GENEMARK PREDICTIONS Sequence: gi|169786889|ref|NC_010404.1| Acinetobacter baumannii plasmid p3ABAYE, complete sequence Sequence file: NC_010404.fna Sequence length: 94413 GC Content: 37.48% 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 -------- -------- ---------- ----- ---- ---- 746 1918 direct fr 2 0.85 0.62 893 1918 direct fr 2 0.86 0.56 1085 1918 direct fr 2 0.82 0.35 1286 1918 direct fr 2 0.79 0.01 2298 2981 complement fr 2 0.72 0.03 2298 2918 complement fr 2 0.77 0.75 2298 2801 complement fr 2 0.73 0.22 2298 2768 complement fr 2 0.74 0.09 3147 5852 complement fr 2 0.92 0.35 3147 5813 complement fr 2 0.93 0.04 3147 5447 complement fr 2 0.95 0.83 3147 5441 complement fr 2 0.95 0.93 3147 5399 complement fr 2 0.95 0.02 5857 6036 complement fr 3 0.52 0.01 5857 5985 complement fr 3 0.55 0.46 6166 7080 complement fr 3 0.88 0.98 6166 7056 complement fr 3 0.90 0.98 6166 7005 complement fr 3 0.90 0.01 6166 6981 complement fr 3 0.90 0.75 7174 8151 complement fr 3 0.89 0.88 7174 7992 complement fr 3 0.91 0.01 7174 7989 complement fr 3 0.91 0.01 7174 7944 complement fr 3 0.90 0.37 8288 9220 direct fr 2 0.74 0.19 8468 9220 direct fr 2 0.77 0.11 8501 9220 direct fr 2 0.79 0.09 8603 9220 direct fr 2 0.88 0.21 8795 9220 direct fr 2 0.84 0.23 9765 9986 complement fr 2 0.59 0.06 9765 9959 complement fr 2 0.69 0.86 9765 9926 complement fr 2 0.67 0.56 9765 9923 complement fr 2 0.65 0.68 10166 10432 direct fr 2 0.72 0.93 10172 10432 direct fr 2 0.72 0.89 10181 10432 direct fr 2 0.72 0.62 10964 12163 complement fr 1 0.80 0.45 10964 11635 complement fr 1 0.73 0.27 10964 11476 complement fr 1 0.80 0.18 10964 11455 complement fr 1 0.79 0.24 12463 12894 direct fr 1 0.57 0.53 12502 12894 direct fr 1 0.63 0.19 12520 12894 direct fr 1 0.64 0.12 12682 12894 direct fr 1 0.71 0.48 13309 13947 complement fr 3 0.86 0.63 13309 13695 complement fr 3 0.87 0.10 13309 13635 complement fr 3 0.85 0.29 13309 13491 complement fr 3 0.74 0.37 13963 14982 complement fr 3 0.91 0.89 13963 14937 complement fr 3 0.93 0.08 13963 14829 complement fr 3 0.92 0.77 13963 14817 complement fr 3 0.92 0.24 15127 15732 direct fr 1 0.75 0.76 15325 15732 direct fr 1 0.89 0.80 15460 15732 direct fr 1 0.85 0.34 15499 15732 direct fr 1 0.82 0.03 15840 16070 direct fr 3 0.51 0.42 15864 16070 direct fr 3 0.57 0.25 15960 16070 direct fr 3 0.67 0.53 15963 16070 direct fr 3 0.64 0.57 15966 16070 direct fr 3 0.64 0.60 16154 17281 complement fr 1 0.91 0.23 16154 17158 complement fr 1 0.94 0.37 16154 17119 complement fr 1 0.94 0.00 16154 17116 complement fr 1 0.94 0.01 17485 18198 complement fr 3 0.90 0.01 17485 18162 complement fr 3 0.92 0.63 17485 17934 complement fr 3 0.90 0.12 17485 17874 complement fr 3 0.89 0.01 18248 19405 complement fr 1 0.86 0.24 18248 19330 complement fr 1 0.89 0.21 18248 19306 complement fr 1 0.89 0.36 18248 19258 complement fr 1 0.88 0.01 20005 20307 complement fr 3 0.79 0.92 20005 20250 complement fr 3 0.81 0.01 20005 20214 complement fr 3 0.78 0.02 20642 21472 complement fr 1 0.77 0.82 20642 21427 complement fr 1 0.80 