GENEMARK PREDICTIONS Sequence: gi|163937941|ref|NC_010183.1| Bacillus weihenstephanensis KBAB4 plasmid pBWB404, complete sequence Sequence file: NC_010183.fna Sequence length: 52830 GC Content: 35.37% 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 -------- -------- ---------- ----- ---- ---- 152 496 complement fr 1 0.61 0.99 152 280 complement fr 1 0.52 0.00 764 1234 complement fr 1 0.75 0.99 764 1171 complement fr 1 0.73 0.01 764 1045 complement fr 1 0.73 0.34 764 967 complement fr 1 0.72 0.22 1935 2360 direct fr 3 0.83 0.35 1974 2360 direct fr 3 0.82 0.37 1998 2360 direct fr 3 0.81 0.04 2472 3287 complement fr 2 0.81 0.92 2472 3224 complement fr 2 0.84 0.17 2472 3083 complement fr 2 0.81 0.03 2472 3062 complement fr 2 0.81 0.06 3344 3814 complement fr 1 0.84 0.60 3344 3769 complement fr 1 0.88 0.38 3344 3592 complement fr 1 0.81 0.00 3344 3532 complement fr 1 0.75 0.01 3840 4322 complement fr 2 0.86 0.97 3840 4250 complement fr 2 0.88 0.01 3840 4172 complement fr 2 0.86 0.18 3840 4073 complement fr 2 0.80 0.51 4439 5149 complement fr 1 0.85 0.30 4439 4843 complement fr 1 0.88 0.03 4439 4822 complement fr 1 0.87 0.05 4439 4744 complement fr 1 0.84 0.05 5198 5728 complement fr 1 0.88 0.98 5198 5716 complement fr 1 0.89 0.96 5198 5671 complement fr 1 0.88 0.02 6643 7077 complement fr 3 0.78 0.97 6643 7074 complement fr 3 0.78 0.99 6643 7068 complement fr 3 0.80 0.96 6643 6804 complement fr 3 0.53 0.00 7334 7528 direct fr 2 0.60 0.98 7343 7528 direct fr 2 0.60 0.99 7361 7528 direct fr 2 0.67 0.02 7367 7528 direct fr 2 0.67 0.03 7394 7528 direct fr 2 0.59 0.01 7530 8300 direct fr 3 0.89 0.93 7641 8300 direct fr 3 0.93 0.08 7692 8300 direct fr 3 0.93 0.02 7767 8300 direct fr 3 0.93 0.77 8216 8410 direct fr 2 0.61 0.00 8327 8410 direct fr 2 0.89 0.18 8414 8551 direct fr 2 0.63 0.93 8417 8551 direct fr 2 0.63 0.85 8972 9157 direct fr 2 0.59 0.55 8981 9157 direct fr 2 0.63 0.45 9059 9157 direct fr 2 0.71 0.25 9158 10006 direct fr 2 0.75 0.10 9176 10006 direct fr 2 0.76 0.92 9218 10006 direct fr 2 0.80 0.23 9254 10006 direct fr 2 0.79 0.39 9308 10006 direct fr 2 0.78 0.15 9939 10748 direct fr 3 0.86 0.72 9984 10748 direct fr 3 0.89 0.07 9990 10748 direct fr 3 0.89 0.18 9996 10748 direct fr 3 0.89 0.07 10763 11236 direct fr 2 0.86 0.34 10847 11236 direct fr 2 0.85 0.54 10865 11236 direct fr 2 0.85 0.02 11214 11414 direct fr 3 0.63 0.85 11223 11414 direct fr 3 0.67 0.95 11268 11414 direct fr 3 0.82 0.02 11274 11414 direct fr 3 0.81 0.03 11328 11414 direct fr 3 0.71 0.05 11411 11692 direct fr 2 0.78 0.52 12098 12364 complement fr 1 0.70 0.93 12098 12346 complement fr 1 0.76 0.95 13662 13838 direct fr 3 0.74 0.98 13698 13838 direct fr 3 0.76 0.05 13707 13838 direct fr 3 0.75 0.02 13719 13838 direct fr 3 0.73 0.06 13814 14470 direct fr 2 0.92 0.97 13841 14470 direct fr 2 0.95 0.98 13862 14470 direct fr 2 0.97 0.03 13898 14470 direct fr 2 0.97 0.01 13916 14470 direct fr 2 0.97 0.06 14655 14990 direct fr 3 0.88 0.13 14664 14990 direct fr 3 0.88 0.04 14856 14990 direct fr 3 0.73 0.01 15865 16143 direct fr 1 0.75 0.98 16006 16143 direct fr 1 0.68 0.00 16925 17095 direct fr 2 0.59 0.75 16964 17095 direct fr 2 0.74 0.03 16985 17095 direct fr 2 0.70 0.96 17912 18160 direct fr 2 0.67 0.98 