GENEMARK PREDICTIONS Sequence: gi|154688247|ref|NC_009726.1| Coxiella burnetii Dugway 5J108-111 plasmid pQpDG, complete sequence Sequence file: NC_009726.fna Sequence length: 54179 GC Content: 39.79% 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 -------- -------- ---------- ----- ---- ---- 79 537 direct fr 1 0.82 .... 247 537 direct fr 1 0.89 0.38 271 537 direct fr 1 0.88 0.50 307 537 direct fr 1 0.88 0.06 671 1129 direct fr 2 0.70 0.04 728 1129 direct fr 2 0.66 0.01 740 1129 direct fr 2 0.66 0.05 800 1129 direct fr 2 0.65 0.54 1211 1345 complement fr 1 0.63 0.71 1722 2666 direct fr 3 0.76 0.23 1764 2666 direct fr 3 0.78 0.95 1785 2666 direct fr 3 0.77 0.25 2019 2666 direct fr 3 0.76 0.15 2064 2666 direct fr 3 0.77 0.29 2914 3642 direct fr 1 0.65 0.30 2923 3642 direct fr 1 0.66 0.30 3184 3642 direct fr 1 0.68 0.12 3208 3642 direct fr 1 0.70 0.42 3262 3642 direct fr 1 0.75 0.30 3361 3642 direct fr 1 0.79 0.63 3617 4513 complement fr 1 0.58 0.01 3617 4261 complement fr 1 0.64 0.55 3617 4120 complement fr 1 0.57 0.34 4405 4638 complement fr 3 0.63 0.10 4405 4626 complement fr 3 0.62 0.27 5013 5276 direct fr 3 0.52 0.60 5507 7366 direct fr 2 0.84 0.01 5558 7366 direct fr 2 0.87 0.18 5663 7366 direct fr 2 0.88 0.15 5981 7366 direct fr 2 0.87 0.18 6143 7366 direct fr 2 0.88 0.05 7840 8298 direct fr 1 0.72 0.75 8483 10069 complement fr 1 0.82 0.62 8483 10033 complement fr 1 0.83 0.59 8483 10000 complement fr 1 0.83 0.01 8483 9808 complement fr 1 0.80 0.12 10097 10882 complement fr 1 0.81 0.86 10097 10807 complement fr 1 0.81 0.07 10097 10726 complement fr 1 0.79 0.20 10097 10687 complement fr 1 0.78 0.04 10828 11694 complement fr 3 0.68 0.51 10828 11562 complement fr 3 0.66 0.06 10828 11544 complement fr 3 0.65 0.13 10828 11277 complement fr 3 0.54 0.44 12240 13127 complement fr 2 0.80 0.01 12240 13082 complement fr 2 0.84 0.01 12240 13079 complement fr 2 0.85 0.02 12240 13016 complement fr 2 0.90 0.67 12240 12959 complement fr 2 0.90 0.21 12240 12926 complement fr 2 0.90 0.34 13018 13512 complement fr 3 0.85 0.44 13018 13437 complement fr 3 0.88 0.30 13018 13179 complement fr 3 0.73 0.15 13018 13137 complement fr 3 0.64 0.57 13514 13963 complement fr 1 0.53 0.01 13514 13939 complement fr 1 0.56 0.20 14939 15304 direct fr 2 0.51 0.23 14948 15304 direct fr 2 0.52 0.48 15194 15304 direct fr 2 0.63 0.01 15335 16189 direct fr 2 0.74 0.25 15353 16189 direct fr 2 0.76 0.14 15446 16189 direct fr 2 0.74 0.04 15464 16189 direct fr 2 0.74 0.02 15488 16189 direct fr 2 0.73 0.05 16590 17693 direct fr 3 0.79 0.11 16611 17693 direct fr 3 0.78 0.07 16713 17693 direct fr 3 0.82 0.24 16722 17693 direct fr 3 0.82 0.34 18749 19015 complement fr 1 0.51 0.24 19124 20362 direct fr 2 0.78 0.50 19127 20362 direct fr 2 0.78 0.23 19169 20362 direct fr 2 0.81 