GENEMARK PREDICTIONS Sequence: gi|118445179|ref|NC_008598.1| Bacillus thuringiensis str. Al Hakam plasmid pALH1, complete sequence Sequence file: NC_008598.fna Sequence length: 55939 GC Content: 36.15% 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 -------- -------- ---------- ----- ---- ---- 1 693 complement fr 3 0.89 0.51 1 687 complement fr 3 0.89 0.67 1 522 complement fr 3 0.94 0.31 1 504 complement fr 3 0.94 0.71 1 495 complement fr 3 0.94 0.13 665 1603 complement fr 1 0.89 0.98 665 1600 complement fr 1 0.89 0.98 665 1594 complement fr 1 0.90 0.79 665 1441 complement fr 1 0.90 0.09 665 1309 complement fr 1 0.93 0.90 665 1246 complement fr 1 0.93 0.00 1910 2098 direct fr 2 0.50 0.93 1919 2098 direct fr 2 0.50 0.83 2151 2975 complement fr 2 0.74 0.78 2151 2957 complement fr 2 0.75 0.95 2151 2720 complement fr 2 0.84 0.71 2151 2615 complement fr 2 0.81 0.89 2151 2591 complement fr 2 0.80 0.07 2988 3599 complement fr 2 0.87 0.97 2988 3572 complement fr 2 0.91 0.98 2988 3485 complement fr 2 0.90 0.06 2988 3431 complement fr 2 0.89 0.02 3833 3958 direct fr 2 0.63 0.71 3951 4046 complement fr 2 0.55 0.12 3951 4037 complement fr 2 0.59 0.02 4075 4305 complement fr 3 0.69 0.98 4394 4720 complement fr 1 0.79 0.99 4394 4591 complement fr 1 0.72 0.47 4394 4582 complement fr 1 0.70 0.07 4394 4567 complement fr 1 0.68 0.01 5796 6182 complement fr 2 0.84 0.95 5796 6077 complement fr 2 0.83 0.04 5796 5981 complement fr 2 0.74 0.53 5796 5903 complement fr 2 0.55 0.55 6320 6949 complement fr 1 0.89 0.90 6320 6928 complement fr 1 0.93 0.91 6320 6892 complement fr 1 0.92 0.07 6320 6874 complement fr 1 0.92 0.03 7156 7344 complement fr 3 0.56 0.98 7156 7320 complement fr 3 0.57 0.39 7347 7544 complement fr 2 0.54 0.53 7347 7538 complement fr 2 0.54 0.07 8941 9540 complement fr 3 0.91 0.94 8941 9420 complement fr 3 0.93 0.00 8941 9384 complement fr 3 0.93 0.41 8941 9354 complement fr 3 0.92 0.04 9581 9790 complement fr 1 0.69 0.73 9581 9754 complement fr 1 0.77 0.86 9581 9718 complement fr 1 0.71 0.00 9828 10325 complement fr 2 0.79 0.94 9828 10274 complement fr 2 0.80 0.04 9828 10211 complement fr 2 0.76 0.29 9828 9905 complement fr 2 0.52 0.09 10330 10506 complement fr 3 0.65 0.95 10330 10440 complement fr 3 0.64 0.04 10330 10422 complement fr 3 0.60 0.46 10517 10798 complement fr 1 0.64 0.97 10517 10786 complement fr 1 0.67 0.52 10517 10783 complement fr 1 0.67 0.54 10517 10774 complement fr 1 0.66 0.22 10788 11183 complement fr 2 0.86 0.01 10788 11126 complement fr 2 0.97 0.81 10788 11117 complement fr 2 1.00 0.99 10788 11069 complement fr 2 1.00 0.00 10788 10868 complement fr 2 1.00 0.02 11250 11963 complement fr 2 0.83 0.41 11250 11951 complement fr 2 0.82 0.56 11250 11891 complement fr 2 0.81 0.00 11975 12238 complement fr 1 0.82 0.98 11975 12211 complement fr 1 0.85 0.14 11975 12091 complement fr 1 0.69 0.26 11975 12058 complement fr 1 0.56 0.00 12235 12522 complement fr 3 0.70 0.16 12235 12480 complement fr 3 0.79 0.40 12235 12456 complement fr 3 0.77 0.77 12235 12369 complement fr 3 0.64 0.07 12437 12700 complement fr 1 0.60 0.46 12437 12649 