0.00 20642 21391 complement fr 1 0.82 0.37 20642 21340 complement fr 1 0.84 0.08 20642 21163 complement fr 1 0.80 0.01 20642 21124 complement fr 1 0.78 0.43 21701 22813 complement fr 1 0.86 0.84 21701 22699 complement fr 1 0.87 0.35 21701 22591 complement fr 1 0.85 0.00 21701 22462 complement fr 1 0.91 0.37 22835 23110 complement fr 1 0.73 0.71 22835 23014 complement fr 1 0.73 0.00 22835 22978 complement fr 1 0.67 0.12 22835 22954 complement fr 1 0.60 0.21 23230 23331 direct fr 1 0.65 0.21 23356 23559 direct fr 1 0.53 0.21 23398 23559 direct fr 1 0.60 0.53 23410 23559 direct fr 1 0.57 0.69 23413 23559 direct fr 1 0.54 0.32 23486 23626 direct fr 2 0.63 0.06 23588 23626 direct fr 2 0.90 0.00 23927 24904 direct fr 2 0.71 0.64 23945 24904 direct fr 2 0.73 0.69 23996 24904 direct fr 2 0.75 0.41 24014 24904 direct fr 2 0.74 0.88 24032 24904 direct fr 2 0.74 0.48 25020 26258 direct fr 3 0.91 0.21 25152 26258 direct fr 3 0.94 0.34 25254 26258 direct fr 3 0.96 0.75 25272 26258 direct fr 3 0.96 0.76 26315 27607 direct fr 2 0.75 0.17 26390 27607 direct fr 2 0.78 0.50 26441 27607 direct fr 2 0.77 0.03 26480 27607 direct fr 2 0.77 0.11 27620 28534 direct fr 2 0.54 0.01 27713 28534 direct fr 2 0.59 0.67 27779 28534 direct fr 2 0.56 0.03 27794 28534 direct fr 2 0.55 0.09 28730 28909 direct fr 2 0.56 0.06 28775 28909 direct fr 2 0.70 0.83 28975 29133 direct fr 1 0.52 0.34 29906 30901 direct fr 2 0.93 0.59 29915 30901 direct fr 2 0.93 0.69 29918 30901 direct fr 2 0.94 0.87 30077 30901 direct fr 2 0.98 0.03 30095 30901 direct fr 2 0.98 0.03 30110 30901 direct fr 2 0.98 0.02 30846 31907 direct fr 3 0.78 0.00 30849 31907 direct fr 3 0.78 0.00 30891 31907 direct fr 3 0.82 0.19 31011 31907 direct fr 3 0.83 0.15 31044 31907 direct fr 3 0.83 0.14 31290 31907 direct fr 3 0.78 0.09 31958 32920 complement fr 1 0.80 0.05 31958 32857 complement fr 1 0.85 0.44 31958 32839 complement fr 1 0.85 0.47 31958 32836 complement fr 1 0.85 0.46 32993 33733 direct fr 2 0.92 0.56 33176 33733 direct fr 2 0.94 0.00 33272 33733 direct fr 2 0.93 0.31 33320 33733 direct fr 2 0.92 0.01 33807 34805 direct fr 3 0.89 0.10 33930 34805 direct fr 3 0.91 0.02 33951 34805 direct fr 3 0.91 0.05 34203 34805 direct fr 3 0.87 0.38 34826 35110 direct fr 2 0.59 0.19 35374 35511 direct fr 1 0.77 0.02 35398 35511 direct fr 1 0.73 0.03 35852 36394 direct fr 2 0.83 0.38 35876 36394 direct fr 2 0.87 0.77 36056 36394 direct fr 2 0.86 0.02 36191 36394 direct fr 2 0.78 0.10 36526 37038 direct fr 1 0.60 0.41 36604 37038 direct fr 1 0.67 0.00 37237 38148 direct fr 1 0.57 0.12 37246 38148 direct fr 1 0.57 0.05 37489 38148 direct fr 1 0.65 0.02 37825 38148 direct fr 1 0.75 0.32 37888 38148 direct fr 1 0.74 0.17 38405 38650 direct fr 2 0.71 0.61 38640 38933 direct fr 3 0.53 0.85 38766 38933 direct fr 3 0.64 0.10 40251 40559 direct fr 3 0.86 0.65 40413 40559 direct fr 3 0.89 0.15 40491 40559 direct fr 3 0.76 0.38 40600 40902 direct fr 1 0.74 0.92 40666 40902 direct fr 1 0.81 0.01 42250 42510 complement fr 3 0.77 0.88 42250 42444 complement fr 3 0.70 0.09 42503 