GENEMARK PREDICTIONS Sequence: gi|81230333|ref|NC_007595.1| Synechococcus elongatus PCC 7942 plasmid 1, complete sequence Sequence file: NC_007595.fna Sequence length: 46366 GC Content: 52.89% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 53 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 -------- -------- ---------- ----- ---- ---- 65 394 complement fr 1 0.60 0.14 65 217 complement fr 1 0.60 0.41 65 211 complement fr 1 0.58 0.45 1318 1929 complement fr 3 0.56 0.51 1318 1755 complement fr 3 0.53 0.17 1318 1749 complement fr 3 0.54 0.21 2720 3070 complement fr 1 0.51 0.93 3160 5040 complement fr 3 0.54 0.03 3160 5010 complement fr 3 0.55 0.06 3160 4941 complement fr 3 0.56 0.53 3160 4659 complement fr 3 0.62 0.01 3160 4602 complement fr 3 0.64 0.02 3160 4596 complement fr 3 0.65 0.01 3160 4272 complement fr 3 0.71 0.05 3160 4161 complement fr 3 0.74 0.18 5275 6195 complement fr 3 0.54 0.14 5275 6087 complement fr 3 0.52 0.23 5275 6063 complement fr 3 0.53 0.69 5275 6009 complement fr 3 0.52 0.13 6290 7249 complement fr 1 0.51 0.02 6290 7069 complement fr 1 0.61 0.32 6290 6904 complement fr 1 0.58 0.27 7246 8235 complement fr 3 0.62 0.15 7246 8157 complement fr 3 0.66 0.27 7246 8073 complement fr 3 0.68 0.58 7246 7980 complement fr 3 0.66 0.20 7246 7944 complement fr 3 0.66 0.33 8417 8599 complement fr 1 0.60 0.68 10022 10381 direct fr 2 0.66 0.10 10253 10381 direct fr 2 0.54 0.66 10256 10381 direct fr 2 0.54 0.36 10567 11178 direct fr 1 0.61 0.28 10600 11178 direct fr 1 0.65 0.76 10711 11178 direct fr 1 0.58 0.61 12463 12948 direct fr 1 0.50 0.19 16875 17042 direct fr 3 0.53 0.61 17143 17676 direct fr 1 0.50 0.74 17149 17676 direct fr 1 0.51 0.81 17513 18748 direct fr 2 0.55 0.00 17585 18748 direct fr 2 0.59 0.72 17597 18748 direct fr 2 0.59 0.29 17615 18748 direct fr 2 0.60 0.01 17621 18748 direct fr 2 0.61 0.01 17687 18748 direct fr 2 0.63 0.63 18014 18748 direct fr 2 0.59 0.12 18026 18748 direct fr 2 0.59 0.21 19033 19557 direct fr 1 0.51 0.25 19318 19557 direct fr 1 0.61 0.83 19583 20806 direct fr 2 0.51 0.00 19889 20806 direct fr 2 0.57 0.19 19910 20806 direct fr 2 0.56 0.02 19958 20806 direct fr 2 0.55 0.05 20048 20806 direct fr 2 0.56 0.07 20706 21608 direct fr 3 0.51 0.01 20742 21608 direct fr 3 0.53 0.33 20808 21608 direct fr 3 0.57 0.06 20952 21608 direct fr 3 0.65 0.58 21120 21608 direct fr 3 0.60 0.32 21162 21608 direct fr 3 0.61 0.06 21183 21608 direct fr 3 0.63 0.57 21198 21608 direct fr 3 0.63 0.73 21733 21879 direct fr 1 0.62 0.88 22356 22625 direct fr 3 0.51 0.08 22362 22625 direct fr 3 0.53 0.16 22482 22625 direct fr 3 0.55 0.26 22675 22869 complement fr 3 0.57 0.86 22675 22857 complement fr 3 0.56 0.61 22675 22824 complement fr 3 0.51 0.01 23609 24181 complement fr 1 0.77 0.11 23609 24160 complement fr 1 0.77 0.44 23609 24148 complement fr 1 0.76 0.37 24871 27870 direct fr 1 0.55 0.13 24979 27870 direct fr 1 0.57 0.17 25015 27870 direct fr 1 0.57 0.45 25306 27870 direct fr 1 0.56 0.29 25480 27870 direct fr 1 0.58 0.03 25732 27870 direct fr 1 0.57 0.31 25744 25929 complement fr 3 0.51 0.31 29941 31365 complement fr 3 0.61 0.48 29941 31323 complement fr 3 0.62 0.22 29941 31320 complement fr 3 0.61 0.26 29941 31284 complement fr 3 0.61 0.68 34543 34836 direct fr 1 0.53 0.78 34802 35131 direct fr 2 0.63 0.21 34826 35131 direct fr 2 0.60 0.86 34841 35131 direct fr 2 0.59 0.70 36501 37499 complement fr 2 0.57 0.17 36501 37493 complement fr 2 0.57 0.32 36501 37475 complement fr 2 0.56 0.24 37703 38233 complement