complement fr 1 0.67 0.24 12437 12595 complement fr 1 0.56 0.02 12713 13630 complement fr 1 0.88 0.11 12713 13609 complement fr 1 0.89 0.10 12713 13594 complement fr 1 0.91 0.07 12713 13561 complement fr 1 0.93 0.56 12713 13537 complement fr 1 0.93 0.64 12713 13486 complement fr 1 0.92 0.11 13545 14360 complement fr 2 0.81 0.42 13545 14321 complement fr 2 0.85 0.66 13545 13979 complement fr 2 0.86 0.88 13545 13964 complement fr 2 0.85 0.16 13545 13898 complement fr 2 0.83 0.00 14361 14582 complement fr 2 0.78 0.99 14361 14552 complement fr 2 0.84 0.99 14361 14543 complement fr 2 0.83 0.22 14782 15456 complement fr 3 0.92 0.98 14782 15282 complement fr 3 0.90 0.18 14782 15189 complement fr 3 0.88 0.33 15453 15941 complement fr 2 0.91 0.65 15453 15935 complement fr 2 0.92 0.80 15453 15893 complement fr 2 0.92 0.32 15453 15890 complement fr 2 0.92 0.23 15948 16103 complement fr 2 0.78 1.00 15948 16097 complement fr 2 0.78 1.00 15948 16088 complement fr 2 0.82 0.99 15948 16043 complement fr 2 0.80 0.01 16555 17343 complement fr 3 0.89 0.36 16555 17325 complement fr 3 0.92 0.24 16555 17295 complement fr 3 0.92 0.49 16555 17226 complement fr 3 0.91 0.00 17365 17517 complement fr 3 0.64 0.31 17365 17475 complement fr 3 0.53 0.07 17718 18068 direct fr 3 0.79 0.91 17760 18068 direct fr 3 0.86 0.13 17802 18068 direct fr 3 0.84 0.00 18107 18238 complement fr 1 0.55 0.63 18107 18229 complement fr 1 0.55 0.81 18107 18211 complement fr 1 0.55 0.93 18389 18502 complement fr 1 0.62 0.96 18389 18493 complement fr 1 0.62 0.26 18578 19798 complement fr 1 0.71 0.06 18578 19759 complement fr 1 0.73 0.01 18578 19726 complement fr 1 0.75 0.93 18578 19600 complement fr 1 0.72 0.19 18578 19570 complement fr 1 0.71 0.20 20223 20570 direct fr 3 0.79 0.35 20775 21479 direct fr 3 0.89 0.04 20895 21479 direct fr 3 0.96 0.86 20904 21479 direct fr 3 0.96 0.82 21586 21843 direct fr 1 0.90 0.15 21682 21843 direct fr 1 0.84 0.23 21715 21843 direct fr 1 0.80 0.00 21978 22541 direct fr 3 0.76 0.80 22344 22541 direct fr 3 0.77 0.03 23171 24130 direct fr 2 0.86 0.68 23192 24130 direct fr 2 0.88 0.87 23201 24130 direct fr 2 0.89 0.82 23207 24130 direct fr 2 0.89 0.07 23369 24130 direct fr 2 0.89 0.07 23399 24130 direct fr 2 0.89 0.78 23609 24130 direct fr 2 0.85 0.14 24988 25209 complement fr 3 0.55 0.15 24988 25152 complement fr 3 0.63 0.31 25603 26979 complement fr 3 0.82 0.95 25603 26808 complement fr 3 0.82 0.18 25603 26673 complement fr 3 0.80 0.01 25603 26565 complement fr 3 0.78 0.17 28635 29465 direct fr 3 0.96 0.95 28644 29465 direct fr 3 0.96 0.97 28791 29465 direct fr 3 0.95 0.42 29458 29841 direct fr 1 0.74 0.60 29467 29841 direct fr 1 0.77 0.93 29722 29841 direct fr 1 0.67 0.01 29957 30316 direct fr 2 0.74 0.53 29999 30316 direct fr 2 0.82 0.56 30053 30316 direct fr 2 0.82 0.08 30182 30316 direct fr 2 0.67 0.40 30215 30316 direct fr 2 0.60 0.01 30333 30599 direct fr 3 0.53 0.16 30360 30599 direct fr 3 0.58 0.74 30483 30599 direct fr 3 0.62 0.46 30492 30599 direct fr 3 0.62 0.13 31028 31876 direct fr 2 0.86 0.84 31352 31876 direct fr 2 0.84 0.05 31394 31876 direct fr 