GENEMARK PREDICTIONS Sequence: gi|121582466|ref|NC_008765.1| Acidovorax sp. JS42 plasmid pAOVO01, complete sequence Sequence file: NC_008765.fna Sequence length: 72689 GC Content: 62.21% 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 -------- -------- ---------- ----- ---- ---- 64 324 complement fr 3 0.81 0.98 64 282 complement fr 3 0.85 0.15 64 267 complement fr 3 0.84 0.07 64 228 complement fr 3 0.80 0.16 332 1057 complement fr 1 0.61 0.17 332 1009 complement fr 1 0.64 0.03 332 982 complement fr 1 0.66 0.00 332 943 complement fr 1 0.65 0.90 332 817 complement fr 1 0.71 0.84 332 751 complement fr 1 0.73 0.00 1546 1800 direct fr 1 0.66 0.74 1555 1800 direct fr 1 0.69 0.92 1576 1800 direct fr 1 0.76 0.63 1594 1800 direct fr 1 0.80 0.17 1672 1800 direct fr 1 0.72 0.74 1699 1800 direct fr 1 0.66 0.25 2127 5174 complement fr 2 0.91 1.00 2127 5114 complement fr 2 0.91 0.01 2127 5105 complement fr 2 0.91 0.01 2127 5102 complement fr 2 0.91 0.01 5186 6592 complement fr 1 0.96 0.49 5186 6565 complement fr 1 0.97 0.71 5186 6529 complement fr 1 0.97 0.17 5186 6523 complement fr 1 0.97 0.04 6603 7415 complement fr 2 0.93 0.96 6603 7412 complement fr 2 0.93 0.87 6603 7298 complement fr 2 0.93 0.21 6603 7274 complement fr 2 0.93 0.01 6603 7148 complement fr 2 0.91 0.01 7420 7782 complement fr 3 0.77 0.03 7420 7686 complement fr 3 0.94 0.90 7420 7644 complement fr 3 0.93 0.01 7420 7632 complement fr 3 0.93 0.09 7779 9065 complement fr 2 0.85 0.01 7779 9050 complement fr 2 0.85 0.16 7779 9023 complement fr 2 0.88 0.42 7779 9020 complement fr 2 0.88 0.38 7779 9017 complement fr 2 0.88 0.25 7779 8906 complement fr 2 0.93 0.29 7779 8837 complement fr 2 0.92 0.05 7779 8777 complement fr 2 0.92 0.97 9020 10318 complement fr 1 0.91 0.97 9020 10291 complement fr 1 0.91 0.97 9020 10279 complement fr 1 0.91 0.59 9020 10273 complement fr 1 0.91 0.15 10315 11310 complement fr 3 0.73 0.00 10315 11091 complement fr 3 0.93 0.92 10315 11064 complement fr 3 0.93 0.57 10315 11034 complement fr 3 0.93 0.09 10315 10962 complement fr 3 0.92 0.05 11091 12092 complement fr 2 0.83 0.28 11091 12074 complement fr 2 0.84 0.63 11091 12065 complement fr 2 0.85 0.42 11091 12062 complement fr 2 0.85 0.35 11091 12032 complement fr 2 0.85 0.76 12089 12727 complement fr 1 0.86 0.69 12089 12607 complement fr 1 0.90 0.13 12089 12601 complement fr 1 0.90 0.18 12089 12529 complement fr 1 0.89 0.12 12714 13277 complement fr 2 0.76 0.00 12714 13193 complement fr 2 0.89 0.90 12714 13190 complement fr 2 0.89 0.89 12714 13151 complement fr 2 0.90 0.12 12714 13142 complement fr 2 0.90 0.10 12714 13061 complement fr 2 0.88 0.00 13190 13618 complement fr 1 0.82 0.10 13190 13540 complement fr 1 0.86 0.08 13190 13531 complement fr 1 0.86 0.10 13190 13519 complement fr 1 0.86 0.02 13608 16232 complement fr 2 0.98 0.94 13608 16220 complement fr 2 0.98 0.96 13608 16217 complement fr 2 0.98 0.88 16270 16935 complement fr 3 0.89 0.87 16270 16920 complement fr 3 0.91 0.95 16270 16884 complement fr 3 0.91 0.03 16270 16881 complement fr 3 0.91 0.00 17063 17812 complement fr 1 0.88 0.19 17063 17800 complement fr 1 0.90 0.18 17063 17731 complement fr 1 0.94 0.97 17063 17710 complement fr 1 0.93 0.04 17063 17647 complement fr 1 0.93 0.08 17805 19154 complement fr 2 0.85 0.49 17805 19118 complement fr 2 