GENEMARK PREDICTIONS Sequence: gi|37595821|ref|NC_005128.1| Vibrio vulnificus YJ016 plasmid pYJ016, complete sequence Sequence file: NC_005128.fna Sequence length: 48508 GC Content: 44.93% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 45 Matrix author: Borodovsky Laboratory - Georgia Tech, School of Biology, Atlanta, GA, USA 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 -------- -------- ---------- ----- ---- ---- 2190 2477 direct fr 3 0.67 0.28 2253 2477 direct fr 3 0.76 0.54 2304 2477 direct fr 3 0.71 0.13 2346 2477 direct fr 3 0.61 0.07 2804 3379 direct fr 2 0.57 0.59 2864 3379 direct fr 2 0.58 0.37 2882 3379 direct fr 2 0.56 0.20 3020 3379 direct fr 2 0.57 0.14 3825 4151 direct fr 3 0.56 0.07 3846 4151 direct fr 3 0.54 0.11 3849 4151 direct fr 3 0.54 0.06 3862 5673 direct fr 1 0.61 0.26 3865 5673 direct fr 1 0.61 0.25 3898 5673 direct fr 1 0.62 0.00 3925 5673 direct fr 1 0.63 0.01 4075 5673 direct fr 1 0.69 0.02 4132 5673 direct fr 1 0.71 0.42 4141 5673 direct fr 1 0.72 0.39 4228 5673 direct fr 1 0.71 0.06 4291 5673 direct fr 1 0.70 0.50 6081 8633 direct fr 3 0.66 0.17 6084 8633 direct fr 3 0.66 0.15 6414 8633 direct fr 3 0.68 0.43 6627 8633 direct fr 3 0.66 0.32 6642 8633 direct fr 3 0.66 0.44 8518 9315 direct fr 1 0.61 0.03 8662 9315 direct fr 1 0.72 0.67 8734 9315 direct fr 1 0.71 0.16 8794 9315 direct fr 1 0.68 0.26 9218 9475 complement fr 1 0.52 0.13 9218 9469 complement fr 1 0.52 0.17 9218 9457 complement fr 1 0.50 0.26 10495 11292 direct fr 1 0.52 0.17 10579 11292 direct fr 1 0.57 0.11 10750 11292 direct fr 1 0.58 0.68 10816 11292 direct fr 1 0.55 0.05 12406 13053 direct fr 1 0.57 0.12 12619 13053 direct fr 1 0.63 0.07 11942 12154 direct fr 2 0.59 0.80 11960 12154 direct fr 2 0.62 0.61 13013 13879 direct fr 2 0.60 0.34 13094 13879 direct fr 2 0.62 0.49 13097 13879 direct fr 2 0.62 0.49 13100 13879 direct fr 2 0.62 0.43 14307 15713 direct fr 3 0.61 0.02 14346 15713 direct fr 3 0.62 0.20 14520 15713 direct fr 3 0.68 0.08 14598 15713 direct fr 3 0.72 0.35 14604 15713 direct fr 3 0.72 0.32 14646 15713 direct fr 3 0.73 0.24 14775 15713 direct fr 3 0.70 0.26 15000 15713 direct fr 3 0.65 0.13 15717 18527 direct fr 3 0.65 0.35 15753 18527 direct fr 3 0.66 0.32 15822 18527 direct fr 3 0.66 0.04 15828 18527 direct fr 3 0.66 0.07 15831 18527 direct fr 3 0.66 0.03 18610 19143 direct fr 1 0.66 0.26 18730 19143 direct fr 1 0.69 0.73 18751 19143 direct fr 1 0.68 0.44 19448 21565 direct fr 2 0.61 0.05 19460 21565 direct fr 2 0.62 0.01 19532 21565 direct fr 2 0.64 0.67 19580 21565 direct fr 2 0.64 0.11 19700 21565 direct fr 2 0.65 0.16 19847 21565 direct fr 2 0.63 0.65 19856 21565 direct fr 2 0.63 0.36 21699 27473 direct fr 3 0.76 0.06 21897 27473 direct fr 3 0.76 0.05 21921 27473 direct fr 3 0.76 0.13 22167 27473 direct fr 3 0.75 0.30 22182 27473 direct fr 3 0.75 0.02 22212 27473 direct fr 3 0.75 0.38 27492 27851 complement fr 2 0.58 0.01 27492 27674 complement fr 2 0.56 0.21 27492 27635 complement fr 2 0.58 0.09 28409 28855 complement fr 1 0.55 0.17 28937 30319 complement fr 1 0.56 0.14 28937 30079 complement fr 1 0.56 0.57 28937 29989 complement fr 1 0.53 0.24 30895 31191 complement fr 3 0.61 0.76 30895 31173 complement fr 3 0.66 0.81 31267 31566 complement fr 3 0.59 0.26 31267 31476 complement fr 3 0.57 0.31 31267 31443 complement fr 3 0.53 0.29 32038 32409 complement fr 3 0.58 0.88 32038 32361 complement fr 3 0.59 0.01 32428 32736 complement fr 3 0.69 0.12 32428 32598 complement fr 3 0.66 0.42 32428 32568 complement fr 3 0.58 0.13 32428 32565 complement fr 3 0.58 0.07 32739 33083 complement fr 2 0.56 0.54 32739 33074 complement fr 2 0.56 0.43 33795 34004 complement fr 2 0.53 0.13 34091 34399 complement fr 1 0.65 0.69 34091 34369 complement fr 1 0.67 0.08 34978 35274 complement fr 3 0.66 0.68 34978 35229 complement fr 3 0.73 0.12 35383 35793 complement fr 3 0.57 0.12 35383 35769 complement fr 3 0.61 0.07 35383 35721 complement fr 3 0.64 0.41 35383 35673 complement fr 3 0.62 0.36 35383 35652 complement fr 3 0.61 0.09 35383 35649 complement fr 3 0.61 0.06 35383 35511 complement fr 3 0.57 0.30 35741 36220 complement fr 1 0.60 0.70 35741 36217 complement