fr 1 0.51 0.71 37703 38194 complement fr 1 0.52 0.25 37703 38191 complement fr 1 0.52 0.10 37703 38134 complement fr 1 0.52 0.03 37703 38110 complement fr 1 0.55 0.30 37703 38035 complement fr 1 0.59 0.15 37703 38020 complement fr 1 0.60 0.08 39571 40194 direct fr 1 0.61 0.40 39643 40194 direct fr 1 0.63 0.02 39652 40194 direct fr 1 0.64 0.01 39700 40194 direct fr 1 0.67 0.51 39754 40194 direct fr 1 0.71 0.56 39784 40194 direct fr 1 0.69 0.24 39874 40194 direct fr 1 0.63 0.08 40470 41786 complement fr 2 0.50 0.29 40470 41705 complement fr 2 0.52 0.47 40470 41672 complement fr 2 0.53 0.00 40470 41615 complement fr 2 0.54 0.11 40470 41606 complement fr 2 0.54 0.06 40470 41483 complement fr 2 0.60 0.44 40470 41447 complement fr 2 0.60 0.13 40470 41420 complement fr 2 0.60 0.07 40470 41408 complement fr 2 0.61 0.06 40470 41330 complement fr 2 0.64 0.19 43307 43585 complement fr 1 0.72 0.32 43307 43531 complement fr 1 0.65 0.23 43307 43432 complement fr 1 0.55 0.57 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 65 436 complement fr 1 497 1393 complement fr 1 1318 1953 complement fr 3 2048 2329 direct fr 2 2283 2450 complement fr 2 2337 2723 direct fr 3 2720 3100 complement fr 1 3160 5070 complement fr 3 5275 6288 complement fr 3 6290 7270 complement fr 1 7246 8238 complement fr 3 8417 8644 complement fr 1 8643 9050 direct fr 3 8864 9049 complement fr 1 9300 9959 complement fr 2 9462 9653 direct fr 3 9690 9917 direct fr 3 9899 10381 direct fr 2 10546 11178 direct fr 1 11148 12299 direct fr 3 12376 12948 direct fr 1 13058 14281 direct fr 2 13146 13502 complement fr 2 14364 15401 direct fr 3 14655 15146 complement fr 2 15243 15458 complement fr 2 15368 16924 direct fr 2 15497 15976 complement fr 1 16277 16666 complement fr 1 16664 16915 complement fr 1 16821 17042 direct fr 3 17119 17676 direct fr 1 17137 17718 complement fr 3 17384 18748 direct fr 2 18628 18939 complement fr 3 18640 19557 direct fr 1 19171 19335 complement fr 3 19547 20806 direct fr 2 19985 20482 complement fr 1 20700 21608 direct fr 3 20699 20866 complement fr 1 21559 21879 direct fr 1 21931 22212 direct fr 1 22154 22417 direct fr 2 22329 22625 direct fr 3 22675 23553 complement fr 3 23609 24235 complement fr 1 24633 24845 direct fr 3 24700 25116 complement fr 3 24832 27870 direct fr 1 25744 26013 complement fr 3 26350 26739 complement fr 3 27436 27693 complement fr 3 27980 28903 complement fr 1 28000 28194 complement fr 3 29204 29389 direct fr 2 29359 29499 direct fr 1 29941 31401 complement fr 3 31732 32697 direct fr 1 31775 32005 direct fr 2 34129 34518 complement fr 3 34492 34836 direct fr 1 34712 35131 direct fr 2 35646 36116 complement fr 2 36198 36392 direct fr 3 36501 37553 complement fr 2 37703 38443 complement fr 1 38515 39228 direct fr 1 39535 40194 direct fr 1 39622 39849 complement fr 3 40177 40344 complement fr 3 40470 41801 complement fr 2 41589 41978 direct fr 3 41755 42438 complement fr 3 41836 42051 direct fr 1 41976 42341 direct fr 3 42637 43134 direct fr 1 43173 43373 complement fr 2 43199 43888 direct fr 2 43307 43639 complement fr 1 43724 43921 complement fr 1 43839 44252 direct fr 3 43998 44207 complement fr 2 44480 44749 direct fr 2 44483 44737 complement fr 1 44779 45747 complement fr 3 45819 45995 direct fr 3 45831 46202 complement fr 2 46136 46318 direct fr 2 46172 46366 complement fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 2 34740 +/- 11 bp (direct) -------------------- 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