GENEMARK PREDICTIONS Sequence: gi|152973731|ref|NC_009651.1| Klebsiella pneumoniae subsp. pneumoniae MGH 78578 plasmid pKPN5, complete sequence Sequence file: NC_009651.fna Sequence length: 88582 GC Content: 53.82% 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 -------- -------- ---------- ----- ---- ---- 39 632 complement fr 2 0.74 0.00 39 596 complement fr 2 0.79 0.27 39 515 complement fr 2 0.85 0.07 39 440 complement fr 2 0.85 0.87 39 434 complement fr 2 0.85 0.69 815 946 complement fr 1 0.56 0.99 1008 1724 complement fr 2 0.86 0.38 1008 1712 complement fr 2 0.88 0.43 1008 1613 complement fr 2 0.88 0.04 1008 1595 complement fr 2 0.88 0.02 1008 1541 complement fr 2 0.87 0.09 1749 2297 complement fr 2 0.69 0.78 1749 2264 complement fr 2 0.72 0.73 1749 2060 complement fr 2 0.60 0.47 1749 1946 complement fr 2 0.54 0.21 2345 3700 complement fr 1 0.82 0.33 2345 3676 complement fr 1 0.82 0.25 2345 3523 complement fr 1 0.81 0.12 4074 4301 complement fr 2 0.57 0.30 4074 4232 complement fr 2 0.65 0.05 4074 4220 complement fr 2 0.63 0.18 4981 5379 complement fr 3 0.53 0.00 4981 5352 complement fr 3 0.58 0.00 4981 5301 complement fr 3 0.66 0.73 4981 5295 complement fr 3 0.66 0.66 4981 5286 complement fr 3 0.68 0.48 4981 5274 complement fr 3 0.70 0.26 4981 5172 complement fr 3 0.67 0.18 4981 5103 complement fr 3 0.54 0.50 5775 5966 complement fr 2 0.52 0.30 6009 6515 complement fr 2 0.85 0.25 6009 6482 complement fr 2 0.89 0.66 6009 6350 complement fr 2 0.86 0.16 6009 6236 complement fr 2 0.79 0.22 6558 7370 complement fr 2 0.51 0.12 6558 7223 complement fr 2 0.60 0.08 6558 7079 complement fr 2 0.69 0.06 6558 6986 complement fr 2 0.81 0.48 6558 6977 complement fr 2 0.83 0.31 6558 6926 complement fr 2 0.86 0.70 6558 6899 complement fr 2 0.84 0.44 7667 8593 complement fr 1 0.70 0.04 7667 8581 complement fr 1 0.71 0.17 7667 8434 complement fr 1 0.80 0.88 7667 8431 complement fr 1 0.80 0.79 7667 8383 complement fr 1 0.80 0.12 8488 8907 complement fr 3 0.77 0.42 8488 8877 complement fr 3 0.84 0.90 8488 8793 complement fr 3 0.80 0.01 8488 8745 complement fr 3 0.77 0.23 8917 9159 complement fr 3 0.72 0.78 8917 9138 complement fr 3 0.79 0.99 8917 9102 complement fr 3 0.83 0.48 8917 9054 complement fr 3 0.78 0.05 9138 9914 complement fr 2 0.80 0.31 9138 9878 complement fr 2 0.84 0.02 9138 9875 complement fr 2 0.85 0.02 9138 9839 complement fr 2 0.87 0.54 9138 9806 complement fr 2 0.87 0.65 9138 9803 complement fr 2 0.87 0.54 10276 10506 complement fr 3 0.59 0.11 10276 10443 complement fr 3 0.65 0.38 10276 10407 complement fr 3 0.58 0.13 10667 11383 complement fr 1 0.86 0.38 10667 11371 complement fr 1 0.87 0.43 10667 11272 complement fr 1 0.88 0.04 10667 11254 complement fr 1 0.87 0.02 10667 11200 complement fr 1 0.86 0.09 