GENEMARK PREDICTIONS Sequence: gi|45478502|ref|NC_005813.1| Yersinia pestis biovar Microtus str. 91001 plasmid pCD1, complete sequence Sequence file: NC_005813.fna Sequence length: 70159 GC Content: 44.85% 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 -------- -------- ---------- ----- ---- ---- 87 1109 direct fr 3 0.74 .... 108 1109 direct fr 3 0.75 0.30 138 1109 direct fr 3 0.75 0.16 366 1109 direct fr 3 0.74 0.15 456 1109 direct fr 3 0.74 0.31 1106 1888 direct fr 2 0.92 0.88 1109 1888 direct fr 2 0.92 0.86 1112 1888 direct fr 2 0.92 0.91 2097 2357 direct fr 3 0.77 0.39 2118 2357 direct fr 3 0.75 0.12 2121 2357 direct fr 3 0.75 0.08 2619 2714 direct fr 3 0.57 0.44 2843 3022 direct fr 2 0.51 0.26 2873 3022 direct fr 2 0.55 0.17 3160 3414 direct fr 1 0.64 0.43 3247 3414 direct fr 1 0.62 0.04 3289 3414 direct fr 1 0.62 0.30 3711 4589 direct fr 3 0.83 0.46 3723 4589 direct fr 3 0.85 0.22 3834 4589 direct fr 3 0.91 0.28 3876 4589 direct fr 3 0.91 0.30 3918 4589 direct fr 3 0.91 0.53 6173 6451 direct fr 2 0.59 0.03 6254 6451 direct fr 2 0.57 0.38 6257 6451 direct fr 2 0.57 0.31 6266 6451 direct fr 2 0.59 0.11 6302 6451 direct fr 2 0.64 0.38 6311 6451 direct fr 2 0.64 0.62 6747 7196 direct fr 3 0.59 0.07 6867 7196 direct fr 3 0.65 0.41 7204 9402 direct fr 1 0.80 0.02 7213 9402 direct fr 1 0.80 0.15 7222 9402 direct fr 1 0.80 0.68 7231 9402 direct fr 1 0.81 0.48 7345 9402 direct fr 1 0.82 0.10 7417 9402 direct fr 1 0.85 0.13 7603 9402 direct fr 1 0.85 0.10 7609 9402 direct fr 1 0.85 0.13 7798 9402 direct fr 1 0.84 0.35 11250 11897 complement fr 2 0.61 0.03 11250 11786 complement fr 2 0.69 0.04 11250 11753 complement fr 2 0.71 0.77 11250 11726 complement fr 2 0.70 0.28 11858 12064 direct fr 2 0.66 0.52 11915 12064 direct fr 2 0.63 0.11 12323 13753 direct fr 2 0.76 0.16 12347 13753 direct fr 2 0.77 0.20 12392 13753 direct fr 2 0.78 0.47 12668 13753 direct fr 2 0.76 0.16 12689 13753 direct fr 2 0.75 0.05 14265 14552 complement fr 2 0.68 0.14 14265 14435 complement fr 2 0.64 0.17 14265 14423 complement fr 2 0.61 0.21 15028 15294 complement fr 3 0.65 0.72 15028 15225 complement fr 3 0.67 0.09 15028 15153 complement fr 3 0.51 0.56 15842 16189 complement fr 1 0.77 0.20 15842 16141 complement fr 1 0.84 0.43 15842 16042 complement fr 1 0.82 0.16 15842 16030 complement fr 1 0.81 0.01 16414 17079 complement fr 3 0.81 0.18 16414 17046 complement fr 3 0.85 0.02 16414 16851 complement fr 3 0.86 0.04 16414 16764 complement fr 3 0.83 0.42 16414 16710 complement fr 3 0.80 0.04 17025 17657 complement fr 2 0.82 0.10 17025 17654 complement fr 2 0.82 0.11 17025 17651 complement fr 2 0.83 0.08 17025 17228 complement fr 2 0.68 0.13 17025 17192 complement fr 2 0.62 0.42 17654 18388 complement fr 1 0.82 0.04 17654 18286 complement fr 1 0.88 0.22 17654 18127 complement fr 1 0.85 0.26 17654 18016 complement fr 1 0.82 0.11 18395 18742 complement fr 1 0.78 0.67 18395 18709 complement