42859 complement fr 1 0.84 0.83 42503 42697 complement fr 1 0.77 0.08 42503 42619 complement fr 1 0.67 0.58 44396 44833 direct fr 2 0.89 0.22 44438 44833 direct fr 2 0.91 0.52 44450 44833 direct fr 2 0.90 0.55 44453 44833 direct fr 2 0.90 0.25 45076 45396 direct fr 1 0.81 0.60 45241 45396 direct fr 1 0.70 0.11 45289 45396 direct fr 1 0.57 0.00 45667 47622 complement fr 3 0.64 0.03 45667 47526 complement fr 3 0.67 0.29 45667 47058 complement fr 3 0.65 0.01 45667 46872 complement fr 3 0.67 0.12 45667 46722 complement fr 3 0.63 0.10 45667 46401 complement fr 3 0.60 0.35 47714 48343 complement fr 1 0.74 0.13 47714 48214 complement fr 1 0.67 0.28 47714 48205 complement fr 1 0.67 0.62 48393 48602 complement fr 2 0.58 0.00 48599 48883 complement fr 1 0.75 0.93 48599 48877 complement fr 1 0.75 0.89 48599 48805 complement fr 1 0.77 0.05 48599 48763 complement fr 1 0.70 0.13 49045 53784 complement fr 3 0.86 0.08 49045 53775 complement fr 3 0.86 0.30 49045 53685 complement fr 3 0.86 0.01 49045 53583 complement fr 3 0.87 0.67 49045 53580 complement fr 3 0.87 0.74 53839 55878 complement fr 3 0.94 0.99 53839 55818 complement fr 3 0.95 0.18 53839 55761 complement fr 3 0.95 0.02 53839 55584 complement fr 3 0.94 0.00 55908 58532 complement fr 2 0.94 0.95 55908 58391 complement fr 2 0.95 0.18 55908 58088 complement fr 2 0.94 0.01 55908 58082 complement fr 2 0.94 0.00 58529 59899 complement fr 1 0.74 0.62 58529 58675 complement fr 1 0.62 0.01 58529 58666 complement fr 1 0.59 0.02 58529 58651 complement fr 1 0.55 0.18 59896 63429 complement fr 3 0.91 0.84 59896 63369 complement fr 3 0.92 0.08 59896 63261 complement fr 3 0.91 0.82 59896 63153 complement fr 3 0.91 0.57 63476 67156 complement fr 1 0.95 0.64 63476 67048 complement fr 1 0.95 0.01 63476 66880 complement fr 1 0.95 0.75 67197 67772 complement fr 2 0.78 0.46 67197 67637 complement fr 2 0.73 0.00 67197 67607 complement fr 2 0.71 0.00 67197 67577 complement fr 2 0.75 0.94 67789 68400 complement fr 3 0.91 0.88 67789 68352 complement fr 3 0.91 0.12 67789 68349 complement fr 3 0.91 0.08 68411 69277 complement fr 1 0.90 0.92 68411 69244 complement fr 1 0.93 0.17 68411 69187 complement fr 1 0.92 0.09 68411 69079 complement fr 1 0.94 0.36 69503 69739 direct fr 2 0.57 0.21 69938 70048 complement fr 1 0.55 0.99 69938 70033 complement fr 1 0.51 0.96 70588 70773 complement fr 3 0.51 0.78 70588 70755 complement fr 3 0.54 0.58 70940 71872 direct fr 2 0.73 0.05 71120 71872 direct fr 2 0.77 0.43 71168 71872 direct fr 2 0.79 0.05 71297 71872 direct fr 2 0.91 0.26 71312 71872 direct fr 2 0.91 0.62 72003 72197 complement fr 2 0.59 0.95 72003 72188 complement fr 2 0.63 0.80 72003 72182 complement fr 2 0.63 0.82 72293 72523 complement fr 1 0.59 0.23 72293 72511 complement fr 1 0.63 0.82 72568 73266 complement fr 3 0.75 0.00 72568 73242 complement fr 3 0.78 0.05 72568 73170 complement fr 3 0.85 0.24 72568 73140 complement fr 3 0.85 0.02 72568 73125 complement fr 3 0.85 0.45 72568 73002 complement fr 3 0.81 0.11 73377 73646 direct fr 3 0.73 0.96 73488 73646 direct fr 3 0.77 