0.87 0.90 17805 19115 complement fr 2 0.88 0.73 17805 19097 complement fr 2 0.87 0.77 19147 19884 complement fr 3 0.84 0.00 19147 19710 complement fr 3 0.96 0.06 19147 19707 complement fr 3 0.96 0.04 19147 19698 complement fr 3 0.96 0.16 19820 20413 complement fr 1 0.81 0.55 19820 20347 complement fr 1 0.85 0.12 19820 20311 complement fr 1 0.84 0.35 19820 20287 complement fr 1 0.83 0.11 20428 20727 complement fr 3 0.71 0.21 20428 20721 complement fr 3 0.73 0.11 20428 20646 complement fr 3 0.73 0.70 20428 20634 complement fr 3 0.72 0.55 20428 20622 complement fr 3 0.70 0.23 20737 21069 complement fr 3 0.90 0.19 20737 21006 complement fr 3 0.99 0.19 20737 20979 complement fr 3 0.99 0.02 20737 20976 complement fr 3 0.99 0.00 21549 22064 complement fr 2 0.78 0.22 21549 22049 complement fr 2 0.80 0.22 21549 22007 complement fr 2 0.84 0.05 21549 21848 complement fr 2 0.80 0.11 21549 21761 complement fr 2 0.73 0.17 22306 23154 direct fr 1 0.63 0.00 22318 23154 direct fr 1 0.64 0.00 22375 23154 direct fr 1 0.69 0.00 22420 23154 direct fr 1 0.73 0.27 22444 23154 direct fr 1 0.76 0.01 22588 23154 direct fr 1 0.91 0.51 22648 23154 direct fr 1 0.90 0.01 22657 23154 direct fr 1 0.90 0.00 23123 24091 complement fr 1 0.87 0.79 23123 24058 complement fr 1 0.90 0.53 23123 24001 complement fr 1 0.90 0.85 23123 23998 complement fr 1 0.90 0.77 24100 24381 complement fr 3 0.78 0.98 24100 24375 complement fr 3 0.78 0.80 24100 24306 complement fr 3 0.78 0.23 24100 24264 complement fr 3 0.72 0.17 24100 24216 complement fr 3 0.62 0.30 24409 25320 complement fr 3 0.62 0.00 24409 25263 complement fr 3 0.66 0.01 24409 25215 complement fr 3 0.67 0.98 24409 25179 complement fr 3 0.69 0.00 24409 25047 complement fr 3 0.67 0.12 24409 25002 complement fr 3 0.64 0.34 24409 24924 complement fr 3 0.59 0.00 25354 25566 complement fr 3 0.51 0.93 25354 25542 complement fr 3 0.57 0.00 25354 25467 complement fr 3 0.55 0.99 25708 28650 complement fr 3 0.94 0.03 25708 28593 complement fr 3 0.96 0.99 25708 28584 complement fr 3 0.96 0.98 25708 28575 complement fr 3 0.96 0.89 28590 29045 complement fr 2 0.70 0.00 28590 28976 complement fr 2 0.82 0.98 28590 28931 complement fr 2 0.82 0.03 28590 28916 complement fr 2 0.82 0.71 28590 28904 complement fr 2 0.81 0.92 29057 31054 complement fr 1 0.87 0.01 29057 30994 complement fr 1 0.88 0.86 29057 30973 complement fr 1 0.88 0.20 29057 30970 complement fr 1 0.88 0.10 31056 31433 complement fr 2 0.64 0.00 31056 31295 complement fr 2 0.71 0.23 31056 31286 complement fr 2 0.71 0.04 31056 31271 complement fr 2 0.68 0.02 31746 32066 direct fr 3 0.62 0.44 31893 32066 direct fr 3 0.55 0.02 31896 32066 direct fr 3 0.55 0.00 32587 32880 direct fr 1 0.57 0.00 32647 32880 direct fr 1 0.71 0.97 32659 32880 direct fr 1 0.74 0.93 32665 32880 direct fr 1 0.75 0.55 32683 32880 direct fr 1 0.77 0.01 32788 32880 direct fr 1 0.65 0.00 33517 34191 complement fr 3 0.63 0.00 33517 34134 complement fr 3 0.69 0.23 33517 34086 complement fr 3 0.71 0.61 33517 33819 complement fr 3 0.68 0.01 33517 33774 complement fr 3 0.62 0.36 34142 34378 complement fr 1 0.65 0.89 34142 34354 complement fr 1 0.61 0.70 34142 34351 complement fr 1 0.61 0.44 34391 34717 complement fr 1 0.94 0.81 34391 34657 complement fr 1 0.94 0.14 34391 34633 complement fr 1 0.93 0.04 34732 35061 