GENEMARK PREDICTIONS Sequence: gi|47104025|ref|NC_005871.1| Photobacterium profundum SS9 plasmid pPBPR1, complete sequence Sequence file: NC_005871.fna Sequence length: 80033 GC Content: 44.03% 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 -------- -------- ---------- ----- ---- ---- 1503 1775 direct fr 3 0.62 0.56 1641 1775 direct fr 3 0.52 0.08 1778 2080 direct fr 2 0.51 0.15 2007 2654 direct fr 3 0.76 0.02 2091 2654 direct fr 3 0.86 0.71 2238 2654 direct fr 3 0.88 0.13 2307 2654 direct fr 3 0.88 0.02 2651 3385 direct fr 2 0.79 0.07 2693 3385 direct fr 2 0.85 0.71 2798 3385 direct fr 2 0.84 0.59 2801 3385 direct fr 2 0.84 0.36 3379 4848 direct fr 1 0.88 0.52 3382 4848 direct fr 1 0.88 0.30 3385 4848 direct fr 1 0.89 0.49 3526 4848 direct fr 1 0.88 0.76 3598 4848 direct fr 1 0.88 0.05 3655 4848 direct fr 1 0.87 0.00 4860 5255 direct fr 3 0.61 0.60 4872 5255 direct fr 3 0.63 0.18 4917 5255 direct fr 3 0.69 0.04 4971 5255 direct fr 3 0.71 0.84 4980 5255 direct fr 3 0.71 0.40 5259 7847 direct fr 3 0.84 0.20 5439 7847 direct fr 3 0.87 0.45 5502 7847 direct fr 3 0.87 0.19 5523 7847 direct fr 3 0.87 0.05 7844 8203 direct fr 2 0.82 0.44 7874 8203 direct fr 2 0.87 0.34 7949 8203 direct fr 2 0.88 0.41 7955 8203 direct fr 2 0.88 0.32 8200 8445 direct fr 1 0.69 0.83 8406 9104 direct fr 3 0.85 0.83 8415 9104 direct fr 3 0.86 0.91 8505 9104 direct fr 3 0.89 0.56 8541 9104 direct fr 3 0.89 0.39 8601 9104 direct fr 3 0.88 0.18 9108 10112 direct fr 3 0.73 0.13 9240 10112 direct fr 3 0.82 0.88 9255 10112 direct fr 3 0.82 0.40 9300 10112 direct fr 3 0.82 0.01 9339 10112 direct fr 3 0.82 0.50 9390 10112 direct fr 3 0.84 0.22 10303 11007 direct fr 1 0.71 0.01 10525 11007 direct fr 1 0.76 0.02 10609 11007 direct fr 1 0.72 0.02 10633 11007 direct fr 1 0.70 0.15 10904 12811 direct fr 2 0.74 0.00 10931 12811 direct fr 2 0.75 0.00 10961 12811 direct fr 2 0.76 0.15 10964 12811 direct fr 2 0.76 0.16 11009 12811 direct fr 2 0.78 0.11 11021 12811 direct fr 2 0.78 0.17 11042 12811 direct fr 2 0.79 0.53 11243 12811 direct fr 2 0.76 0.01 11294 12811 direct fr 2 0.75 0.00 12808 13599 direct fr 1 0.78 0.02 12865 13599 direct fr 1 0.84 0.83 12868 13599 direct fr 1 0.84 0.79 12991 13599 direct fr 1 0.84 0.15 13021 13599 direct fr 1 0.85 0.57 13105 13599 direct fr 1 0.83 0.01 13132 13599 direct fr 1 0.82 0.16 13611 14051 direct fr 3 0.68 0.10 13656 14051 direct fr 3 0.74 0.71 13833 14051 direct fr 3 0.77 0.06 13848 14051 direct fr 3 0.76 0.11 13911 14051 direct fr 3 0.65 0.14 14048 15409 direct fr 2 0.90 0.09 14219 15409 direct fr 2 0.93 0.09 14297 15409 direct fr 2 0.93 0.08 15384 18218 direct fr 3 0.87 0.20 15414 18218 direct fr 3 0.89 0.94 15510 18218 direct fr 3 0.89 0.06 15564 18218 direct fr 3 0.89 0.47 18222 18677 complement fr 2 0.61 0.09 18222 18665 complement fr 2 0.63 0.09 18222 18632 complement fr 2 0.64 0.93 18222 18626 complement fr 2 0.64 0.63 