2 0.83 0.45 31436 31876 direct fr 2 0.82 0.13 32177 33106 direct fr 2 0.77 0.47 32264 33106 direct fr 2 0.76 0.00 32303 33106 direct fr 2 0.75 0.76 33427 34017 complement fr 3 0.85 0.69 33427 33939 complement fr 3 0.90 0.86 33427 33909 complement fr 3 0.89 0.15 33427 33861 complement fr 3 0.88 0.01 34128 34391 complement fr 2 0.72 0.49 34128 34292 complement fr 2 0.65 0.08 34887 36152 direct fr 3 0.69 0.12 34971 36152 direct fr 3 0.73 0.83 35004 36152 direct fr 3 0.73 0.74 35016 36152 direct fr 3 0.73 0.02 36149 36490 direct fr 2 0.66 0.69 36164 36490 direct fr 2 0.68 0.92 36182 36490 direct fr 2 0.74 0.99 36209 36490 direct fr 2 0.75 0.17 36308 36490 direct fr 2 0.62 0.01 36660 37568 direct fr 3 0.89 1.00 36687 37568 direct fr 3 0.91 0.79 36819 37568 direct fr 3 0.93 0.32 37050 37568 direct fr 3 0.91 0.00 37581 37934 direct fr 3 0.79 0.99 37812 37934 direct fr 3 0.73 0.18 37860 37934 direct fr 3 0.57 0.26 38131 38892 complement fr 3 0.88 0.34 38131 38817 complement fr 3 0.92 0.01 38131 38739 complement fr 3 0.91 0.04 38131 38619 complement fr 3 0.89 0.01 38892 39026 complement fr 2 0.65 0.94 38892 38987 complement fr 2 0.50 0.19 39119 39400 complement fr 1 0.82 0.82 39119 39382 complement fr 1 0.82 0.05 39119 39286 complement fr 1 0.71 0.04 39442 40110 complement fr 3 0.90 0.92 39442 40059 complement fr 3 0.93 0.05 39442 39831 complement fr 3 0.90 0.31 39442 39726 complement fr 3 0.86 0.09 40125 41714 complement fr 2 0.91 0.09 40125 41528 complement fr 2 0.90 0.16 40125 41519 complement fr 2 0.90 0.08 41775 42041 complement fr 2 0.53 0.95 42051 43898 complement fr 2 0.91 0.60 42051 43817 complement fr 2 0.93 0.00 42051 43787 complement fr 2 0.94 0.19 42051 43754 complement fr 2 0.94 0.78 43910 44791 complement fr 1 0.78 0.73 43910 44785 complement fr 1 0.78 0.88 43910 44770 complement fr 1 0.78 0.75 43910 44755 complement fr 1 0.78 0.49 43910 44728 complement fr 1 0.77 0.07 44791 47466 complement fr 3 0.92 0.00 44791 47445 complement fr 3 0.91 0.00 44791 47433 complement fr 3 0.91 0.00 47533 47793 complement fr 3 0.82 0.18 47533 47760 complement fr 3 0.80 0.25 47533 47712 complement fr 3 0.78 0.16 47871 48287 complement fr 2 0.81 0.82 47871 48185 complement fr 2 0.87 0.20 47871 48176 complement fr 2 0.86 0.41 47871 48128 complement fr 2 0.84 0.01 48353 48826 complement fr 1 0.90 0.99 48353 48817 complement fr 1 0.90 1.00 48353 48784 complement fr 1 0.91 0.02 48353 48532 complement fr 1 0.79 0.09 48353 48511 complement fr 1 0.75 0.10 48832 49260 complement fr 3 0.74 0.51 48832 49233 complement fr 3 0.78 0.14 48832 49209 complement fr 3 0.80 0.33 48832 49056 complement fr 3 0.72 0.34 48832 49017 complement fr 3 0.67 0.22 49236 49727 complement fr 2 0.85 0.32 49236 49670 complement fr 2 0.89 0.56 49236 49601 complement fr 2 0.87 0.01 49236 49571 complement fr 2 0.86 0.05 49712 50104 complement fr 1 0.68 0.03 49712 50089 complement fr 1 0.70 0.28 49712 50086 complement fr 1 0.72 0.18 50104 50502 complement fr 3 0.76 0.98 50104 50493 complement fr 3 0.78 0.99 50104 50442 complement fr 3 0.77 0.00 50104 50322 complement fr 3 0.65 0.01 50698 51615 