0.09 19304 20362 direct fr 2 0.82 0.13 19358 20362 direct fr 2 0.82 0.62 19421 20362 direct fr 2 0.81 0.01 20544 21035 direct fr 3 0.71 0.23 20586 21035 direct fr 3 0.75 0.95 20607 21035 direct fr 3 0.74 0.25 20841 21035 direct fr 3 0.59 0.15 21368 22393 direct fr 2 0.79 0.39 21374 22393 direct fr 2 0.80 0.39 21464 22393 direct fr 2 0.83 0.36 21617 22393 direct fr 2 0.82 0.04 21626 22393 direct fr 2 0.82 0.05 22591 23676 complement fr 3 0.80 0.07 22591 23586 complement fr 3 0.85 0.48 22591 23442 complement fr 3 0.87 0.39 22591 23409 complement fr 3 0.86 0.01 24130 24882 direct fr 1 0.66 0.53 24136 24882 direct fr 1 0.67 0.24 24229 24882 direct fr 1 0.72 0.10 24373 24882 direct fr 1 0.69 0.02 24376 24882 direct fr 1 0.69 0.02 24514 24882 direct fr 1 0.59 0.53 24933 25142 direct fr 3 0.56 0.06 25044 25142 direct fr 3 0.72 0.51 26010 27590 direct fr 3 0.78 0.76 26094 27590 direct fr 3 0.78 0.26 26100 27590 direct fr 3 0.78 0.12 26637 27590 direct fr 3 0.87 0.15 27587 31033 direct fr 2 0.85 0.72 27605 31033 direct fr 2 0.85 0.08 27788 31033 direct fr 2 0.85 0.53 28166 31033 direct fr 2 0.83 0.18 31061 32293 complement fr 1 0.77 0.33 31061 32281 complement fr 1 0.78 0.41 31061 31957 complement fr 1 0.80 0.05 31061 31888 complement fr 1 0.80 0.27 31061 31681 complement fr 1 0.83 0.41 32307 32537 complement fr 2 0.60 0.46 32307 32522 complement fr 2 0.63 0.42 32307 32513 complement fr 2 0.66 0.11 32307 32396 complement fr 2 0.55 0.03 32588 32686 direct fr 2 0.53 0.02 32931 33446 complement fr 2 0.50 0.13 32931 33407 complement fr 2 0.55 0.13 32931 33395 complement fr 2 0.55 0.26 34107 34838 direct fr 3 0.65 0.11 34140 34838 direct fr 3 0.67 0.57 34197 34838 direct fr 3 0.69 0.49 34410 34838 direct fr 3 0.57 0.33 34446 34838 direct fr 3 0.57 0.28 35466 35798 direct fr 3 0.73 0.11 35577 35798 direct fr 3 0.75 0.62 35655 35798 direct fr 3 0.61 0.03 35714 36235 direct fr 2 0.73 0.04 36357 37109 complement fr 2 0.71 0.99 36357 36941 complement fr 2 0.70 0.40 36357 36893 complement fr 2 0.68 0.34 37123 38205 complement fr 3 0.70 0.21 37123 38193 complement fr 3 0.70 0.21 37123 38181 complement fr 3 0.70 0.04 39859 40020 complement fr 3 0.50 0.94 40007 40111 complement fr 1 0.58 0.03 40007 40099 complement fr 1 0.53 0.01 40876 41178 direct fr 1 0.60 0.94 40993 41178 direct fr 1 0.54 0.80 41241 41585 complement fr 2 0.80 0.15 41241 41582 complement fr 2 0.80 0.12 41241 41468 complement fr 2 0.72 0.06 41582 42037 complement fr 1 0.59 0.60 41582 41947 complement fr 1 0.70 0.06 41582 41857 complement fr 1 0.74 0.11 42034 42516 complement fr 3 0.85 0.64 42034 42267 complement fr 3 0.76 0.01 42034 42246 complement fr 3 0.75 0.08 42528 45155 complement fr 2 0.92 0.44 42528 45035 complement fr 2 0.93 0.15 42528 45002 complement fr 2 0.93 0.37 42528 44927 complement