17930 18160 direct fr 2 0.74 0.99 17933 18160 direct fr 2 0.74 0.99 17960 18160 direct fr 2 0.77 0.02 18047 18160 direct fr 2 0.63 0.85 18059 18160 direct fr 2 0.60 0.37 18160 18417 direct fr 1 0.73 0.97 18202 18417 direct fr 1 0.84 0.01 18265 18417 direct fr 1 0.77 0.00 18331 18417 direct fr 1 0.62 0.04 18798 19244 direct fr 3 0.80 0.99 18861 19244 direct fr 3 0.87 0.01 19337 19720 direct fr 2 0.74 0.73 19346 19720 direct fr 2 0.76 0.96 19424 19720 direct fr 2 0.85 0.71 19448 19720 direct fr 2 0.87 0.95 19535 19720 direct fr 2 0.82 0.00 19604 19720 direct fr 2 0.73 0.17 19713 21398 direct fr 3 0.94 0.66 19926 21398 direct fr 3 0.96 0.49 19968 21398 direct fr 3 0.96 0.03 20031 21398 direct fr 3 0.96 0.59 21474 22640 direct fr 3 0.95 0.05 21621 22640 direct fr 3 0.94 0.10 21639 22640 direct fr 3 0.94 0.21 22573 23175 direct fr 1 0.85 0.00 22582 23175 direct fr 1 0.85 0.01 22591 23175 direct fr 1 0.87 0.08 22630 23175 direct fr 1 0.90 0.92 22663 23175 direct fr 1 0.90 0.01 22681 23175 direct fr 1 0.89 0.02 23189 24355 direct fr 2 0.93 0.98 23309 24355 direct fr 2 0.95 0.00 23426 24355 direct fr 2 0.94 0.00 23465 24355 direct fr 2 0.94 0.00 24392 24682 direct fr 2 0.72 0.99 24407 24682 direct fr 2 0.75 0.88 24455 24682 direct fr 2 0.86 0.11 24685 24957 direct fr 1 0.74 0.74 24688 24957 direct fr 1 0.74 0.44 24697 24957 direct fr 1 0.77 0.59 24954 25253 direct fr 3 0.66 0.95 25246 25602 direct fr 1 0.79 0.99 25309 25602 direct fr 1 0.86 0.20 25357 25602 direct fr 1 0.83 0.00 25599 25928 direct fr 3 0.78 0.99 25647 25928 direct fr 3 0.82 0.00 25686 25928 direct fr 3 0.80 0.42 25716 25928 direct fr 3 0.78 0.75 25929 26522 direct fr 3 0.83 0.37 25974 26522 direct fr 3 0.90 0.81 26091 26522 direct fr 3 0.90 0.00 26274 26522 direct fr 3 0.83 0.00 26295 26522 direct fr 3 0.82 0.00 26527 26871 direct fr 1 0.84 0.98 26665 26871 direct fr 1 0.86 0.02 26734 26871 direct fr 1 0.81 0.11 26770 26871 direct fr 1 0.75 0.01 26982 27089 direct fr 3 0.81 0.74 26994 27089 direct fr 3 0.79 0.03 27027 27089 direct fr 3 0.69 0.02 27107 28570 direct fr 2 0.97 1.00 27464 28570 direct fr 2 0.97 0.12 27575 28570 direct fr 2 0.97 0.03 27809 28570 direct fr 2 0.96 0.02 28795 31155 direct fr 1 0.86 0.86 28867 31155 direct fr 1 0.87 0.05 28891 31155 direct fr 1 0.87 0.01 28903 31155 direct fr 1 0.87 0.08 31197 32669 direct fr 3 0.90 0.10 31365 32669 direct fr 3 0.93 0.08 31524 32669 direct fr 3 0.92 0.00 31563 32669 direct fr 3 0.92 0.65 32666 38626 direct fr 2 0.95 0.81 32804 38626 direct fr 2 0.96 0.65 32831 38626 direct fr 2 0.96 0.02 32837 38626 direct fr 2 0.96 0.03 38663 39088 direct fr 2 0.79 0.99 38768 39088 direct fr 2 0.88 0.51 38861 39088 direct fr 2 0.83 0.04 38864 39088 direct fr 2 0.83 0.05 39088 40023 direct fr 1 0.88 0.98 39148 40023 direct fr 1 0.93 0.14 39208 40023 direct fr 1 0.92 0.03 39217 40023 direct fr 1 0.92 0.02 40075 40566 complement fr 3 0.88 0.98 40075 40542 complement fr 3 0.92 0.32 40075 40518 complement fr 3 0.91 0.02 40075 40449 complement fr 3 0.89 0.00 40729 41220 complement fr 3 0.94 0.85 40729 41211 complement fr 3 0.94 0.95 40729 41187 complement fr 3 0.94 0.51 41497 41985 complement fr 3 0.89 0.96 41497 41976 complement fr 3 0.91 0.86 41497 41928 complement fr 3 0.93 