complement fr 3 0.94 0.97 50698 51249 complement fr 3 0.91 0.02 50698 50997 complement fr 3 0.84 0.20 51631 52818 complement fr 3 0.95 0.15 51631 52698 complement fr 3 0.99 0.05 51631 52569 complement fr 3 0.99 0.00 51631 52482 complement fr 3 0.99 0.02 52865 53815 complement fr 1 0.88 0.96 52865 53791 complement fr 1 0.90 1.00 52865 53686 complement fr 1 0.90 0.10 52865 53461 complement fr 1 0.88 0.84 52865 53452 complement fr 1 0.88 0.46 53778 55316 complement fr 2 0.91 0.89 53778 55256 complement fr 2 0.93 0.01 53778 55091 complement fr 2 0.93 0.30 53778 55052 complement fr 2 0.92 0.04 55316 55939 complement fr 1 0.78 .... 55316 55894 complement fr 1 0.78 .... 55316 55804 complement fr 1 0.80 0.45 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 4 708 complement fr 3 665 1624 complement fr 1 1907 2098 direct fr 2 2151 2990 complement fr 2 2988 3611 complement fr 2 3701 3958 direct fr 2 3951 4085 complement fr 2 4075 4311 complement fr 3 4394 4741 complement fr 1 5796 6227 complement fr 2 6320 6973 complement fr 1 6952 7149 complement fr 3 7156 7371 complement fr 3 7347 7667 complement fr 2 8941 9546 complement fr 3 9581 9796 complement fr 1 9828 10343 complement fr 2 10330 10527 complement fr 3 10517 10825 complement fr 1 10788 11213 complement fr 2 11101 11274 complement fr 3 11250 12011 complement fr 2 11975 12265 complement fr 1 12235 12561 complement fr 3 12437 12715 complement fr 1 12713 13633 complement fr 1 13545 14363 complement fr 2 14361 14591 complement fr 2 14782 15474 complement fr 3 15453 15950 complement fr 2 15948 16118 complement fr 2 16308 16454 complement fr 2 16445 16651 complement fr 1 16555 17367 complement fr 3 17365 17607 complement fr 3 17700 18068 direct fr 3 18107 18286 complement fr 1 18389 18541 complement fr 1 18578 19825 complement fr 1 20199 20570 direct fr 3 20697 21479 direct fr 3 21484 21843 direct fr 1 21954 22541 direct fr 3 23156 24130 direct fr 2 24482 24658 direct fr 2 24988 25221 complement fr 3 25603 26994 complement fr 3 28521 29465 direct fr 3 29449 29841 direct fr 1 29948 30316 direct fr 2 30324 30599 direct fr 3 30938 31876 direct fr 2 32063 33106 direct fr 2 33427 34059 complement fr 3 34128 34418 complement fr 2 34581 34811 complement fr 2 34851 36152 direct fr 3 36143 36490 direct fr 2 36588 37568 direct fr 3 37566 37934 direct fr 3 38131 38898 complement fr 3 38892 39125 complement fr 2 39119 39469 complement fr 1 39442 40131 complement fr 3 40125 41765 complement fr 2 41775 42053 complement fr 2 42051 43907 complement fr 2 43910 44833 complement fr 1 44791 47535 complement fr 3 47533 48024 complement fr 3 47871 48290 complement fr 2 48353 48859 complement fr 1 48832 49266 complement fr 3 49236 49733 complement fr 2 49712 50134 complement fr 1 50104 50520 complement fr 3 50499 50684 complement fr 2 50698 51633 complement fr 3 51631 52821 complement fr 3 52865 53827 complement fr 1 53778 55328 complement fr 2 55316 55939 complement fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 2 1 10776 +/- 11 bp (complement) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 14:08:27 2007