11546 12160 direct fr 2 0.74 0.90 11726 12160 direct fr 2 0.74 0.27 11732 12160 direct fr 2 0.74 0.09 11786 12160 direct fr 2 0.70 0.58 12412 13029 direct fr 1 0.68 0.72 12427 13029 direct fr 1 0.67 0.74 12466 13029 direct fr 1 0.66 0.08 13029 13865 direct fr 3 0.64 0.00 13035 13865 direct fr 3 0.65 0.00 13260 13865 direct fr 3 0.74 0.40 13287 13865 direct fr 3 0.74 0.13 13350 13865 direct fr 3 0.71 0.02 14176 16476 direct fr 1 0.85 0.86 14245 16476 direct fr 1 0.85 0.11 14290 16476 direct fr 1 0.85 0.69 16555 17559 direct fr 1 0.54 0.97 16708 17559 direct fr 1 0.55 0.74 16735 17559 direct fr 1 0.54 0.24 16870 17559 direct fr 1 0.57 0.12 18529 19344 direct fr 1 0.74 0.26 18640 19344 direct fr 1 0.77 0.10 18658 19344 direct fr 1 0.76 0.01 18739 19344 direct fr 1 0.73 0.45 19909 21402 complement fr 3 0.68 0.24 19909 21393 complement fr 3 0.69 0.39 19909 21276 complement fr 3 0.71 0.09 19909 21243 complement fr 3 0.70 0.25 19909 21096 complement fr 3 0.73 0.95 21613 21801 complement fr 3 0.53 0.99 21613 21777 complement fr 3 0.59 0.89 21758 22489 complement fr 1 0.86 0.16 21758 22459 complement fr 1 0.90 0.99 21758 22456 complement fr 1 0.90 0.98 21758 22300 complement fr 1 0.88 0.12 23121 23837 complement fr 2 0.85 0.38 23121 23825 complement fr 2 0.87 0.43 23121 23726 complement fr 2 0.87 0.04 23121 23708 complement fr 2 0.87 0.02 23121 23654 complement fr 2 0.86 0.09 23837 24472 complement fr 1 0.81 0.38 23837 24460 complement fr 1 0.82 0.43 23837 24361 complement fr 1 0.82 0.04 23837 24343 complement fr 1 0.82 0.02 23837 24289 complement fr 1 0.80 0.09 24519 24767 direct fr 3 0.75 0.97 24591 24767 direct fr 3 0.79 0.04 24618 24767 direct fr 3 0.75 0.02 24764 25315 direct fr 2 0.75 0.41 24896 25315 direct fr 2 0.76 0.15 24914 25315 direct fr 2 0.74 0.40 25061 25315 direct fr 2 0.64 0.66 25448 26200 direct fr 2 0.78 0.10 25517 26200 direct fr 2 0.86 0.26 25544 26200 direct fr 2 0.87 0.20 25634 26200 direct fr 2 0.90 0.28 25661 26200 direct fr 2 0.90 0.00 25709 26200 direct fr 2 0.90 0.90 26253 26909 direct fr 3 0.75 0.04 26331 26909 direct fr 3 0.84 0.80 26454 26909 direct fr 3 0.82 0.63 26463 26909 direct fr 3 0.82 0.23 26858 27136 direct fr 2 0.58 0.03 26906 27136 direct fr 2 0.70 0.49 26912 27136 direct fr 2 0.70 0.53 26957 27136 direct fr 2 0.72 0.71 28245 28961 complement fr 2 0.86 0.38 28245 28949 complement fr 2 0.87 0.43 28245 28850 complement fr 2 0.88 0.04 28245 28832 complement fr 2 0.87 0.02 28245 28778 complement fr 2 0.86 0.09 31008 31718 complement fr 2 0.50 0.21 31008 31619 complement fr 2 0.51 0.97 31008 31616 complement fr 2 0.51 0.86 32129 33670 complement fr 1 0.61 0.00 32129 33454 complement fr 1 0.63 0.11 32129 33361 complement fr 1 0.65 0.78 32129 33298 complement fr 1 0.64 0.03 32129 