18779 19150 direct fr 2 0.63 0.10 18926 19150 direct fr 2 0.74 0.42 18938 19150 direct fr 2 0.73 0.03 19147 21252 direct fr 1 0.92 0.43 19216 21252 direct fr 1 0.93 0.23 19252 21252 direct fr 1 0.94 0.08 19348 21252 direct fr 1 0.94 0.00 19537 21252 direct fr 1 0.95 0.58 21904 22164 direct fr 1 0.52 0.77 22102 22194 complement fr 3 0.64 0.02 22102 22185 complement fr 3 0.71 0.02 22182 23330 complement fr 2 0.72 0.20 22182 23318 complement fr 2 0.73 0.54 22182 23303 complement fr 2 0.73 0.46 22182 23273 complement fr 2 0.74 0.07 22182 23240 complement fr 2 0.74 0.66 23447 29434 direct fr 2 0.94 0.06 23492 29434 direct fr 2 0.95 0.82 23693 29434 direct fr 2 0.95 0.02 23732 29434 direct fr 2 0.95 0.02 23762 29434 direct fr 2 0.95 0.01 29463 29849 complement fr 2 0.79 0.24 29463 29837 complement fr 2 0.81 0.72 29463 29831 complement fr 2 0.84 0.83 29463 29813 complement fr 2 0.87 0.86 29463 29762 complement fr 2 0.89 0.05 29463 29714 complement fr 2 0.87 0.36 29463 29654 complement fr 2 0.83 0.08 31512 31727 complement fr 2 0.58 0.01 31512 31715 complement fr 2 0.62 0.09 31512 31706 complement fr 2 0.62 0.35 31512 31658 complement fr 2 0.60 0.31 31512 31652 complement fr 2 0.59 0.12 31938 32915 complement fr 2 0.77 0.15 31938 32795 complement fr 2 0.77 0.37 31938 32786 complement fr 2 0.77 0.29 31938 32774 complement fr 2 0.77 0.26 33557 34747 direct fr 2 0.66 0.82 33650 34747 direct fr 2 0.65 0.02 33692 34747 direct fr 2 0.64 0.55 33725 34747 direct fr 2 0.63 0.24 34750 35835 direct fr 1 0.85 0.56 35017 35835 direct fr 1 0.89 0.06 35074 35835 direct fr 1 0.89 0.38 35341 35835 direct fr 1 0.88 0.22 36319 36435 direct fr 1 0.50 0.18 36432 36779 complement fr 2 0.75 0.18 36432 36722 complement fr 2 0.82 0.37 36432 36683 complement fr 2 0.78 0.24 36432 36587 complement fr 2 0.74 0.61 36895 37698 complement fr 3 0.73 0.16 36895 37692 complement fr 3 0.74 0.07 36895 37683 complement fr 3 0.74 0.10 36895 37614 complement fr 3 0.80 0.25 36895 37593 complement fr 3 0.83 0.42 36895 37410 complement fr 3 0.81 0.21 36895 37392 complement fr 3 0.82 0.29 36895 37377 complement fr 3 0.81 0.17 38487 38996 complement fr 2 0.80 0.15 38487 38879 complement fr 2 0.83 0.18 38487 38816 complement fr 2 0.81 0.17 43366 43674 complement fr 3 0.51 0.00 43366 43668 complement fr 3 0.53 0.00 43366 43551 complement fr 3 0.69 0.87 43366 43536 complement fr 3 0.66 0.61 43366 43506 complement fr 3 0.61 0.03 43683 44603 complement fr 2 0.67 0.14 43683 44555 complement fr 2 0.68 0.58 43683 44477 complement fr 2 0.67 0.05 43683 44465 complement fr 2 0.66 0.07 43683 44444 complement fr 2 0.67 0.56 44619 46121 complement fr 2 0.67 0.38 44619 46115 complement fr 2 0.68 0.31 44619 46091 complement fr 2 0.69 0.46 44619 46046 complement fr 2 0.69 0.21 44619 45971 complement fr 2 0.67 0.03 44619 45923 complement fr 2 0.66 0.57 46078 46740 complement fr 3 0.52 0.62 46078 