0.06 41497 41862 complement fr 3 0.92 0.00 41497 41850 complement fr 3 0.91 0.00 42606 42857 direct fr 3 0.52 0.00 42663 42857 direct fr 3 0.68 0.34 42868 44034 direct fr 1 0.81 0.50 42949 44034 direct fr 1 0.83 0.08 42976 44034 direct fr 1 0.83 0.01 43240 44034 direct fr 1 0.85 0.65 44348 44635 direct fr 2 0.55 0.02 44719 45309 direct fr 1 0.73 0.61 44797 45309 direct fr 1 0.81 0.95 44875 45309 direct fr 1 0.79 0.01 44917 45309 direct fr 1 0.77 0.00 45635 46159 direct fr 2 0.91 0.04 45719 46159 direct fr 2 0.90 0.00 46016 46159 direct fr 2 0.74 0.00 46891 47085 complement fr 3 0.77 0.22 47439 48413 complement fr 2 0.72 0.78 47439 48404 complement fr 2 0.72 0.57 47439 48191 complement fr 2 0.66 0.01 48481 48882 complement fr 3 0.72 0.65 48481 48819 complement fr 3 0.78 0.08 48481 48759 complement fr 3 0.76 0.38 48481 48732 complement fr 3 0.73 0.42 48897 49784 complement fr 2 0.87 0.01 48897 49736 complement fr 2 0.92 0.92 48897 49727 complement fr 2 0.92 0.99 48897 49655 complement fr 2 0.92 0.02 51402 51608 direct fr 3 0.58 0.08 51465 51608 direct fr 3 0.74 0.42 51492 51608 direct fr 3 0.69 0.00 51525 51608 direct fr 3 0.58 0.00 51647 51763 complement fr 1 0.55 0.88 52249 52794 direct fr 1 0.85 0.29 52315 52794 direct fr 1 0.92 0.89 52381 52794 direct fr 1 0.91 0.00 52402 52794 direct fr 1 0.91 0.00 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 152 517 complement fr 1 764 1249 complement fr 1 1881 2360 direct fr 3 2472 3293 complement fr 2 3344 3838 complement fr 1 3840 4355 complement fr 2 4439 5158 complement fr 1 5198 5779 complement fr 1 6102 6305 direct fr 3 6205 6645 complement fr 3 6643 7107 complement fr 3 7307 7528 direct fr 2 7512 8300 direct fr 3 8186 8410 direct fr 2 8408 8551 direct fr 2 8963 9157 direct fr 2 9155 10006 direct fr 2 9912 10748 direct fr 3 10691 11236 direct fr 2 11202 11414 direct fr 3 11333 11692 direct fr 2 12098 12370 complement fr 1 13617 13838 direct fr 3 13808 14470 direct fr 2 14595 14990 direct fr 3 15838 16143 direct fr 1 16907 17095 direct fr 2 17900 18160 direct fr 2 18145 18417 direct fr 1 18478 18795 direct fr 1 18783 19244 direct fr 3 19328 19720 direct fr 2 19704 21398 direct fr 3 21396 22640 direct fr 3 22549 23175 direct fr 1 23183 24355 direct fr 2 24377 24682 direct fr 2 24676 24957 direct fr 1 24951 25253 direct fr 3 25240 25602 direct fr 1 25572 25928 direct fr 3 25926 26522 direct fr 3 26524 26871 direct fr 1 26856 27089 direct fr 3 27077 28570 direct fr 2 28759 31155 direct fr 1 28929 29366 complement fr 2 31185 32669 direct fr 3 32663 38626 direct fr 2 38645 39088 direct fr 2 39082 40023 direct fr 1 40075 40596 complement fr 3 40729 41307 complement fr 3 41497 42006 complement fr 3 42196 42624 complement fr 3 42497 42649 direct fr 2 42585 42857 direct fr 3 42844 44034 direct fr 1 44018 44635 direct fr 2 44677 45309 direct fr 1 44994 45158 direct fr 3 45557 46159 direct fr 2 46891 47121 complement fr 3 47235 47402 direct fr 3 47439 48461 complement fr 2 48481 48906 complement fr 3 48897 49787 complement fr 2 51399 51608 direct fr 3 51647 51835 complement fr 1 52231 52794 direct fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 3 45048 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Dec 28 10:34:52 2007