33244 complement fr 1 0.64 0.38 34075 35001 complement fr 3 0.60 0.00 34075 34941 complement fr 3 0.63 0.97 34075 34914 complement fr 3 0.63 0.13 34075 34911 complement fr 3 0.63 0.06 34171 34302 direct fr 1 0.51 0.68 34207 34302 direct fr 1 0.51 0.23 36996 37247 complement fr 2 0.52 0.08 36996 37184 complement fr 2 0.60 0.19 36996 37121 complement fr 2 0.59 0.81 37667 38416 complement fr 1 0.55 0.27 37667 38359 complement fr 1 0.59 0.03 37667 38347 complement fr 1 0.59 0.01 37667 38314 complement fr 1 0.60 0.05 37667 38278 complement fr 1 0.64 0.04 37667 38263 complement fr 1 0.65 0.14 37667 38200 complement fr 1 0.71 0.24 37667 38014 complement fr 1 0.66 0.68 37667 37996 complement fr 1 0.64 0.35 38346 39359 direct fr 3 0.70 0.20 38493 39359 direct fr 3 0.71 0.41 38622 39359 direct fr 3 0.66 0.09 38688 39359 direct fr 3 0.63 0.97 39675 40391 complement fr 2 0.85 0.38 39675 40379 complement fr 2 0.87 0.43 39675 40280 complement fr 2 0.87 0.04 39675 40262 complement fr 2 0.87 0.02 39675 40208 complement fr 2 0.85 0.09 40625 41215 complement fr 1 0.77 0.09 40625 41206 complement fr 1 0.78 0.44 40625 41155 complement fr 1 0.81 0.35 40625 41146 complement fr 1 0.80 0.47 40625 41134 complement fr 1 0.80 0.42 41509 42855 direct fr 1 0.56 0.01 41515 42855 direct fr 1 0.56 0.01 41623 42855 direct fr 1 0.60 0.05 41722 42855 direct fr 1 0.58 0.16 41770 42855 direct fr 1 0.59 0.28 41863 42855 direct fr 1 0.62 0.12 42391 42855 direct fr 1 0.53 0.68 42427 42855 direct fr 1 0.52 0.82 42906 43328 complement fr 2 0.63 0.35 42906 43283 complement fr 2 0.65 0.56 42906 43259 complement fr 2 0.63 0.14 42906 43220 complement fr 2 0.61 0.72 43727 44647 complement fr 1 0.57 0.27 43727 44638 complement fr 1 0.58 0.69 43727 44389 complement fr 1 0.55 0.45 43727 44329 complement fr 1 0.50 0.00 46342 48528 complement fr 3 0.80 0.84 46342 48390 complement fr 3 0.79 0.14 46342 48291 complement fr 3 0.78 0.14 48529 49632 complement fr 3 0.87 0.51 48529 49620 complement fr 3 0.88 0.65 48529 49617 complement fr 3 0.88 0.48 48529 49563 complement fr 3 0.87 0.27 50184 51128 direct fr 3 0.71 0.81 50247 51128 direct fr 3 0.70 0.05 50604 51128 direct fr 3 0.64 0.11 50616 51128 direct fr 3 0.63 0.02 51165 51557 direct fr 3 0.79 0.93 51204 51557 direct fr 3 0.84 0.10 51207 51557 direct fr 3 0.84 0.04 51243 51557 direct fr 3 0.83 0.30 51582 52136 direct fr 3 0.65 0.01 51615 52136 direct fr 3 0.70 0.25 51732 52136 direct fr 3 0.72 0.05 51840 52136 direct fr 3 0.71 0.81 51906 52136 direct fr 3 0.62 0.07 52182 52385 direct fr 3 0.51 0.03 52185 52385 direct fr 3 0.51 0.05 52236 52385 direct fr 3 0.65 0.80 52239 52385 direct fr 3 0.67 0.66 52296 52385 direct fr 3 0.55 0.28 52298 53419 direct fr 2 0.69 0.01 52415 53419 direct fr 2 0.73 0.31 52466 53419 