0.94 73701 74030 direct fr 3 0.76 0.53 73797 74030 direct fr 3 0.80 0.12 73800 74030 direct fr 3 0.80 0.08 73842 74030 direct fr 3 0.78 0.25 74017 74304 direct fr 1 0.57 0.90 74035 74304 direct fr 1 0.59 0.95 74065 74304 direct fr 1 0.64 0.10 74101 74304 direct fr 1 0.58 0.01 74116 74304 direct fr 1 0.55 0.01 75532 75738 complement fr 3 0.64 0.28 76201 76734 complement fr 3 0.79 0.12 76201 76719 complement fr 3 0.81 0.81 76201 76569 complement fr 3 0.84 0.29 76703 76960 complement fr 1 0.67 0.38 76703 76954 complement fr 1 0.70 0.11 76703 76939 complement fr 1 0.73 0.25 76703 76918 complement fr 1 0.77 0.60 76957 77208 complement fr 3 0.74 0.67 77317 77958 complement fr 3 0.83 0.91 77317 77793 complement fr 3 0.84 0.07 77317 77724 complement fr 3 0.81 0.12 77317 77721 complement fr 3 0.81 0.03 77927 78388 complement fr 1 0.74 0.29 77927 78166 complement fr 1 0.71 0.80 77927 78094 complement fr 1 0.59 0.28 77927 78082 complement fr 1 0.56 0.04 78449 78904 complement fr 1 0.66 0.54 78449 78889 complement fr 1 0.68 0.42 78449 78820 complement fr 1 0.69 0.14 78449 78808 complement fr 1 0.69 0.10 78449 78694 complement fr 1 0.72 0.30 80214 80708 complement fr 2 0.69 0.11 80214 80684 complement fr 2 0.72 0.15 80214 80621 complement fr 2 0.77 0.89 80214 80603 complement fr 2 0.76 0.39 80214 80522 complement fr 2 0.70 0.02 80900 83284 complement fr 1 0.84 0.12 80900 83212 complement fr 1 0.83 0.00 80900 83206 complement fr 1 0.83 0.00 83693 84100 complement fr 1 0.64 0.50 83693 84034 complement fr 1 0.68 0.60 83693 83980 complement fr 1 0.62 0.07 84105 86456 complement fr 2 0.73 0.98 84105 86372 complement fr 2 0.73 0.07 84105 86063 complement fr 2 0.72 0.54 84105 85619 complement fr 2 0.70 0.23 84105 85586 complement fr 2 0.70 0.15 85411 85530 direct fr 1 0.52 0.37 87254 87610 direct fr 2 0.77 0.26 87383 87610 direct fr 2 0.68 0.20 87395 87610 direct fr 2 0.69 0.11 89486 89791 direct fr 2 0.73 0.65 89519 89791 direct fr 2 0.79 0.82 89567 89791 direct fr 2 0.79 0.06 89606 89791 direct fr 2 0.74 0.02 89672 89791 direct fr 2 0.63 0.00 89791 90321 direct fr 1 0.65 0.15 89995 90321 direct fr 1 0.63 0.43 90043 90321 direct fr 1 0.57 0.01 90052 90321 direct fr 1 0.55 0.00 90131 91042 direct fr 2 0.71 0.01 90140 91042 direct fr 2 0.72 0.01 90161 91042 direct fr 2 0.74 0.00 90488 91042 direct fr 2 0.85 0.83 90527 91042 direct fr 2 0.85 0.02 90539 91042 direct fr 2 0.85 0.07 91548 92402 complement fr 2 0.79 0.02 91548 92255 complement fr 2 0.89 0.07 91548 92231 complement fr 2 0.88 0.11 91548 92081 complement fr 2 0.85 0.00 92551 93450 complement fr 3 0.90 0.86 92551 92979 complement fr 3 0.85 0.24 92551 92964 complement fr 3 0.84 0.02 92551 92868 complement fr 3 0.80 0.24 93469 94245 complement fr 3 0.89 0.53 93469 93591 complement fr 3 0.67 0.08 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 713 1918 direct fr 2 2049 2300 complement fr 2 2298 2984 complement fr 2 3147 5873 complement fr 2 5857 6168 complement fr 3 6166 7098 complement fr 3 7174 8166 complement fr 3 8258 9220 direct fr 2 9765 10001 