GENEMARK PREDICTIONS Sequence: gi|159046605|ref|NC_009958.1| Dinoroseobacter shibae DFL 12 plasmid pDSHI04, complete sequence Sequence file: NC_009958.fna Sequence length: 86208 GC Content: 61.05% 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 -------- -------- ---------- ----- ---- ---- 2525 2776 complement fr 1 0.62 0.40 2525 2647 complement fr 1 0.52 0.47 2525 2644 complement fr 1 0.52 0.40 2937 6497 direct fr 3 0.78 0.00 2964 6497 direct fr 3 0.78 0.00 3168 6497 direct fr 3 0.83 0.30 3255 6497 direct fr 3 0.84 0.78 3447 6497 direct fr 3 0.84 0.02 3546 6497 direct fr 3 0.83 0.12 6617 7027 complement fr 1 0.66 0.45 6617 7000 complement fr 1 0.64 0.25 6617 6967 complement fr 1 0.62 0.01 7067 7495 complement fr 1 0.82 0.51 7067 7444 complement fr 1 0.88 0.51 7067 7435 complement fr 1 0.88 0.76 7067 7249 complement fr 1 0.88 0.27 7492 7638 complement fr 3 0.51 0.43 8880 9245 direct fr 3 1.00 0.03 8931 9245 direct fr 3 1.00 0.02 9087 9245 direct fr 3 0.99 0.01 9370 10845 direct fr 1 0.80 0.02 9760 10845 direct fr 1 0.98 0.42 9778 10845 direct fr 1 0.98 0.10 9781 10845 direct fr 1 0.98 0.16 10862 11521 direct fr 2 0.96 0.88 10895 11521 direct fr 2 0.95 0.10 10919 11521 direct fr 2 0.95 0.00 11557 11931 direct fr 1 0.83 0.16 11725 11931 direct fr 1 0.81 0.06 11854 11931 direct fr 1 0.60 0.34 11866 11931 direct fr 1 0.55 0.37 12125 13507 direct fr 2 0.56 0.28 12128 13507 direct fr 2 0.56 0.17 12305 13507 direct fr 2 0.60 0.14 12314 13507 direct fr 2 0.60 0.12 12371 13507 direct fr 2 0.58 0.30 13911 15719 complement fr 2 0.77 0.00 13911 15623 complement fr 2 0.81 0.17 13911 15449 complement fr 2 0.83 0.05 13911 15407 complement fr 2 0.83 0.04 13911 15344 complement fr 2 0.82 0.61 16240 17085 complement fr 3 0.53 0.22 16240 16839 complement fr 3 0.72 0.78 16240 16644 complement fr 3 0.68 0.47 16240 16569 complement fr 3 0.62 0.10 17959 18471 direct fr 1 0.51 0.16 19191 19292 direct fr 3 0.63 0.80 19224 19292 direct fr 3 0.55 0.20 19415 19981 direct fr 2 0.73 0.99 19502 19981 direct fr 2 0.76 0.22 19556 19981 direct fr 2 0.76 0.98 19586 19981 direct fr 2 0.74 0.36 19968 20222 direct fr 3 0.70 0.17 20031 20222 direct fr 3 0.81 0.23 20058 20222 direct fr 3 0.79 0.34 20685 20852 direct fr 3 0.55 0.44 20972 21250 direct fr 2 0.57 0.20 21011 21250 direct fr 2 0.59 0.56 21044 21250 direct fr 2 0.53 0.04 21412 22251 complement fr 3 0.85 0.29 21412 22221 complement fr 3 0.89 0.12 21412 22209 complement fr 3 0.89 0.60 21412 22194 complement fr 3 0.89 0.43 22245 22511 complement fr 2 0.68 0.53 22245 22472 complement fr 2 0.77 0.91 22245 22448 complement fr 2 0.76 0.01 23371 23529 direct fr 1 0.55 0.30 23416 23529 direct fr 1 0.51 0.70 24188 25330 complement fr 1 0.55 0.02 24188 25219 complement fr 1 0.61 0.21 24188 25168 complement fr 1 0.62 0.37 24188 25000 complement fr 1 0.58 0.05 24188 24997 complement fr 1 0.58 0.02 25327 25485 complement fr 3 0.51 0.88 25737 26090 complement fr 2 0.58 0.95 25737 26084 complement fr 2 0.58 0.89 25737 26051 complement fr 2 0.56 0.02 26979 27338 direct fr 3 0.50 0.00 26997 27338 direct fr 3 0.52 0.00 27234 27338 direct fr 3 0.75 0.81 27240 27338 direct fr 3 0.75 0.48 28140 28574 complement fr 2 0.86 0.29 28140 28526 complement fr 2 0.84 0.22 28140 28484 complement fr 2 0.82 0.23 28656 28772 complement fr 2 0.81 0.77 28656 28739 