complement fr 3 0.57 0.16 34732 34998 complement fr 3 0.67 0.03 34732 34887 complement fr 3 0.73 0.39 35234 35728 complement fr 1 0.86 0.93 35234 35620 complement fr 1 0.86 0.09 35234 35617 complement fr 1 0.86 0.01 35234 35539 complement fr 1 0.82 0.11 36284 36529 complement fr 1 0.67 0.00 36284 36502 complement fr 1 0.78 0.25 36284 36439 complement fr 1 0.94 0.57 36284 36400 complement fr 1 0.93 0.31 36284 36394 complement fr 1 0.92 0.07 36546 36995 complement fr 2 0.88 0.76 36546 36965 complement fr 2 0.93 0.53 36546 36932 complement fr 2 0.92 0.14 36546 36902 complement fr 2 0.92 0.00 37009 37476 complement fr 3 0.89 0.73 37009 37461 complement fr 3 0.90 0.95 37009 37434 complement fr 3 0.90 0.70 37530 39575 complement fr 2 0.93 0.00 37530 39569 complement fr 2 0.93 0.00 37530 39506 complement fr 2 0.96 1.00 37530 39416 complement fr 2 0.97 0.46 37530 39371 complement fr 2 0.97 0.25 37530 39362 complement fr 2 0.97 0.50 40603 40830 complement fr 3 0.69 1.00 40939 41280 complement fr 3 0.64 0.00 40939 41244 complement fr 3 0.70 0.68 40939 41136 complement fr 3 0.68 0.68 41280 41621 complement fr 2 0.65 0.07 41280 41558 complement fr 2 0.69 0.74 41280 41555 complement fr 2 0.68 0.55 41280 41528 complement fr 2 0.67 0.03 41691 42704 complement fr 2 0.78 0.10 41691 42695 complement fr 2 0.79 0.13 41691 42515 complement fr 2 0.96 0.44 41691 42467 complement fr 2 0.97 0.30 41691 42437 complement fr 2 0.97 0.03 41691 42323 complement fr 2 0.97 0.27 42604 43035 complement fr 3 0.96 1.00 42604 42999 complement fr 3 0.97 0.14 42604 42987 complement fr 3 0.97 0.00 43800 44351 complement fr 2 0.65 0.22 43800 44312 complement fr 2 0.67 0.42 43800 44297 complement fr 2 0.66 0.83 43800 44099 complement fr 2 0.61 0.59 44370 44987 complement fr 2 0.82 0.01 44370 44963 complement fr 2 0.86 0.23 44370 44855 complement fr 2 0.87 0.00 44370 44831 complement fr 2 0.87 0.15 44370 44786 complement fr 2 0.86 0.30 45009 45923 complement fr 2 0.78 0.90 45009 45854 complement fr 2 0.80 0.32 45009 45851 complement fr 2 0.79 0.21 45009 45746 complement fr 2 0.77 0.01 45009 45728 complement fr 2 0.79 0.00 45009 45638 complement fr 2 0.89 0.21 45928 46218 complement fr 3 0.54 0.00 45928 46212 complement fr 3 0.57 0.00 45928 46149 complement fr 3 0.72 0.24 45928 46086 complement fr 3 0.77 0.06 45928 46050 complement fr 3 0.70 0.00 46360 46860 complement fr 3 0.69 0.36 46360 46812 complement fr 3 0.67 0.38 46360 46797 complement fr 3 0.67 0.15 46857 47765 complement fr 2 0.74 0.88 46857 47669 complement fr 2 0.73 0.26 46857 47615 complement fr 2 0.71 0.01 46857 47609 complement fr 2 0.71 0.02 47762 48805 complement fr 1 0.92 0.84 47762 48736 complement fr 1 0.92 0.19 47762 48715 complement fr 1 0.92 0.01 47762 48652 complement fr 1 0.92 0.01 50359 51387 complement fr 3 0.83 0.40 50359 51294 complement fr 3 0.91 0.80 50359 51204 complement fr 3 0.91 0.74 50359 51168 complement fr 3 0.91 0.03 51494 51808 complement fr 1 0.80 0.98 51494 51781 complement fr 1 0.80 0.69 51494 51694 complement fr 1 0.71 0.25 51805 52128 complement fr 3 0.81 0.99 51805 52035 complement fr 3 0.75 0.09 51805 52023 complement fr 3 0.74 0.03 52202 52600 complement fr 1 0.82 0.14 52202 52591 complement fr 1 0.84 0.20 52202 52582 complement fr 1 0.86 0.19 52202 52504 complement fr 1 0.83 0.03 52202 