GENEMARK PREDICTIONS Sequence: gi|29171546|ref|NC_004632.1| Pseudomonas syringae pv. tomato str. DC3000 plasmid pDC3000B, complete sequence Sequence file: NC_004632.fna Sequence length: 67473 GC Content: 56.17% 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 -------- -------- ---------- ----- ---- ---- 350 1723 direct fr 2 0.69 0.22 497 1723 direct fr 2 0.69 0.03 569 1723 direct fr 2 0.68 0.46 590 1723 direct fr 2 0.67 0.19 1841 3070 complement fr 1 0.64 0.95 1841 3037 complement fr 1 0.65 0.23 1841 2920 complement fr 1 0.62 0.02 1841 2731 complement fr 1 0.65 0.67 4424 6106 complement fr 1 0.94 0.63 4424 6040 complement fr 1 0.94 0.41 4424 5917 complement fr 1 0.96 0.51 7588 8028 direct fr 1 0.54 0.41 7609 8028 direct fr 1 0.57 0.38 7612 8028 direct fr 1 0.57 0.48 7627 8028 direct fr 1 0.59 0.41 7636 8028 direct fr 1 0.60 0.46 7681 8028 direct fr 1 0.57 0.25 8099 8356 complement fr 1 0.63 0.86 8099 8323 complement fr 1 0.70 0.12 8099 8209 complement fr 1 0.53 0.02 8450 9316 complement fr 1 0.89 0.66 8450 9295 complement fr 1 0.90 0.20 8450 9232 complement fr 1 0.91 0.56 8450 9214 complement fr 1 0.90 0.01 9517 10932 direct fr 1 0.91 0.01 9553 10932 direct fr 1 0.93 0.69 9604 10932 direct fr 1 0.94 0.24 9718 10932 direct fr 1 0.94 0.34 9775 10932 direct fr 1 0.94 0.06 11077 12045 direct fr 1 0.80 0.18 11146 12045 direct fr 1 0.81 0.97 11152 12045 direct fr 1 0.81 0.93 12398 12532 direct fr 2 0.57 0.96 12419 12532 direct fr 2 0.62 0.97 12434 12532 direct fr 2 0.65 0.24 12597 13721 complement fr 2 0.90 0.33 12597 13712 complement fr 2 0.91 0.40 12597 13655 complement fr 2 0.94 0.46 12597 13589 complement fr 2 0.93 0.01 12597 13511 complement fr 2 0.93 0.05 14664 15446 complement fr 2 0.73 0.01 14664 15407 complement fr 2 0.74 0.94 14664 15359 complement fr 2 0.73 0.04 14664 15320 complement fr 2 0.72 0.00 14664 15245 complement fr 2 0.81 0.45 14664 15188 complement fr 2 0.87 0.23 16269 16424 direct fr 3 0.62 0.30 16581 16799 direct fr 3 0.61 0.16 16659 16799 direct fr 3 0.59 0.74 16668 16799 direct fr 3 0.59 0.81 17384 18283 direct fr 2 0.89 0.08 17396 18283 direct fr 2 0.89 0.10 17474 18283 direct fr 2 0.88 0.18 18458 18877 complement fr 1 0.73 0.41 18458 18730 complement fr 1 0.78 0.29 18458 18670 complement fr 1 0.73 0.01 18458 18655 complement fr 1 0.71 0.10 18874 19167 complement fr 3 0.58 0.11 18874 19155 complement fr 3 0.60 0.07 18874 19131 complement fr 3 0.65 0.22 18874 19122 complement fr 3 0.68 0.25 18874 19095 complement fr 3 0.71 0.23 18874 18996 complement fr 3 0.51 0.08 19504 20490 complement fr 3 0.57 0.41 19504 20466 complement fr 3 0.59 0.82 19504 20451 complement fr 3 0.59 0.43 19504 20445 complement fr 3 0.59 0.42 19504 20280 complement fr 3 0.53 0.14 19504 20040 complement fr 3 0.70 0.00 20813 21094 complement fr 1 0.51 0.06 21094 21783 complement fr 3 0.66 0.13 21094 21777 complement fr 3 0.67 0.14 21094 21762 complement fr 3 0.68 0.10 21094 21681 complement fr 3 0.71 0.53 21094 21552 complement fr 3 0.65 0.67 21094 21522 complement fr 3 0.63 0.01 22205 22372 direct fr 2 