complement fr 2 0.73 0.18 28656 28736 complement fr 2 0.73 0.07 28862 30055 complement fr 1 0.84 0.16 28862 29956 complement fr 1 0.83 0.04 28862 29911 complement fr 1 0.83 0.76 30113 30364 complement fr 1 0.62 0.00 30113 30340 complement fr 1 0.68 0.19 30113 30307 complement fr 1 0.80 0.25 30113 30244 complement fr 1 0.84 0.19 30488 30886 complement fr 1 0.50 0.84 30488 30877 complement fr 1 0.50 0.64 30488 30868 complement fr 1 0.50 0.66 32370 32585 direct fr 3 0.53 0.83 32424 32585 direct fr 3 0.67 0.11 34155 35036 complement fr 2 0.72 0.65 34155 34904 complement fr 2 0.71 0.12 34155 34808 complement fr 2 0.67 0.29 34155 34550 complement fr 2 0.52 0.02 37751 37960 direct fr 2 0.52 0.03 39501 39818 direct fr 3 0.51 0.09 39504 39818 direct fr 3 0.51 0.04 39555 39818 direct fr 3 0.60 0.58 39579 39818 direct fr 3 0.60 0.62 39585 39818 direct fr 3 0.60 0.33 39815 41992 direct fr 2 0.52 0.14 39929 41992 direct fr 2 0.53 0.05 39968 41992 direct fr 2 0.53 0.34 40091 41992 direct fr 2 0.55 0.88 40196 41992 direct fr 2 0.55 0.04 40382 41992 direct fr 2 0.57 0.54 40547 41992 direct fr 2 0.55 0.25 41989 44979 direct fr 1 0.73 0.29 42016 44979 direct fr 1 0.73 0.98 42019 44979 direct fr 1 0.73 0.86 42097 44979 direct fr 1 0.72 0.15 45610 45843 direct fr 1 0.75 0.72 45616 45843 direct fr 1 0.79 0.99 45652 45843 direct fr 1 0.87 0.52 45688 45843 direct fr 1 0.84 0.05 45721 45843 direct fr 1 0.80 0.03 45840 46232 direct fr 3 0.82 0.83 45873 46232 direct fr 3 0.89 0.64 46002 46232 direct fr 3 0.86 0.01 46050 46232 direct fr 3 0.83 0.01 46077 46232 direct fr 3 0.81 0.12 46419 46973 direct fr 3 0.91 0.96 46449 46973 direct fr 3 0.95 0.96 46518 46973 direct fr 3 0.97 0.12 46551 46973 direct fr 3 0.96 0.01 46581 46973 direct fr 3 0.96 0.02 46918 48018 direct fr 1 0.91 0.00 46978 48018 direct fr 1 0.96 0.93 46990 48018 direct fr 1 0.97 0.85 47023 48018 direct fr 1 0.99 0.13 47026 48018 direct fr 1 0.99 0.06 47056 48018 direct fr 1 0.99 0.10 48022 48855 direct fr 1 0.90 0.80 48127 48855 direct fr 1 0.94 0.22 48148 48855 direct fr 1 0.94 0.02 48244 48855 direct fr 1 0.93 0.00 48852 49709 direct fr 3 0.90 0.60 48882 49709 direct fr 3 0.94 0.99 48906 49709 direct fr 3 0.94 0.36 48999 49709 direct fr 3 0.93 0.18 49744 50616 direct fr 1 0.97 0.76 49813 50616 direct fr 1 0.98 0.01 49849 50616 direct fr 1 0.97 0.01 49962 51629 direct fr 3 0.52 0.01 50682 51629 direct fr 3 0.91 0.23 50691 51629 direct fr 3 0.92 0.08 50712 51629 direct fr 3 0.93 0.04 50748 51629 direct fr 3 0.95 0.98 50754 51629 direct fr 3 0.95 0.95 50796 51629 direct fr 3 0.95 0.01 51575 52234 direct fr 2 0.88 0.00 51626 52234 direct fr 2 0.96 1.00 51668 52234 direct fr 2 0.96 0.03 51680 52234 direct fr 2 0.95 0.02 52379 54934 direct fr 2 0.96 0.66 52493 54934 direct fr 2 0.98 0.96 52502 54934 direct fr 2 0.98 0.87 52529 54934 direct fr 2 0.98 0.08 54931 55707 direct fr 1 0.93 0.50 55042 55707 direct fr 1 0.97 0.12 55060 55707 direct fr 1 0.97 0.02 55081 55707 direct fr 1 0.97 0.04 56306 56557 complement fr 1 0.63 0.40 56306 56428 complement fr 1 0.51 0.47 56306 56425 complement fr 1 0.51 0.40 57015 59051 direct fr 3 0.87 0.08 57018 59051 direct fr 3 0.87 0.12 57060 59051 direct fr 3 0.88 0.82 57063 59051 direct fr 3 0.89 0.63 57168 59051 direct fr 3 0.88 0.55 57171 59051 direct fr 3 0.88 0.43 59283 59666 direct fr 3 0.84 