46725 complement fr 3 0.53 0.24 46078 46716 complement fr 3 0.54 0.07 46078 46713 complement fr 3 0.54 0.10 46078 46611 complement fr 3 0.61 0.16 46078 46500 complement fr 3 0.63 0.33 46078 46497 complement fr 3 0.63 0.17 46078 46482 complement fr 3 0.63 0.41 46753 47778 complement fr 3 0.83 0.02 46753 47730 complement fr 3 0.86 0.89 46753 47727 complement fr 3 0.86 0.91 46753 47577 complement fr 3 0.87 0.04 47819 48235 complement fr 1 0.61 0.21 47819 48070 complement fr 1 0.69 0.76 47819 48028 complement fr 1 0.64 0.00 47819 48001 complement fr 1 0.59 0.01 48251 48799 complement fr 1 0.55 0.22 48251 48796 complement fr 1 0.55 0.39 48251 48784 complement fr 1 0.56 0.22 48251 48781 complement fr 1 0.56 0.21 48251 48655 complement fr 1 0.68 0.83 48251 48652 complement fr 1 0.68 0.73 48251 48604 complement fr 1 0.66 0.17 48841 51273 complement fr 3 0.70 0.25 48841 51165 complement fr 3 0.71 0.31 48841 51075 complement fr 3 0.71 0.00 48841 50973 complement fr 3 0.70 0.04 48841 50898 complement fr 3 0.71 0.14 48841 50889 complement fr 3 0.71 0.04 51938 52891 complement fr 1 0.64 0.11 51938 52579 complement fr 1 0.59 0.07 51938 52456 complement fr 1 0.51 0.19 54037 56025 direct fr 1 0.56 0.19 54178 56025 direct fr 1 0.55 0.52 54244 56025 direct fr 1 0.55 0.27 54313 56025 direct fr 1 0.54 0.05 54370 56025 direct fr 1 0.53 0.36 54373 56025 direct fr 1 0.53 0.36 54586 56025 direct fr 1 0.52 0.57 55252 56025 direct fr 1 0.55 0.12 56287 57750 direct fr 1 0.51 0.13 56353 57750 direct fr 1 0.53 0.54 56497 57750 direct fr 1 0.53 0.08 56575 57750 direct fr 1 0.55 0.02 56641 57750 direct fr 1 0.56 0.49 57799 57882 direct fr 1 0.63 0.60 57823 57882 direct fr 1 0.65 0.20 57943 58239 complement fr 3 0.56 0.80 57943 58203 complement fr 3 0.58 0.23 59613 59972 complement fr 2 0.71 0.44 61198 61812 direct fr 1 0.69 0.07 61543 61812 direct fr 1 0.75 0.56 61600 61812 direct fr 1 0.80 0.76 61612 61812 direct fr 1 0.80 0.64 61636 61812 direct fr 1 0.78 0.08 61899 62543 complement fr 2 0.60 0.15 61899 62456 complement fr 2 0.60 0.10 61899 62315 complement fr 2 0.57 0.59 63869 64501 direct fr 2 0.76 0.29 63947 64501 direct fr 2 0.80 0.10 64025 64501 direct fr 2 0.78 0.79 64223 64501 direct fr 2 0.69 0.78 65355 65864 complement fr 2 0.51 0.77 66908 67033 direct fr 2 0.57 0.79 66932 67033 direct fr 2 0.54 0.40 67701 67967 complement fr 2 0.67 0.61 67701 67883 complement fr 2 0.65 0.33 67701 67847 complement fr 2 0.57 0.35 69510 70019 direct fr 3 0.51 0.18 69630 70019 direct fr 3 0.54 0.02 69681 70019 direct fr 3 0.55 0.21 69732 70019 direct fr 3 0.59 0.16 71507 72244 complement fr 1 0.63 0.55 71507 72163 complement fr 1 0.68 0.87 71507 72139 complement fr 1 0.68 0.32 71507 71992 complement fr 1 0.64 0.13 71507 71749 complement fr 1 0.58 0.13 74859 75119 direct fr 3 0.64 0.89 74910 75119 direct fr 3 0.78 0.01 74916 75119 direct fr 3 0.78 0.04 74970 75119 direct