complement fr 2 10028 10432 direct fr 2 10709 10828 complement fr 1 10964 12202 complement fr 1 12451 12894 direct fr 1 13309 13965 complement fr 3 13963 15006 complement fr 3 15115 15732 direct fr 1 15831 16070 direct fr 3 16154 17299 complement fr 1 17485 18246 complement fr 3 18248 19417 complement fr 1 19587 19799 direct fr 3 20005 20337 complement fr 3 20642 21481 complement fr 1 21701 22837 complement fr 1 22835 23122 complement fr 1 23152 23331 direct fr 1 23329 23559 direct fr 1 23477 23626 direct fr 2 23861 24904 direct fr 2 24990 26258 direct fr 3 26297 27607 direct fr 2 27614 28534 direct fr 2 28709 28909 direct fr 2 28897 29133 direct fr 1 29127 29276 direct fr 3 29894 30901 direct fr 2 30825 31907 direct fr 3 31958 32923 complement fr 1 32963 33733 direct fr 2 33747 34805 direct fr 3 34760 35110 direct fr 2 35284 35511 direct fr 1 35822 36394 direct fr 2 36523 37038 direct fr 1 37231 38148 direct fr 1 38351 38650 direct fr 2 38637 38933 direct fr 3 39042 39236 direct fr 3 40215 40559 direct fr 3 40585 40902 direct fr 1 41214 41624 complement fr 2 42250 42567 complement fr 3 42503 42895 complement fr 1 43399 44100 direct fr 1 44179 44394 direct fr 1 44348 44833 direct fr 2 45034 45396 direct fr 1 45667 47637 complement fr 3 47714 48454 complement fr 1 48393 48656 complement fr 2 48599 48907 complement fr 1 49045 53796 complement fr 3 53839 55893 complement fr 3 55908 58538 complement fr 2 58529 59908 complement fr 1 59752 59937 direct fr 1 59896 63468 complement fr 3 63476 67207 complement fr 1 67197 67880 complement fr 2 67789 68472 complement fr 3 68411 69307 complement fr 1 69464 69739 direct fr 2 69608 69808 complement fr 1 69938 70075 complement fr 1 70073 70609 complement fr 1 70588 70788 complement fr 3 70910 71872 direct fr 2 72003 72239 complement fr 2 72293 72541 complement fr 1 72568 73284 complement fr 3 73353 73646 direct fr 3 73686 74030 direct fr 3 73986 74303 complement fr 2 74011 74304 direct fr 1 74341 74532 complement fr 3 74533 74766 complement fr 3 74742 74930 complement fr 2 74952 75203 complement fr 2 75284 75469 complement fr 1 75532 75873 complement fr 3 76201 76743 complement fr 3 76703 76972 complement fr 1 76957 77247 complement fr 3 77246 77473 direct fr 2 77317 77976 complement fr 3 77927 78451 complement fr 1 78449 78919 complement fr 1 79566 79847 complement fr 2 79995 80153 complement fr 2 80214 80744 complement fr 2 80900 83695 complement fr 1 83693 84118 complement fr 1 84105 86471 complement fr 2 85282 85530 direct fr 1 86469 87005 complement fr 2 87128 87610 direct fr 2 87526 87735 direct fr 1 87733 87975 direct fr 1 88325 88492 direct fr 2 89465 89791 direct fr 2 89776 90321 direct fr 1 90113 91042 direct fr 2 90153 90362 direct fr 3 91548 92414 complement fr 2 92551 93471 complement fr 3 93469 94275 complement fr 3 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 2 23496 +/- 11 bp (direct) 1 3 29076 +/- 11 bp (direct) 2 3 30900 +/- 11 bp (direct) 1 3 90204 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Wed Mar 19 11:56:14 2008