0.07 59355 59666 direct fr 3 0.96 0.97 59409 59666 direct fr 3 0.96 0.02 59478 59666 direct fr 3 0.94 0.00 59739 60020 direct fr 3 0.82 0.68 59847 60020 direct fr 3 0.74 0.91 59910 60020 direct fr 3 0.61 0.01 60514 61974 complement fr 3 0.78 0.09 60514 61947 complement fr 3 0.79 0.78 60514 61929 complement fr 3 0.80 0.87 60514 61926 complement fr 3 0.80 0.71 60514 61899 complement fr 3 0.80 0.02 60514 61854 complement fr 3 0.80 0.87 60514 61788 complement fr 3 0.79 0.15 62343 64739 direct fr 3 0.91 0.30 62430 64739 direct fr 3 0.92 0.78 62622 64739 direct fr 3 0.92 0.02 62721 64739 direct fr 3 0.92 0.12 65200 65451 complement fr 3 0.63 0.40 65200 65322 complement fr 3 0.52 0.47 65200 65319 complement fr 3 0.52 0.40 65809 66255 direct fr 1 0.86 0.54 65860 66255 direct fr 1 0.88 0.28 65866 66255 direct fr 1 0.88 0.22 65893 66255 direct fr 1 0.87 0.06 66201 66728 direct fr 3 0.76 0.00 66252 66728 direct fr 3 0.83 0.98 66261 66728 direct fr 3 0.84 0.92 66267 66728 direct fr 3 0.86 0.80 66306 66728 direct fr 3 0.84 0.02 66351 66728 direct fr 3 0.83 0.04 66718 68040 direct fr 1 0.73 0.43 66739 68040 direct fr 1 0.74 0.43 66772 68040 direct fr 1 0.77 0.30 66868 68040 direct fr 1 0.76 0.48 66877 68040 direct fr 1 0.76 0.40 68033 69217 direct fr 2 0.95 0.81 68081 69217 direct fr 2 0.96 0.17 68114 69217 direct fr 2 0.96 0.05 68210 69217 direct fr 2 0.95 0.02 69126 70538 complement fr 2 0.50 0.46 70715 71725 complement fr 1 0.89 0.25 70715 71716 complement fr 1 0.90 0.45 70715 71707 complement fr 1 0.91 0.80 70715 71659 complement fr 1 0.93 0.20 70715 71620 complement fr 1 0.93 0.00 70715 71566 complement fr 1 0.93 0.01 71700 72740 complement fr 2 0.97 0.98 71700 72683 complement fr 2 0.97 0.00 71700 72590 complement fr 2 0.97 0.16 72811 73245 complement fr 3 0.50 0.06 72811 73236 complement fr 3 0.52 0.01 73755 74669 complement fr 2 0.69 0.06 73755 74666 complement fr 2 0.69 0.05 73755 74558 complement fr 2 0.78 0.00 73755 74486 complement fr 2 0.85 0.01 73755 74468 complement fr 2 0.88 0.45 73755 74459 complement fr 2 0.90 0.86 73755 74372 complement fr 2 0.93 0.09 73755 74345 complement fr 2 0.93 0.26 73755 74264 complement fr 2 0.92 0.07 74668 75609 direct fr 1 0.95 0.79 74692 75609 direct fr 1 0.97 0.10 74710 75609 direct fr 1 0.99 0.24 74713 75609 direct fr 1 1.00 0.25 74809 75609 direct fr 1 1.00 0.01 74845 75609 direct fr 1 1.00 0.03 75619 76494 direct fr 1 0.91 0.51 75700 76494 direct fr 1 0.92 0.78 75712 76494 direct fr 1 0.92 0.19 76612 77184 complement fr 3 0.77 0.65 76612 77109 complement fr 3 0.79 0.16 76612 77079 complement fr 3 0.78 0.01 76612 77070 complement fr 3 0.78 0.00 77191 78195 complement fr 3 0.89 0.79 77191 78102 complement fr 3 0.90 0.35 77191 78096 complement fr 3 0.89 0.21 78217 79641 complement fr 3 0.97 0.06 78217 79479 complement fr 3 1.00 0.08 78217 79428 complement fr 3 1.00 0.09 78217 79320 complement fr 3 1.00 0.05 79830 80822 complement fr 2 0.96 0.83 79830 80747 complement fr 2 0.98 0.34 79830 80735 complement fr 2 0.98 0.15 79830 80615 complement fr 2 0.98 0.06 82051 83457 direct fr 1 0.55 0.00 82519 83457 direct fr 1 0.82 0.00 82522 83457 direct fr 1 0.82 0.00 82654 83457 direct fr 1 0.96 0.82 82711 83457 direct fr 1 0.99 0.34 82918 83457 direct fr 1 0.99 0.04 83023 83457 direct fr 1 0.99 0.19 80815 81669 complement fr 3 0.81 0.00 