fr 1 0.82 0.84 18395 18652 complement fr 1 0.82 0.33 18395 18634 complement fr 1 0.80 0.78 18395 18502 complement fr 1 0.62 0.40 18743 19240 complement fr 1 0.74 0.03 18743 19201 complement fr 1 0.77 0.89 19237 19584 complement fr 3 0.75 0.72 19237 19437 complement fr 3 0.66 0.04 19586 19795 complement fr 1 0.53 0.19 19850 20050 complement fr 1 0.58 0.99 19850 20020 complement fr 1 0.63 0.94 19850 20011 complement fr 1 0.64 0.03 19850 19996 complement fr 1 0.62 0.02 19850 19984 complement fr 1 0.58 0.04 20047 21306 complement fr 3 0.84 0.70 20047 21174 complement fr 3 0.88 0.51 20047 21165 complement fr 3 0.88 0.53 20047 21159 complement fr 3 0.88 0.48 21303 23141 complement fr 2 0.89 0.40 21303 23126 complement fr 2 0.90 0.10 21303 23012 complement fr 2 0.90 0.08 21303 22949 complement fr 2 0.90 0.17 21303 22829 complement fr 2 0.91 0.20 21303 22511 complement fr 2 0.90 0.22 23132 23545 complement fr 1 0.72 0.17 23132 23443 complement fr 1 0.76 0.22 23132 23389 complement fr 1 0.72 0.18 23132 23341 complement fr 1 0.67 0.42 23948 24763 complement fr 1 0.64 0.38 23948 24616 complement fr 1 0.61 0.20 23948 24247 complement fr 1 0.72 0.09 23948 24190 complement fr 1 0.67 0.18 24887 25282 complement fr 1 0.53 0.09 24887 25243 complement fr 1 0.57 0.47 24887 25222 complement fr 1 0.57 0.85 24887 25204 complement fr 1 0.56 0.57 25858 26922 complement fr 3 0.73 0.76 25858 26838 complement fr 3 0.72 0.05 25858 26802 complement fr 3 0.71 0.05 26922 27707 complement fr 2 0.63 0.23 26922 27647 complement fr 2 0.64 0.19 26922 27623 complement fr 2 0.64 0.67 27704 27970 complement fr 1 0.71 0.84 27704 27922 complement fr 1 0.73 0.08 27704 27907 complement fr 1 0.71 0.32 27704 27898 complement fr 1 0.70 0.17 27972 28625 complement fr 2 0.72 0.53 27972 28550 complement fr 2 0.75 0.28 27972 28523 complement fr 2 0.76 0.35 27972 28469 complement fr 2 0.75 0.46 27972 28463 complement fr 2 0.75 0.26 28622 29545 complement fr 1 0.80 0.83 28622 29005 complement fr 1 0.82 0.12 28622 28894 complement fr 1 0.80 0.45 28622 28816 complement fr 1 0.75 0.27 29542 30909 complement fr 3 0.86 0.56 29542 30513 complement fr 3 0.83 0.09 29542 30486 complement fr 3 0.83 0.01 29542 30141 complement fr 3 0.88 0.35 30909 31373 complement fr 2 0.85 0.94 30909 31262 complement fr 2 0.83 0.55 30909 31046 complement fr 2 0.62 0.03 31370 32689 complement fr 1 0.87 0.63 31370 32602 complement fr 1 0.89 0.41 31370 32575 complement fr 1 0.89 0.33 31370 32566 complement fr 1 0.89 0.17 32887 33768 direct fr 1 0.87 0.40 33001 33768 direct fr 1 0.88 0.58 33040 33768 direct fr 1 0.88 0.10 33193 33768 direct fr 1 0.85 0.14 33701 34027 direct fr 2 0.63 0.01 33749 34027 direct fr 2 0.73 0.74 33773 34027 direct fr 2 0.78 0.94 33872 34027 direct fr 2 0.69 0.11 33899 34027 direct fr 2 0.66 0.26 34014 34385 direct fr 3 0.72 0.10 34062 34385 direct fr 3 0.83 0.49 34104 34385 direct fr 3 0.87 0.59 34200 