0.58 0.21 22964 23584 complement fr 1 0.74 0.64 22964 23470 complement fr 1 0.70 0.05 22964 23395 complement fr 1 0.65 0.79 23822 24130 direct fr 2 0.55 0.03 23897 24130 direct fr 2 0.57 0.76 23903 24130 direct fr 2 0.57 0.37 24130 24417 direct fr 1 0.65 0.68 24202 24417 direct fr 1 0.77 0.01 24223 24417 direct fr 1 0.74 0.27 24250 24417 direct fr 1 0.73 0.56 24479 24895 direct fr 2 0.62 0.71 24563 24895 direct fr 2 0.64 0.05 24593 24895 direct fr 2 0.60 0.81 24620 24895 direct fr 2 0.57 0.13 25355 25732 direct fr 2 0.74 0.24 25382 25732 direct fr 2 0.81 0.84 25478 25732 direct fr 2 0.84 0.34 25583 25732 direct fr 2 0.79 0.39 25601 25732 direct fr 2 0.75 0.06 25632 26615 direct fr 3 0.69 0.01 25779 26615 direct fr 3 0.81 0.11 25785 26615 direct fr 3 0.81 0.05 25812 26615 direct fr 3 0.83 0.75 25860 26615 direct fr 3 0.85 0.05 25926 26615 direct fr 3 0.84 0.10 25971 26615 direct fr 3 0.83 0.61 26950 27228 complement fr 3 0.69 0.84 26950 27141 complement fr 3 0.63 0.04 26950 27126 complement fr 3 0.61 0.01 27526 27870 complement fr 3 0.63 0.72 27526 27792 complement fr 3 0.52 0.06 28130 28459 direct fr 2 0.67 0.09 28160 28459 direct fr 2 0.72 0.64 28247 28459 direct fr 2 0.73 0.35 28301 28459 direct fr 2 0.64 0.20 28352 28459 direct fr 2 0.50 0.01 28416 30425 direct fr 3 0.66 0.00 28425 30425 direct fr 3 0.67 0.00 28470 30425 direct fr 3 0.68 0.36 28527 30425 direct fr 3 0.69 0.46 28620 30425 direct fr 3 0.68 0.32 28677 30425 direct fr 3 0.67 0.66 31003 31812 complement fr 3 0.87 0.05 31003 31749 complement fr 3 0.90 0.60 31003 31605 complement fr 3 0.88 0.30 31003 31500 complement fr 3 0.86 0.06 31809 32831 complement fr 2 0.82 0.97 31809 32810 complement fr 2 0.83 0.87 31809 32798 complement fr 2 0.83 0.71 31809 32732 complement fr 2 0.83 0.09 31809 32687 complement fr 2 0.82 0.15 36937 37470 direct fr 1 0.53 0.00 36958 37470 direct fr 1 0.54 0.05 37012 37470 direct fr 1 0.60 0.88 37018 37470 direct fr 1 0.60 0.54 37081 37470 direct fr 1 0.55 0.54 37652 37768 direct fr 2 0.56 0.20 37810 38058 direct fr 1 0.54 0.32 37882 38058 direct fr 1 0.54 0.44 38061 38552 direct fr 3 0.73 0.07 38100 38552 direct fr 3 0.78 0.43 38157 38552 direct fr 3 0.79 0.72 38208 38552 direct fr 3 0.77 0.13 38238 38552 direct fr 3 0.74 0.69 38589 39062 direct fr 3 0.63 0.18 38739 39062 direct fr 3 0.80 0.18 38889 39062 direct fr 3 0.81 0.61 38907 39062 direct fr 3 0.79 0.14 39059 39859 direct fr 2 0.81 0.62 39194 39859 direct fr 2 0.88 0.61 39269 39859 direct fr 2 0.88 0.29 39383 39859 direct fr 2 0.85 0.01 39826 41037 direct fr 1 0.79 0.82 39856 41037 direct fr 1 0.80 0.73 39877 41037 direct fr 1 0.81 0.28 39997 41037 direct fr 1 0.81 0.03 40039 41037 direct fr 1 0.82 0.78 40210 41037 direct fr 1 0.83 0.30 41137 41733 direct fr 1 0.77 0.67 41272 41733 direct fr 1 0.82 0.54 41350 41733 direct fr 1 0.81 0.22 41371 41733 direct fr 1 0.81 0.08 41730 42281 direct fr 3 0.83 0.02 41772 42281 direct fr 3 0.89 0.93 41775 42281 direct fr 3 0.90 0.92 41784 42281 direct fr 3 0.90 0.56 41832 42281 direct fr 3 0.89 0.34 42318 42563 direct