fr 3 0.75 0.65 75119 75421 direct fr 2 0.74 0.78 75239 75421 direct fr 2 0.80 0.31 75589 76602 direct fr 1 0.88 0.01 75616 76602 direct fr 1 0.90 0.56 75646 76602 direct fr 1 0.92 0.85 75757 76602 direct fr 1 0.93 0.62 75790 76602 direct fr 1 0.93 0.11 76913 77149 complement fr 1 0.53 0.70 76913 77134 complement fr 1 0.58 0.70 76913 77131 complement fr 1 0.58 0.62 77981 78859 complement fr 1 0.72 0.01 77981 78850 complement fr 1 0.73 0.01 77981 78841 complement fr 1 0.73 0.01 77981 78709 complement fr 1 0.76 0.20 77981 78475 complement fr 1 0.70 0.01 77981 78424 complement fr 1 0.74 0.90 77981 78271 complement fr 1 0.65 0.42 79373 79657 direct fr 2 0.85 0.26 79436 79657 direct fr 2 0.82 0.02 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 293 709 direct fr 2 777 1037 direct fr 3 1488 1775 direct fr 3 1694 2080 direct fr 2 1820 2296 complement fr 1 1992 2654 direct fr 3 2639 3385 direct fr 2 3250 4848 direct fr 1 4812 5255 direct fr 3 5055 5444 complement fr 2 5253 7847 direct fr 3 7793 8203 direct fr 2 8185 8445 direct fr 1 8376 9104 direct fr 3 9102 10112 direct fr 3 10084 10290 complement fr 3 10243 11007 direct fr 1 10853 12811 direct fr 2 12730 13599 direct fr 1 13605 14051 direct fr 3 13889 15409 direct fr 2 15357 18218 direct fr 3 18222 18704 complement fr 2 18749 19150 direct fr 2 19039 21252 direct fr 1 21640 22164 direct fr 1 22000 22104 complement fr 3 22047 22451 direct fr 3 22102 22302 complement fr 3 22182 23366 complement fr 2 22941 23198 direct fr 3 23444 29434 direct fr 2 29463 29852 complement fr 2 30909 31370 complement fr 2 31512 31760 complement fr 2 31938 32933 complement fr 2 33193 33393 direct fr 1 33524 34747 direct fr 2 34741 35835 direct fr 1 36003 36158 complement fr 2 36139 36435 direct fr 1 36432 36797 complement fr 2 36818 36964 complement fr 1 36895 37788 complement fr 3 37791 38294 complement fr 2 38487 39083 complement fr 2 43366 43704 complement fr 3 43683 44621 complement fr 2 44619 46133 complement fr 2 46078 46746 complement fr 3 46753 47799 complement fr 3 47819 48253 complement fr 1 48251 48811 complement fr 1 48841 51321 complement fr 3 51569 51868 direct fr 2 51938 53011 complement fr 1 54007 56025 direct fr 1 56023 57750 direct fr 1 57748 57882 direct fr 1 57943 58266 complement fr 3 59613 60008 complement fr 2 61156 61812 direct fr 1 61899 62561 complement fr 2 63086 63328 complement fr 1 63842 64501 direct fr 2 64511 64918 direct fr 2 64818 65036 direct fr 3 65355 66410 complement fr 2 66812 67033 direct fr 2 66957 67478 direct fr 3 67701 67982 complement fr 2 68253 70019 direct fr 3 70380 71471 complement fr 2 71507 72259 complement fr 1 73613 74278 direct fr 2 74853 75119 direct fr 3 75089 75421 direct fr 2 75586 76602 direct fr 1 76913 77182 complement fr 1 77981 78880 complement fr 1 79265 79657 direct fr 2 -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 18:33:45 2007