34385 direct fr 3 0.80 0.32 34284 34385 direct fr 3 0.67 0.04 34382 34750 direct fr 2 0.76 0.10 34747 35091 direct fr 1 0.66 0.74 35078 37192 direct fr 2 0.89 0.72 35132 37192 direct fr 2 0.91 0.08 35141 37192 direct fr 2 0.91 0.00 35156 37192 direct fr 2 0.91 0.00 37189 37629 direct fr 1 0.69 0.83 37192 37629 direct fr 1 0.69 0.45 37348 37629 direct fr 1 0.75 0.31 37363 37629 direct fr 1 0.74 0.36 37408 37629 direct fr 1 0.69 0.19 37671 37958 direct fr 3 0.67 0.66 37767 37958 direct fr 3 0.75 0.01 37803 37958 direct fr 3 0.70 0.06 37960 38934 direct fr 1 0.65 0.23 38020 38934 direct fr 1 0.68 0.76 38314 38934 direct fr 1 0.64 0.32 38323 38934 direct fr 1 0.64 0.36 38937 39443 direct fr 3 0.71 0.98 38979 39443 direct fr 3 0.78 0.02 39015 39443 direct fr 3 0.76 0.37 39126 39443 direct fr 3 0.76 0.26 39421 40626 direct fr 1 0.73 0.13 39553 40626 direct fr 1 0.78 0.01 39592 40626 direct fr 1 0.77 0.55 39700 40626 direct fr 1 0.75 0.65 40645 41565 direct fr 1 0.88 0.05 40813 41565 direct fr 1 0.91 0.60 40939 41565 direct fr 1 0.89 0.02 41008 41565 direct fr 1 0.88 0.10 42691 42900 direct fr 1 0.53 0.00 42757 42900 direct fr 1 0.65 0.83 43231 44397 direct fr 1 0.73 0.01 43294 44397 direct fr 1 0.77 0.04 43369 44397 direct fr 1 0.80 0.14 43471 44397 direct fr 1 0.80 0.07 43582 44397 direct fr 1 0.78 0.11 45633 45803 complement fr 2 0.55 0.63 45633 45770 complement fr 2 0.51 0.02 46757 47155 complement fr 1 0.77 0.68 46757 47131 complement fr 1 0.82 0.41 46757 47056 complement fr 1 0.78 0.33 47155 48123 complement fr 3 0.52 0.02 47155 48036 complement fr 3 0.55 0.08 47155 48018 complement fr 3 0.54 0.10 47155 48012 complement fr 3 0.54 0.09 49769 50398 direct fr 2 0.85 0.89 49781 50398 direct fr 2 0.86 0.65 49859 50398 direct fr 2 0.87 0.85 50505 50822 direct fr 3 0.75 0.80 50676 50822 direct fr 3 0.77 0.04 50846 51304 direct fr 2 0.81 0.35 50993 51304 direct fr 2 0.80 0.39 51014 51304 direct fr 2 0.79 0.12 51017 51304 direct fr 2 0.79 0.08 51413 51610 direct fr 2 0.57 0.38 51416 51610 direct fr 2 0.57 0.31 51425 51610 direct fr 2 0.59 0.11 51461 51610 direct fr 2 0.65 0.47 51470 51610 direct fr 2 0.63 0.72 51515 51610 direct fr 2 0.53 0.34 52368 53576 direct fr 3 0.77 0.08 52410 53576 direct fr 3 0.81 0.68 52458 53576 direct fr 3 0.81 0.29 52623 53576 direct fr 3 0.78 0.07 52677 53576 direct fr 3 0.77 0.09 53573 54538 direct fr 2 0.75 0.05 53576 54538 direct fr 2 0.75 0.12 53591 54538 direct fr 2 0.76 0.51 53675 54538 direct fr 2 0.80 0.65 53705 54538 direct fr 2 0.80 0.01 53765 54538 direct fr 2 0.83 0.33 54017 54538 direct fr 2 0.81 0.04 54311 54538 direct fr 2 0.62 0.56 54698 54934 direct fr 2 0.70 0.68 54743 54934 direct fr 2 0.71 0.19 54788 54934 direct fr 2 0.64 0.14 54833 54934 direct fr 2 0.51 0.33 55083 55256 complement fr 2 0.56 0.19 55083 55199 complement fr 2 0.50 0.68 55800 56042 direct fr 3 0.68 0.08 55848 56042 direct fr 3 0.81 0.71 55857 56042 