direct fr 2 0.73 0.61 52511 53419 direct fr 2 0.73 0.13 52517 53419 direct fr 2 0.72 0.10 53603 54382 direct fr 2 0.70 0.01 53657 54382 direct fr 2 0.75 0.84 53696 54382 direct fr 2 0.75 0.46 53705 54382 direct fr 2 0.74 0.16 54440 54631 complement fr 1 0.61 0.56 54440 54547 complement fr 1 0.53 0.23 55475 56341 direct fr 2 0.50 0.01 55514 56341 direct fr 2 0.53 0.55 55523 56341 direct fr 2 0.53 0.41 55538 56341 direct fr 2 0.55 0.07 55589 56341 direct fr 2 0.56 0.08 55619 56341 direct fr 2 0.58 0.01 55733 56341 direct fr 2 0.69 0.52 55751 56341 direct fr 2 0.69 0.75 55871 56341 direct fr 2 0.64 0.26 56426 57037 complement fr 1 0.53 0.85 59469 59630 direct fr 3 0.67 0.63 59523 59630 direct fr 3 0.66 0.25 59712 60983 complement fr 2 0.75 0.97 59712 60965 complement fr 2 0.75 0.19 59712 60836 complement fr 2 0.75 0.02 59712 60749 complement fr 2 0.79 0.68 60983 61429 complement fr 1 0.68 0.06 60983 61414 complement fr 1 0.72 0.16 60983 61228 complement fr 1 0.80 0.39 60983 61189 complement fr 1 0.77 0.04 60983 61123 complement fr 1 0.66 0.61 61648 62619 direct fr 1 0.89 0.69 61756 62619 direct fr 1 0.93 0.72 61792 62619 direct fr 1 0.93 0.04 61852 62619 direct fr 1 0.93 0.75 62622 63272 direct fr 3 0.80 0.88 62682 63272 direct fr 3 0.86 0.07 62754 63272 direct fr 3 0.86 0.45 62766 63272 direct fr 3 0.86 0.37 63307 64023 direct fr 1 0.85 0.38 63319 64023 direct fr 1 0.86 0.39 63418 64023 direct fr 1 0.89 0.05 63436 64023 direct fr 1 0.88 0.01 63490 64023 direct fr 1 0.87 0.08 63914 64528 complement fr 1 0.61 0.91 63914 64477 complement fr 1 0.58 0.10 63914 64441 complement fr 1 0.55 0.00 64574 64849 complement fr 1 0.68 0.10 64574 64693 complement fr 1 0.63 0.43 64574 64684 complement fr 1 0.59 0.19 64574 64681 complement fr 1 0.59 0.08 66239 66700 complement fr 1 0.55 0.45 66239 66676 complement fr 1 0.52 0.20 66239 66670 complement fr 1 0.51 0.04 67105 67821 complement fr 3 0.85 0.38 67105 67809 complement fr 3 0.87 0.43 67105 67710 complement fr 3 0.87 0.04 67105 67692 complement fr 3 0.87 0.02 67105 67638 complement fr 3 0.85 0.09 68154 69146 direct fr 3 0.74 0.24 68190 69146 direct fr 3 0.76 0.81 68268 69146 direct fr 3 0.75 0.06 68451 69146 direct fr 3 0.77 0.49 69173 69334 direct fr 2 0.53 0.10 69251 69334 direct fr 2 0.55 0.04 69331 69942 complement fr 3 0.57 0.87 69331 69783 complement fr 3 0.51 0.50 69996 70277 complement fr 2 0.60 0.20 69996 70124 complement fr 2 0.64 0.24 70296 70427 direct fr 3 0.63 0.03 70317 70427 direct fr 3 0.55 0.25 71654 72370 direct fr 2 0.85 0.38 71666 72370 direct fr 2 0.87 0.39 71765 72370 direct fr 2 0.89 0.05 71783 72370 direct fr 2 0.89 0.01 71837 72370 direct fr 2 0.87 0.08 72418 73521 direct fr 1 0.91 0.67 72490 73521 direct fr 1 0.94 0.47 72502 73521 direct fr 1 0.94 0.86 