fr 1 0.60 0.47 36637 37125 complement fr 3 0.68 0.36 36637 37104 complement fr 3 0.69 0.03 36637 36801 complement fr 3 0.61 0.88 36637 36780 complement fr 3 0.57 0.42 37143 37295 complement fr 2 0.51 0.73 37143 37292 complement fr 2 0.51 0.73 37304 37870 complement fr 1 0.67 0.24 37304 37858 complement fr 1 0.68 0.02 37304 37783 complement fr 1 0.69 0.60 37304 37675 complement fr 1 0.65 0.14 37304 37561 complement fr 1 0.56 0.18 37886 38017 complement fr 1 0.57 0.95 38911 39288 complement fr 3 0.59 0.66 38911 39171 complement fr 3 0.53 0.23 38911 39168 complement fr 3 0.53 0.19 40847 41989 direct fr 2 0.60 0.29 40964 41989 direct fr 2 0.65 0.70 41024 41989 direct fr 2 0.65 0.22 41135 41989 direct fr 2 0.65 0.01 43002 43502 complement fr 2 0.68 0.78 43002 43493 complement fr 2 0.70 0.11 43002 43469 complement fr 2 0.70 0.01 43002 43442 complement fr 2 0.71 0.41 43002 43412 complement fr 2 0.72 0.75 43002 43358 complement fr 2 0.69 0.08 44214 44390 complement fr 2 0.54 0.07 44214 44384 complement fr 2 0.54 0.04 44546 44764 complement fr 1 0.61 0.61 44546 44701 complement fr 1 0.62 0.08 44766 45401 complement fr 2 0.66 0.78 44766 45299 complement fr 2 0.70 0.14 44766 45128 complement fr 2 0.69 0.16 44766 45113 complement fr 2 0.68 0.01 46044 46304 direct fr 3 0.54 0.21 46065 46304 direct fr 3 0.50 0.04 47028 47906 complement fr 2 0.51 0.01 47028 47882 complement fr 2 0.52 0.11 47028 47879 complement fr 2 0.53 0.07 47028 47867 complement fr 2 0.54 0.05 47028 47858 complement fr 2 0.54 0.16 47028 47531 complement fr 2 0.57 0.06 47028 47327 complement fr 2 0.60 0.62 47028 47321 complement fr 2 0.60 0.77 47028 47300 complement fr 2 0.57 0.25 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 530 772 complement fr 1 1127 1669 direct fr 2 1633 1824 direct fr 1 1720 1908 complement fr 3 1802 1993 direct fr 2 1947 2135 complement fr 2 2106 2477 direct fr 3 2385 2546 complement fr 2 2475 2789 direct fr 3 2747 3379 direct fr 2 3041 3274 complement fr 1 3327 4151 direct fr 3 3491 3775 complement fr 1 3847 5673 direct fr 1 3870 4055 complement fr 2 4564 4962 complement fr 3 5646 6071 direct fr 3 6072 8633 direct fr 3 8331 8492 complement fr 2 8443 9315 direct fr 1 9218 9523 complement fr 1 9306 10322 direct fr 3 10462 11292 direct fr 1 11290 13053 direct fr 1 11594 12154 direct fr 2 12152 12556 direct fr 2 12382 12555 complement fr 3 12917 13879 direct fr 2 13445 13765 complement fr 1 14023 14322 complement fr 3 14280 15713 direct fr 3 14418 14693 complement fr 2 15711 18527 direct fr 3 16158 16433 complement fr 2 16443 16676 complement fr 2 18544 19143 direct fr 1 19276 19467 direct fr 1 19412 21565 direct fr 2 21026 21253 complement fr 1 21593 21748 complement fr 1 21684 27473 direct fr 3 26154 26324 complement fr 2 27492 27857 complement fr 2 27918 28160 direct fr 3 28277 28567 direct fr 2 28409 28867 complement fr 1 28815 29117 direct fr 3 28937 30364 complement fr 1 29434 29679 direct fr 1 30790 30996 direct fr 1 30895 31215 complement fr 3 31267 31590 complement fr 3 31867 32040 complement fr 3 32038 32430 complement fr 3 32428 32754 complement fr 3 32739 33287 complement fr 2 33683 33922 direct fr 2 33795 34055 complement fr 2 34091 34429 complement fr 1 34408 34659 complement fr 3 34661 34906 complement fr 1 34978 35289 complement fr 3 35383 35796 complement fr 3 35741 36256 complement fr 1 36444 36635 complement fr 2 36637 37164 complement fr 3 37143 37334 complement fr 2 37304 37888 complement fr 1 37886 38065 complement fr 1 38035 38295 complement fr 3 38258 38692 complement fr 1 38911 39315 complement fr 3 39447 39659 complement fr 2 39721 39960 complement fr 3 39988 40683 complement fr 3 40841 41989 direct fr 2 41951 42463 complement fr 1 43002 43538 complement fr 2 44214 44456 complement fr 2 44546 44785 complement fr 1 44766 45410 complement fr 2 45855 46304 direct fr 3 47028 47909 complement fr 2 47157 47639 direct fr 3 47985 48143 direct fr 3 -------------------- ABOUT THE MATRIX USED: For details on the model building procedure see: Besemer J. and Borodovsky M. "Heuristic approach to deriving models for gene finding" NAR, 1999, Vol. 27, No. 19, pp. 3911-3920