direct fr 3 0.80 0.42 55893 56042 direct fr 3 0.76 0.43 56474 57133 complement fr 1 0.73 0.01 56474 57085 complement fr 1 0.79 0.05 56474 57058 complement fr 1 0.82 0.19 56474 56938 complement fr 1 0.79 0.09 56474 56926 complement fr 1 0.79 0.30 57327 57719 direct fr 3 0.65 0.41 57468 57719 direct fr 3 0.63 0.55 57588 57719 direct fr 3 0.52 0.33 57782 58396 complement fr 1 0.59 0.01 57782 58279 complement fr 1 0.54 0.06 57782 58267 complement fr 1 0.55 0.04 57782 58222 complement fr 1 0.60 0.23 57782 58165 complement fr 1 0.59 0.43 57782 58042 complement fr 1 0.64 0.19 58529 59701 direct fr 2 0.65 0.19 58553 59701 direct fr 2 0.67 0.24 58565 59701 direct fr 2 0.67 0.53 58607 59701 direct fr 2 0.69 0.04 58682 59701 direct fr 2 0.71 0.77 58703 59701 direct fr 2 0.71 0.67 58718 59701 direct fr 2 0.71 0.45 59698 60132 direct fr 1 0.68 0.99 59701 60132 direct fr 1 0.69 0.98 59737 60132 direct fr 1 0.73 0.01 59818 60132 direct fr 1 0.67 0.11 59860 60132 direct fr 1 0.65 0.60 59980 60132 direct fr 1 0.73 0.13 60476 60901 direct fr 2 0.70 0.98 60620 60901 direct fr 2 0.69 0.13 60629 60901 direct fr 2 0.68 0.05 61049 61858 complement fr 1 0.71 0.27 61049 61804 complement fr 1 0.70 0.36 61049 61801 complement fr 1 0.70 0.40 61882 62148 complement fr 3 0.79 0.90 61882 62079 complement fr 3 0.74 0.05 61882 62058 complement fr 3 0.71 0.01 63199 63834 complement fr 3 0.67 0.01 63199 63831 complement fr 3 0.67 0.01 63199 63822 complement fr 3 0.68 0.00 63199 63750 complement fr 3 0.77 0.08 63199 63669 complement fr 3 0.82 0.16 63199 63594 complement fr 3 0.80 0.07 63199 63588 complement fr 3 0.79 0.06 63914 66229 direct fr 2 0.84 0.36 63983 66229 direct fr 2 0.86 0.22 63992 66229 direct fr 2 0.86 0.24 64346 66229 direct fr 2 0.87 0.04 64565 66229 direct fr 2 0.85 0.03 66226 66606 complement fr 3 0.62 0.36 66226 66435 complement fr 3 0.77 0.05 66226 66396 complement fr 3 0.72 0.16 66226 66375 complement fr 3 0.70 0.47 67542 67634 direct fr 3 0.51 0.88 67580 68515 direct fr 2 0.76 0.03 67595 68515 direct fr 2 0.77 0.21 67940 68515 direct fr 2 0.82 0.14 67967 68515 direct fr 2 0.81 0.03 68129 68515 direct fr 2 0.74 0.04 68841 68987 complement fr 2 0.63 0.03 69146 69637 direct fr 2 0.72 0.26 69179 69637 direct fr 2 0.75 0.06 69188 69637 direct fr 2 0.77 0.01 69221 69637 direct fr 2 0.82 0.19 69329 69637 direct fr 2 0.84 0.37 69365 69637 direct fr 2 0.83 0.22 69401 69637 direct fr 2 0.81 0.70 69809 70126 direct fr 2 0.75 0.80 69980 70126 direct fr 2 0.77 0.04 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 39 1109 direct fr 3 492 830 complement fr 2 1028 1888 direct fr 2 1950 2357 direct fr 3 2229 2789 complement fr 2 2541 2714 direct fr 3 2651 3022 direct fr 2 3088 3414 direct fr 1 3708 4589 direct fr 3 4915 5097 direct fr 1 5416 5646 complement fr 3 5669 5968 complement fr 1 5899 6222 direct fr 1 5993 6238 complement fr 1 5999 6451 direct fr 2 6723 7196 direct fr 3 