fr 3 0.64 0.01 42423 42563 direct fr 3 0.77 0.13 42447 42563 direct fr 3 0.73 0.36 42471 42563 direct fr 3 0.66 0.66 42592 42879 direct fr 1 0.63 0.83 42709 42879 direct fr 1 0.69 0.43 42790 42879 direct fr 1 0.54 0.48 42922 47595 direct fr 1 0.80 0.02 42955 47595 direct fr 1 0.81 0.81 43252 47595 direct fr 1 0.83 0.05 43306 47595 direct fr 1 0.83 0.01 43423 47595 direct fr 1 0.85 0.58 43456 47595 direct fr 1 0.85 0.22 47459 47974 direct fr 2 0.54 0.00 47621 47974 direct fr 2 0.78 0.54 47633 47974 direct fr 2 0.79 0.50 47651 47974 direct fr 2 0.81 0.05 47657 47974 direct fr 2 0.82 0.00 47675 47974 direct fr 2 0.82 0.11 47764 48678 direct fr 1 0.66 0.00 47893 48678 direct fr 1 0.77 0.01 47971 48678 direct fr 1 0.85 0.64 48001 48678 direct fr 1 0.89 0.62 48067 48678 direct fr 1 0.90 0.62 48127 48678 direct fr 1 0.89 0.23 48136 48678 direct fr 1 0.89 0.68 48735 49793 direct fr 3 0.71 0.10 48897 49793 direct fr 3 0.74 0.30 48954 49793 direct fr 3 0.74 0.01 49107 49793 direct fr 3 0.83 0.07 49131 49793 direct fr 3 0.83 0.01 48889 49011 complement fr 3 0.54 0.88 49799 51157 direct fr 2 0.84 0.87 49829 51157 direct fr 2 0.84 0.03 49865 51157 direct fr 2 0.84 0.21 50069 51157 direct fr 2 0.81 0.21 51094 51864 direct fr 1 0.75 0.01 51154 51864 direct fr 1 0.82 0.33 51199 51864 direct fr 1 0.87 0.14 51232 51864 direct fr 1 0.90 0.57 51253 51864 direct fr 1 0.90 0.47 51469 51864 direct fr 1 0.88 0.08 51481 51864 direct fr 1 0.88 0.13 51873 52415 direct fr 3 0.72 0.62 51900 52415 direct fr 3 0.75 0.44 51987 52415 direct fr 3 0.77 0.32 52065 52415 direct fr 3 0.74 0.09 52104 52415 direct fr 3 0.73 0.36 52491 52886 direct fr 3 0.76 0.16 52506 52886 direct fr 3 0.78 0.36 52599 52886 direct fr 3 0.98 0.76 52641 52886 direct fr 3 0.99 0.17 52659 52886 direct fr 3 0.99 0.14 52902 53579 direct fr 3 0.67 0.11 52968 53579 direct fr 3 0.70 0.31 52998 53579 direct fr 3 0.72 0.66 53043 53579 direct fr 3 0.71 0.01 53187 53579 direct fr 3 0.76 0.28 53545 56610 direct fr 1 0.95 0.45 53554 56610 direct fr 1 0.95 0.72 53740 56610 direct fr 1 0.97 0.06 53827 56610 direct fr 1 0.96 0.01 53830 56610 direct fr 1 0.96 0.01 56615 57835 direct fr 2 0.89 0.02 56621 57835 direct fr 2 0.90 0.03 56654 57835 direct fr 2 0.93 0.84 56699 57835 direct fr 2 0.94 0.08 56717 57835 direct fr 2 0.94 0.07 56738 57835 direct fr 2 0.93 0.37 57825 58427 direct fr 3 0.61 0.32 57918 58427 direct fr 3 0.62 0.28 57957 58427 direct fr 3 0.59 0.05 58110 58427 direct fr 3 0.52 0.09 58152 58427 direct fr 3 0.58 0.85 58458 60602 direct fr 3 0.88 0.04 58509 60602 direct fr 3 0.90 0.97 58518 60602 direct fr 3 0.90 0.83 58530 60602 direct fr 3 0.90 0.75 60705 60950 direct fr 3 0.53 0.37 60708 60950 direct fr 3 0.53 0.21 60807 60950 direct fr 3 0.52 0.45 60989 61594 direct fr 2 0.51 0.01 61337 61594 direct fr 2 0.81 0.75 61340 61594 direct fr 2 0.81 0.72 61352 61594 direct fr 2 0.80 0.23 61687 62889 direct fr 1 0.89 0.11 61735 62889 direct fr 1 0.92 0.18 61774 62889 direct fr 1 0.93 0.52 61792 62889 direct fr 1 0.93 0.22 61831 62889 direct fr 1 0.94 0.83 62879 