72544 73521 direct fr 1 0.94 0.38 75482 75712 direct fr 2 0.57 0.93 75485 75712 direct fr 2 0.57 0.93 75515 75712 direct fr 2 0.56 0.78 76555 76707 complement fr 3 0.63 0.31 76555 76701 complement fr 3 0.60 0.26 76801 77517 direct fr 1 0.86 0.38 76813 77517 direct fr 1 0.87 0.39 76912 77517 direct fr 1 0.89 0.05 76930 77517 direct fr 1 0.89 0.01 76984 77517 direct fr 1 0.88 0.08 77573 79057 direct fr 2 0.92 0.97 77579 79057 direct fr 2 0.92 0.98 77645 79057 direct fr 2 0.93 0.02 77747 79057 direct fr 2 0.93 0.07 77774 79057 direct fr 2 0.93 0.31 79076 79903 direct fr 2 0.88 0.27 79187 79903 direct fr 2 0.92 0.01 79214 79903 direct fr 2 0.91 0.04 79307 79903 direct fr 2 0.90 0.01 79975 81171 complement fr 3 0.87 0.04 79975 81150 complement fr 3 0.88 0.51 79975 81114 complement fr 3 0.90 0.70 79975 81108 complement fr 3 0.90 0.47 81700 82074 direct fr 1 0.86 0.78 81814 82074 direct fr 1 0.83 0.12 81862 82074 direct fr 1 0.80 0.05 82316 83497 direct fr 2 0.85 0.00 82349 83497 direct fr 2 0.88 0.03 82358 83497 direct fr 2 0.89 0.08 82400 83497 direct fr 2 0.92 0.72 82433 83497 direct fr 2 0.93 0.06 82526 83497 direct fr 2 0.93 0.28 82532 83497 direct fr 2 0.93 0.19 84446 85162 complement fr 1 0.86 0.38 84446 85150 complement fr 1 0.87 0.43 84446 85051 complement fr 1 0.87 0.04 84446 85033 complement fr 1 0.87 0.02 84446 84979 complement fr 1 0.86 0.09 85162 85818 complement fr 3 0.82 0.97 85162 85686 complement fr 3 0.82 0.18 85162 85650 complement fr 3 0.81 0.03 85162 85569 complement fr 3 0.77 0.43 85914 87098 direct fr 3 0.89 0.95 85941 87098 direct fr 3 0.91 0.95 85962 87098 direct fr 3 0.93 0.04 85980 87098 direct fr 3 0.93 0.00 86028 87098 direct fr 3 0.92 0.28 87124 87483 direct fr 1 0.58 0.00 87163 87483 direct fr 1 0.64 0.01 87193 87483 direct fr 1 0.71 0.13 87256 87483 direct fr 1 0.79 0.51 87280 87483 direct fr 1 0.77 0.08 87286 87483 direct fr 1 0.77 0.01 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 39 701 complement fr 2 815 973 complement fr 1 1008 1748 complement fr 2 1749 2363 complement fr 2 2345 3751 complement fr 1 3632 3964 direct fr 2 4074 4322 complement fr 2 4381 4719 direct fr 1 4981 5406 complement fr 3 5336 5623 complement fr 1 5775 6011 complement fr 2 6009 6560 complement fr 2 6430 6627 complement fr 3 6558 7484 complement fr 2 7667 8626 complement fr 1 8488 8919 complement fr 3 8917 9162 complement fr 3 9138 9926 complement fr 2 10276 10575 complement fr 3 10667 11407 complement fr 1 11540 12160 direct fr 2 11716 13029 direct fr 1 12047 12202 complement fr 1 12921 13865 direct fr 3 13837 15150 complement fr 3 13936 16476 direct fr 1 15538 16455 complement fr 3 16525 17559 direct fr 1 17741 18052 complement fr 1 18490 19344 direct fr 1 19341 19799 complement fr 2 19398 19733 