52492 complement fr 1 0.82 0.15 52662 53954 complement fr 2 0.95 0.28 52662 53897 complement fr 2 0.95 0.04 52662 53819 complement fr 2 0.95 0.00 53967 54749 complement fr 2 0.96 0.96 53967 54584 complement fr 2 0.99 0.10 53967 54479 complement fr 2 0.99 0.27 53967 54458 complement fr 2 0.99 0.11 54778 55290 complement fr 3 0.68 0.01 54778 55197 complement fr 3 0.83 0.89 54778 55083 complement fr 3 0.85 0.91 54778 55077 complement fr 3 0.84 0.68 55353 56339 complement fr 2 0.89 0.68 55353 56123 complement fr 2 0.90 0.01 55353 56072 complement fr 2 0.89 0.00 55353 56042 complement fr 2 0.89 0.02 56343 56606 complement fr 2 0.95 0.13 56343 56585 complement fr 2 0.95 0.02 56343 56573 complement fr 2 0.94 0.00 56797 59712 direct fr 1 0.58 0.01 56827 59712 direct fr 1 0.58 0.88 56863 59712 direct fr 1 0.59 0.54 56968 59712 direct fr 1 0.59 0.00 57076 59712 direct fr 1 0.61 0.14 57145 59712 direct fr 1 0.62 0.96 61154 61681 complement fr 1 0.78 0.93 61154 61639 complement fr 1 0.80 0.20 61154 61543 complement fr 1 0.75 0.31 61154 61540 complement fr 1 0.75 0.06 61678 62418 complement fr 3 0.84 0.08 61678 62340 complement fr 3 0.89 0.27 61678 62286 complement fr 3 0.88 0.49 61678 62160 complement fr 3 0.85 0.12 63107 63808 complement fr 1 0.67 0.01 63107 63655 complement fr 1 0.71 0.00 63107 63586 complement fr 1 0.76 0.07 63107 63475 complement fr 1 0.77 0.26 63107 63469 complement fr 1 0.77 0.23 63818 64861 complement fr 1 0.63 0.24 63818 64795 complement fr 1 0.63 0.01 63818 64780 complement fr 1 0.64 0.00 63818 64726 complement fr 1 0.64 0.95 63818 64723 complement fr 1 0.64 0.89 64865 65140 complement fr 1 0.88 0.93 64865 65047 complement fr 1 0.83 0.05 64865 65035 complement fr 1 0.81 0.02 65156 65311 complement fr 1 0.52 0.98 65156 65299 complement fr 1 0.54 0.68 65156 65293 complement fr 1 0.54 0.58 65296 65883 complement fr 3 0.59 0.29 65296 65877 complement fr 3 0.60 0.07 65296 65820 complement fr 3 0.62 0.28 65296 65817 complement fr 3 0.62 0.14 65296 65688 complement fr 3 0.81 0.87 65296 65589 complement fr 3 0.77 0.60 65296 65586 complement fr 3 0.77 0.42 65817 67028 complement fr 2 0.93 0.84 65817 66902 complement fr 2 0.94 0.85 65817 66896 complement fr 2 0.94 0.24 65817 66860 complement fr 2 0.93 0.01 67044 68726 complement fr 2 0.94 1.00 67044 68699 complement fr 2 0.96 0.93 67044 68543 complement fr 2 0.96 0.00 67044 68540 complement fr 2 0.96 0.00 68744 69055 complement fr 1 0.75 0.07 68744 69004 complement fr 1 0.84 0.87 68744 68962 complement fr 1 0.81 0.05 69018 69479 complement fr 2 0.88 0.42 69018 69446 complement fr 2 0.90 0.21 69018 69440 complement fr 2 0.90 0.10 69018 69413 complement fr 2 0.89 0.04 69512 70600 complement fr 1 0.96 1.00 69512 70402 complement fr 1 0.96 0.88 69512 70381 complement fr 1 0.96 0.07 70597 70824 complement fr 3 0.83 0.85 70597 70785 complement fr 3 0.84 0.01 70597 70761 complement fr 3 0.82 0.32 70837 71082 complement fr 3 0.86 0.87 70837 71067 complement fr 3 0.91 0.91 70837 71037 complement fr 3 0.94 0.19 70837 71022 complement fr 3 0.95 0.06 70837 70929 complement fr 3 1.00 0.94 71208 71306 complement fr 2 0.62 0.99 71208 71294 complement fr 2 0.57 0.99 71328 71648 complement fr 2 0.62 0.00 71328 71639 complement fr 2 0.65 0.00 71328 71621 complement fr 2 0.67 0.01 71328 71591 complement fr 