7198 9402 direct fr 1 9795 10664 direct fr 3 10608 10820 complement fr 2 11250 11954 complement fr 2 11816 12064 direct fr 2 11830 12171 direct fr 1 12266 13753 direct fr 2 12648 12938 complement fr 2 13974 14261 complement fr 2 13996 14169 complement fr 3 14265 14657 complement fr 2 14570 15055 complement fr 1 15028 15312 complement fr 3 15842 16228 complement fr 1 16414 17166 complement fr 3 17025 17756 complement fr 2 17654 18397 complement fr 1 18395 18745 complement fr 1 18743 19285 complement fr 1 19237 19617 complement fr 3 19586 19852 complement fr 1 19850 20059 complement fr 1 20047 21321 complement fr 3 20628 21329 direct fr 3 21303 23210 complement fr 2 23059 23319 direct fr 1 23132 23611 complement fr 1 23948 24781 complement fr 1 24887 25321 complement fr 1 25858 26982 complement fr 3 26922 27758 complement fr 2 27704 27991 complement fr 1 27972 28652 complement fr 2 28622 29551 complement fr 1 29542 30981 complement fr 3 30909 31406 complement fr 2 31370 32713 complement fr 1 32821 33768 direct fr 1 33698 34027 direct fr 2 34011 34385 direct fr 3 34304 34750 direct fr 2 34729 35091 direct fr 1 35066 37192 direct fr 2 37159 37629 direct fr 1 37665 37958 direct fr 3 37936 38934 direct fr 1 38922 39443 direct fr 3 39326 39610 complement fr 1 39403 40626 direct fr 1 39849 40403 complement fr 2 40630 41565 direct fr 1 42033 42257 complement fr 2 42199 42558 complement fr 3 42652 42900 direct fr 1 43177 44397 direct fr 1 44440 44760 complement fr 3 44639 44908 complement fr 1 44830 45105 direct fr 1 45633 46088 complement fr 2 46196 46354 complement fr 1 46757 47173 complement fr 1 47155 48135 complement fr 3 48572 49171 direct fr 2 49285 49554 direct fr 1 49482 49658 direct fr 3 49736 50398 direct fr 2 50496 50822 direct fr 3 50741 51304 direct fr 2 51302 51610 direct fr 2 51663 51848 complement fr 2 52314 53576 direct fr 3 53360 53587 complement fr 1 53552 54538 direct fr 2 54650 54934 direct fr 2 55083 55286 complement fr 2 55327 55656 direct fr 1 55764 56042 direct fr 3 56023 56334 direct fr 1 56474 57142 complement fr 1 57291 57719 direct fr 3 57770 58171 direct fr 2 57782 58432 complement fr 1 58463 58843 complement fr 1 58499 59701 direct fr 2 58910 59581 complement fr 1 59594 59785 complement fr 1 59686 60132 direct fr 1 60461 60901 direct fr 2 61049 61921 complement fr 1 61882 62199 complement fr 3 62248 62619 complement fr 3 63199 63855 complement fr 3 63890 66229 direct fr 2 66226 66654 complement fr 3 67197 67463 direct fr 3 67358 68515 direct fr 2 67488 67634 direct fr 3 67698 67904 direct fr 3 68518 68922 complement fr 3 68841 69137 complement fr 2 69113 69637 direct fr 2 69380 69688 complement fr 1 69800 70126 direct fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 3 49476 +/- 11 bp (direct) 2 3 67776 +/- 11 bp (direct) 2 3 67824 +/- 11 bp (direct) 2 3 67836 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 22:02:23 2007