direct fr 3 19909 21441 complement fr 3 20788 21189 direct fr 1 21613 21813 complement fr 3 21758 22534 complement fr 1 22432 23175 direct fr 1 22593 23087 direct fr 3 23121 23861 complement fr 2 23837 24496 complement fr 1 24489 24767 direct fr 3 24743 25315 direct fr 2 25394 26200 direct fr 2 26217 26909 direct fr 3 26813 27136 direct fr 2 27115 27276 complement fr 3 27290 28153 complement fr 1 28245 28985 complement fr 2 30429 30995 complement fr 2 31008 31811 complement fr 2 32129 33697 complement fr 1 32150 32647 direct fr 2 33275 33544 direct fr 2 34075 35007 complement fr 3 34087 34302 direct fr 1 34908 35297 complement fr 2 35447 36763 complement fr 1 36399 36689 complement fr 2 36996 37355 complement fr 2 37005 37625 direct fr 3 37667 38422 complement fr 1 38337 39359 direct fr 3 38883 39320 complement fr 2 39318 39536 complement fr 2 39675 40415 complement fr 2 40625 41257 complement fr 1 41482 42855 direct fr 1 42906 43415 complement fr 2 43211 43729 complement fr 1 43727 44914 complement fr 1 44075 44368 direct fr 2 44962 45798 complement fr 3 46342 48531 complement fr 3 48265 49674 direct fr 1 48529 49659 complement fr 3 50079 51128 direct fr 3 50526 50933 complement fr 2 51126 51557 direct fr 3 51555 52136 direct fr 3 52173 52385 direct fr 3 52280 53419 direct fr 2 53555 54382 direct fr 2 54440 54745 complement fr 1 55418 56341 direct fr 2 56367 57143 complement fr 2 56426 57097 complement fr 1 57448 58656 direct fr 1 58303 58467 complement fr 3 58641 59630 direct fr 3 59712 61052 complement fr 2 60983 61447 complement fr 1 61633 62619 direct fr 1 62607 63272 direct fr 3 63283 64023 direct fr 1 63914 64573 complement fr 1 64574 64870 complement fr 1 65054 65404 complement fr 1 65532 66038 direct fr 3 66239 67009 complement fr 1 67105 67845 complement fr 3 67896 68105 direct fr 3 68109 69146 direct fr 3 69140 69334 direct fr 2 69331 69960 complement fr 3 69996 70292 complement fr 2 70200 70427 direct fr 3 71211 71522 direct fr 3 71630 72370 direct fr 2 72361 73521 direct fr 1 73772 74368 complement fr 1 73790 74050 direct fr 2 74359 74736 complement fr 3 74798 75451 complement fr 1 75231 75473 direct fr 3 75401 75712 direct fr 2 75442 75939 direct fr 1 76555 77436 complement fr 3 76777 77517 direct fr 1 77552 79057 direct fr 2 79055 79903 direct fr 2 79870 80205 direct fr 1 79975 81207 complement fr 3 81607 82074 direct fr 1 82298 83497 direct fr 2 83851 84195 complement fr 3 84446 85186 complement fr 1 85162 85839 complement fr 3 85908 87098 direct fr 3 87061 87483 direct fr 1 87578 88453 complement fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 2 43296 +/- 11 bp (complement) 1 2 56688 +/- 11 bp (complement) 2 1 75624 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Jul 27 16:16:54 2007