2 0.76 0.77 71328 71576 complement fr 2 0.80 0.62 71328 71546 complement fr 2 0.86 0.16 71328 71492 complement fr 2 0.81 0.79 71328 71483 complement fr 2 0.80 0.09 71600 72199 complement fr 1 0.70 0.40 71600 72187 complement fr 1 0.71 0.00 71600 72124 complement fr 1 0.77 0.95 71600 72082 complement fr 1 0.75 0.10 71600 72061 complement fr 1 0.75 0.11 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 64 465 complement fr 3 332 1075 complement fr 1 1133 1522 complement fr 1 1501 1800 direct fr 1 2127 5219 complement fr 2 2154 3359 direct fr 3 5186 6664 complement fr 1 6603 7475 complement fr 2 7420 7893 complement fr 3 7779 9071 complement fr 2 9020 10363 complement fr 1 10315 11319 complement fr 3 11091 12116 complement fr 2 12089 12757 complement fr 1 12714 13433 complement fr 2 13190 13756 complement fr 1 13608 16316 complement fr 2 16270 17115 complement fr 3 17063 17848 complement fr 1 17805 19205 complement fr 2 19147 19989 complement fr 3 19820 20455 complement fr 1 20428 20739 complement fr 3 20737 21084 complement fr 3 21164 21667 complement fr 1 21549 22094 complement fr 2 22303 23154 direct fr 1 22348 22626 complement fr 3 23123 24097 complement fr 1 24100 24411 complement fr 3 24409 25356 complement fr 3 25354 25596 complement fr 3 25708 28788 complement fr 3 28590 29120 complement fr 2 29057 31069 complement fr 1 31056 31442 complement fr 2 31719 32066 direct fr 3 32578 32880 direct fr 1 33517 34353 complement fr 3 34142 34393 complement fr 1 34391 34777 complement fr 1 34732 35331 complement fr 3 35234 35830 complement fr 1 35954 36286 complement fr 1 36284 36595 complement fr 1 36546 37028 complement fr 2 37009 37560 complement fr 3 37530 39596 complement fr 2 40290 40742 complement fr 2 40603 40857 complement fr 3 40939 41487 complement fr 3 41280 41693 complement fr 2 41691 42806 complement fr 2 42604 43050 complement fr 3 43719 45599 direct fr 3 43800 44372 complement fr 2 44370 45011 complement fr 2 45009 45944 complement fr 2 45928 46239 complement fr 3 46360 46917 complement fr 3 46857 47906 complement fr 2 47762 49045 complement fr 1 48772 49116 complement fr 3 50359 51426 complement fr 3 51494 51880 complement fr 1 51805 52218 complement fr 3 52202 52765 complement fr 1 52662 53969 complement fr 2 53967 54827 complement fr 2 54778 55308 complement fr 3 55353 56345 complement fr 2 56343 56669 complement fr 2 56695 57099 complement fr 3 56722 59712 direct fr 1 58279 59025 complement fr 3 60112 60558 complement fr 3 60393 60800 direct fr 3 60495 61274 complement fr 2 61154 61726 complement fr 1 61678 62508 complement fr 3 62289 62885 direct fr 3 62466 63128 complement fr 2 63107 63820 complement fr 1 63818 64867 complement fr 1 64865 65158 complement fr 1 65156 65410 complement fr 1 65296 65913 complement fr 3 65817 67046 complement fr 2 67044 68807 complement fr 2 68744 69109 complement fr 1 69018 69593 complement fr 2 69512 70648 complement fr 1 70597 70839 complement fr 3 70837 71106 complement fr 3 71208 71330 complement fr 2 71328 71765 complement fr 2 71600 72283 complement fr 1 72121 72549 complement fr 3 72531 72689 complement fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 2 7416 +/- 11 bp (complement) 2 1 45744 +/- 11 bp (complement) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 13:23:19 2007