fr 2 0.93 0.03 46653 47006 direct fr 3 0.57 0.37 47551 48171 complement fr 3 0.61 0.00 47551 48084 complement fr 3 0.66 0.59 47551 48012 complement fr 3 0.61 0.06 47551 47775 complement fr 3 0.57 0.13 48413 49282 complement fr 1 0.79 0.53 48413 49105 complement fr 1 0.82 0.21 48413 48847 complement fr 1 0.76 0.18 49647 50867 direct fr 3 0.70 0.95 49698 50867 direct fr 3 0.72 0.04 49728 50867 direct fr 3 0.71 0.01 49812 50867 direct fr 3 0.70 0.01 50860 51864 direct fr 1 0.74 0.32 50905 51864 direct fr 1 0.78 0.46 50911 51864 direct fr 1 0.78 0.50 51046 51864 direct fr 1 0.75 0.17 51908 53209 direct fr 2 0.64 0.49 51920 53209 direct fr 2 0.63 0.61 51932 53209 direct fr 2 0.63 0.79 53300 53878 complement fr 1 0.87 0.60 53300 53857 complement fr 1 0.87 0.34 53300 53755 complement fr 1 0.87 0.60 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 70 537 direct fr 1 495 674 direct fr 3 554 1129 direct fr 2 1211 1429 complement fr 1 1668 2666 direct fr 3 2911 3642 direct fr 1 3617 4528 complement fr 1 4405 4701 complement fr 3 4842 5276 direct fr 3 5504 7366 direct fr 2 7405 7728 complement fr 3 7553 7774 direct fr 2 7819 8298 direct fr 1 8483 10096 complement fr 1 10097 10915 complement fr 1 10828 11733 complement fr 3 12240 13136 complement fr 2 13018 13533 complement fr 3 13514 13969 complement fr 1 13926 14201 complement fr 2 14818 15096 direct fr 1 14879 15304 direct fr 2 15302 16189 direct fr 2 16017 16298 complement fr 2 16452 17693 direct fr 3 17644 17892 complement fr 3 18013 18264 complement fr 3 18575 18748 complement fr 1 18749 19030 complement fr 1 18955 19140 complement fr 3 19097 20362 direct fr 2 20490 21035 direct fr 3 21356 22393 direct fr 2 22591 23718 complement fr 3 24121 24882 direct fr 1 24921 25142 direct fr 3 25140 25958 direct fr 3 25971 27590 direct fr 3 27542 31033 direct fr 2 31061 32317 complement fr 1 32307 32543 complement fr 2 32474 32686 direct fr 2 32931 33479 complement fr 2 33259 33576 complement fr 3 34092 34838 direct fr 3 35325 35798 direct fr 3 35690 36235 direct fr 2 36357 37115 complement fr 2 37123 38331 complement fr 3 37136 37321 complement fr 1 38612 38962 direct fr 2 39095 39805 complement fr 1 39859 40035 complement fr 3 40007 40285 complement fr 1 40858 41178 direct fr 1 41241 41645 complement fr 2 41582 42049 complement fr 1 42034 42552 complement fr 3 42528 45164 complement fr 2 45708 46430 direct fr 3 46602 47006 direct fr 3 47551 48180 complement fr 3 47689 47973 direct fr 1 48116 48256 complement fr 1 48413 49372 complement fr 1 49626 50867 direct fr 3 50845 51864 direct fr 1 51839 53209 direct fr 2 53300 53962 complement fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 1 37284 +/- 11 bp (complement) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Thu Jan 24 14:21:12 2008