63256 complement fr 1 0.68 0.04 62879 63190 complement fr 1 0.74 0.17 62879 63151 complement fr 1 0.73 0.54 62879 63148 complement fr 1 0.73 0.41 63253 63453 complement fr 3 0.64 0.52 63253 63387 complement fr 3 0.59 0.12 63546 64631 direct fr 3 0.77 0.12 63579 64631 direct fr 3 0.79 0.86 63636 64631 direct fr 3 0.78 0.13 63702 64631 direct fr 3 0.78 0.10 63834 64631 direct fr 3 0.79 0.37 64582 66906 direct fr 1 0.92 0.00 64618 66906 direct fr 1 0.94 0.54 64696 66906 direct fr 1 0.96 0.54 64735 66906 direct fr 1 0.96 0.35 64738 66906 direct fr 1 0.96 0.27 66984 67412 direct fr 3 0.59 0.44 67023 67412 direct fr 3 0.66 0.49 67086 67412 direct fr 3 0.66 0.34 67179 67412 direct fr 3 0.71 0.89 67185 67412 direct fr 3 0.71 0.67 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 150 353 direct fr 3 344 1723 direct fr 2 1841 3091 complement fr 1 2483 2758 direct fr 2 3798 3959 complement fr 2 4424 6166 complement fr 1 7083 7556 direct fr 3 7250 7405 complement fr 1 7483 8028 direct fr 1 8099 8377 complement fr 1 8378 8782 direct fr 2 8450 9391 complement fr 1 9514 10932 direct fr 1 10945 12045 direct fr 1 11062 12123 complement fr 3 12335 12532 direct fr 2 12597 13730 complement fr 2 14664 15488 complement fr 2 14904 15632 direct fr 3 15895 16062 direct fr 1 16104 16424 direct fr 3 16422 16799 direct fr 3 17276 18283 direct fr 2 18458 18880 complement fr 1 18874 19215 complement fr 3 19504 20544 complement fr 3 20813 21109 complement fr 1 21094 21798 complement fr 3 22148 22372 direct fr 2 22582 22938 direct fr 1 22964 23644 complement fr 1 23786 24130 direct fr 2 24115 24417 direct fr 1 24452 24895 direct fr 2 24917 25171 direct fr 2 25346 25732 direct fr 2 25614 26615 direct fr 3 26653 26883 direct fr 1 26950 27264 complement fr 3 27526 27969 complement fr 3 28124 28459 direct fr 2 28313 28534 complement fr 1 28365 30425 direct fr 3 30003 30512 complement fr 2 30504 30728 direct fr 3 31003 31836 complement fr 3 31809 32843 complement fr 2 32887 33429 direct fr 1 33440 34693 direct fr 2 34612 36081 direct fr 1 36703 37470 direct fr 1 37066 37476 complement fr 3 37352 37768 direct fr 2 37753 38058 direct fr 1 37998 38552 direct fr 3 38549 38869 complement fr 1 38553 39062 direct fr 3 38834 39859 direct fr 2 39628 41037 direct fr 1 41035 41733 direct fr 1 41712 42281 direct fr 3 42279 42563 direct fr 3 42580 42879 direct fr 1 42904 47595 direct fr 1 46091 46531 complement fr 1 47282 47974 direct fr 2 47737 48678 direct fr 1 48672 49793 direct fr 3 48889 49143 complement fr 3 49661 51157 direct fr 2 51088 51864 direct fr 1 51867 52415 direct fr 3 52479 52886 direct fr 3 52884 53579 direct fr 3 53440 56610 direct fr 1 56582 57835 direct fr 2 57804 58427 direct fr 3 58425 60602 direct fr 3 60672 60950 direct fr 3 60911 61594 direct fr 2 61178 61849 complement fr 1 61600 62889 direct fr 1 62879 63328 complement fr 1 63253 63492 complement fr 3 63516 64631 direct fr 3 63771 63941 complement fr 2 64579 66906 direct fr 1 66981 67412 direct fr 3 -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 19:21:22 2007