89482 direct fr 2 89018 89539 complement fr 1 89644 89991 complement fr 3 89949 90161 complement fr 2 90089 90241 complement fr 1 90198 90761 complement fr 2 90327 91022 direct fr 3 90759 91181 complement fr 2 90995 91243 direct fr 2 91155 91673 direct fr 3 91703 92506 direct fr 2 92463 92645 complement fr 2 92680 93411 direct fr 1 92765 92905 complement fr 1 93541 93930 complement fr 3 93727 93963 direct fr 1 94091 94354 direct fr 2 94352 96436 direct fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 2 3 21972 +/- 11 bp (complement) 1 2 78948 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 21:55:44 2007