80815 81660 complement fr 3 0.82 0.00 80815 81588 complement fr 3 0.89 0.87 80815 81543 complement fr 3 0.89 0.14 80815 81531 complement fr 3 0.88 0.04 81926 82657 direct fr 2 0.85 0.00 81971 82657 direct fr 2 0.90 0.98 81977 82657 direct fr 2 0.91 0.89 82100 82657 direct fr 2 0.91 0.30 82157 82657 direct fr 2 0.90 0.04 85466 85624 complement fr 1 0.66 0.60 85652 85972 complement fr 1 0.50 0.53 85652 85969 complement fr 1 0.50 0.30 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 1065 1526 direct fr 3 1393 2064 direct fr 1 2525 2908 complement fr 1 2712 6497 direct fr 3 6617 7069 complement fr 1 7067 7594 complement fr 1 7492 7788 complement fr 3 8745 9494 complement fr 2 8754 9245 direct fr 3 9243 9575 direct fr 3 9313 10845 direct fr 1 10772 11521 direct fr 2 11467 11931 direct fr 1 12107 13507 direct fr 2 13911 15725 complement fr 2 16240 17232 complement fr 3 16939 18471 direct fr 1 18450 19292 direct fr 3 19385 19981 direct fr 2 19767 20222 direct fr 3 20252 20572 direct fr 2 20529 20852 direct fr 3 20792 21250 direct fr 2 21412 22539 complement fr 3 22245 22544 complement fr 2 22571 23308 complement fr 1 23260 23529 direct fr 1 23947 24159 complement fr 3 24176 24430 direct fr 2 24188 25567 complement fr 1 24494 25339 direct fr 2 25327 25998 complement fr 3 25737 26150 complement fr 2 26210 26716 direct fr 2 26728 27168 direct fr 1 26868 27338 direct fr 3 27336 27536 direct fr 3 27358 28074 complement fr 3 28140 28658 complement fr 2 28656 28928 complement fr 2 28862 30115 complement fr 1 30113 30370 complement fr 1 30488 31774 complement fr 1 31133 31546 direct fr 2 31914 32888 complement fr 2 32355 32585 direct fr 3 32583 32867 direct fr 3 32827 34050 complement fr 3 33250 33558 direct fr 1 34155 35150 complement fr 2 35233 36330 direct fr 1 35285 35560 direct fr 2 35518 36402 complement fr 3 36418 37227 direct fr 1 36612 37103 complement fr 2 36892 37122 complement fr 3 37469 37960 direct fr 2 39267 39818 direct fr 3 39572 41992 direct fr 2 41932 44979 direct fr 1 45580 45843 direct fr 1 45741 46382 complement fr 2 45822 46232 direct fr 3 46401 46973 direct fr 3 46903 48018 direct fr 1 48016 48855 direct fr 1 48744 49709 direct fr 3 49666 50616 direct fr 1 49839 51629 direct fr 3 51119 52234 direct fr 2 52232 54934 direct fr 2 54745 55707 direct fr 1 56306 56689 complement fr 1 57003 59051 direct fr 3 59049 59258 direct fr 3 59256 59666 direct fr 3 59664 60020 direct fr 3 59950 60174 direct fr 1 60063 60374 direct fr 3 60514 62040 complement fr 3 62250 64739 direct fr 3 65200 65583 complement fr 3 65770 66255 direct fr 1 65889 66728 direct fr 3 66207 66905 complement fr 2 66691 68040 direct fr 1 67967 69217 direct fr 2 69126 70610 complement fr 2 70715 71740 complement fr 1 71700 72839 complement fr 2 72811 73731 complement fr 3 73755 74690 complement fr 2 74533 75609 direct fr 1 75607 76494 direct fr 1 76492 77748 direct fr 1 76612 77193 complement fr 3 77191 78219 complement fr 3 78217 79710 complement fr 3 79830 80873 complement fr 2 80677 83457 direct fr 1 80815 81693 complement fr 3 81518 81838 direct fr 2 81836 82657 direct fr 2 83814 84323 direct fr 3 83949 84380 complement fr 2 85121 85468 complement fr 1 85466 85654 complement fr 1 85652 86206 complement fr 1 -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Thu Nov 8 14:18:43 2007