GENEMARK PREDICTIONS Sequence: gi|116326493|ref|NC_008496.1| Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 plasmid pLEUM1, complete sequence Sequence file: NC_008496.fna Sequence length: 37367 GC Content: 35.39% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 35 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 -------- -------- ---------- ----- ---- ---- 1 258 direct fr 1 0.76 .... 82 258 direct fr 1 0.73 .... 543 734 direct fr 3 0.56 0.55 561 734 direct fr 3 0.60 0.72 627 734 direct fr 3 0.67 0.07 651 734 direct fr 3 0.57 0.14 1323 1475 complement fr 2 0.51 0.68 1323 1466 complement fr 2 0.51 0.55 1880 3730 direct fr 2 0.87 0.52 1916 3730 direct fr 2 0.89 0.09 2054 3730 direct fr 2 0.93 0.42 2228 3730 direct fr 2 0.94 0.74 2453 3730 direct fr 2 0.92 0.04 3785 4030 direct fr 2 0.75 0.23 3794 4030 direct fr 2 0.74 0.01 3929 4030 direct fr 2 0.56 0.12 4023 4583 direct fr 3 0.78 0.85 4032 4583 direct fr 3 0.78 0.96 4380 4583 direct fr 3 0.77 0.31 4600 5292 direct fr 1 0.63 0.09 4645 5292 direct fr 1 0.68 0.57 4678 5292 direct fr 1 0.68 0.52 4855 5292 direct fr 1 0.64 0.24 6038 6523 direct fr 2 0.55 0.61 6188 6523 direct fr 2 0.65 0.46 7334 7789 complement fr 1 0.51 0.68 7334 7780 complement fr 1 0.51 0.43 7334 7777 complement fr 1 0.51 0.43 8451 9206 complement fr 2 0.58 0.33 8451 9164 complement fr 2 0.57 0.45 8451 9158 complement fr 2 0.57 0.50 8451 9089 complement fr 2 0.53 0.17 9203 9853 complement fr 1 0.66 0.10 9203 9697 complement fr 1 0.59 0.47 9203 9631 complement fr 1 0.62 0.01 9203 9574 complement fr 1 0.67 0.52 10343 10759 complement fr 1 0.67 0.05 10343 10711 complement fr 1 0.71 0.86 10343 10609 complement fr 1 0.66 0.05 10343 10492 complement fr 1 0.60 0.01 11211 12308 complement fr 2 0.65 0.49 11211 12077 complement fr 2 0.62 0.30 11211 12008 complement fr 2 0.59 0.21 11211 11888 complement fr 2 0.59 0.31 11211 11834 complement fr 2 0.58 0.24 12362 13033 complement fr 1 0.59 0.12 12362 12676 complement fr 1 0.77 0.61 12362 12610 complement fr 1 0.72 0.04 13155 13451 direct fr 3 0.62 0.70 13167 13451 direct fr 3 0.64 0.65 13284 13451 direct fr 3 0.69 0.83 13326 13451 direct fr 3 0.60 0.19 13356 13451 direct fr 3 0.52 0.08 15704 15841 direct fr 2 0.72 0.56 15740 15841 direct fr 2 0.65 0.11 15752 15841 direct fr 2 0.61 0.05 16304 16927 complement fr 1 0.61 0.57 16304 16879 complement fr 1 0.61 0.02 16304 16681 complement fr 1 0.61 0.07 16304 16666 complement fr 1 0.60 0.06 16973 17215 complement fr 1 0.61 0.26 17699 18511 complement fr 1 0.79 0.84 17699 18472 complement fr 1 0.80 0.02 17699 18448 complement fr 1 0.80 0.35 17699 18424 complement fr 1 0.80 0.81 20163 20267 direct fr 3 0.55 0.37 20172 20267 direct fr 3 0.55 0.08 20333 20905 direct fr 2 0.80 0.63 20366 20905 direct fr 2 0.78 0.05 20372 20905 direct fr 2 0.78 0.02 20937 21470 direct fr 3 0.82 0.77 20964 21470 direct fr 3 0.83 0.09 21072 21470 direct fr 3 0.81 0.58 21672 21953 complement fr 2 0.64 0.22 21672 21908 complement fr 2 0.57 0.23 22523 22777 complement fr 1 0.55 0.08 22523 22657 complement fr 1 0.54 0.62 22986 23549 complement fr 2 0.74 0.18 22986 23462 complement fr 2 0.71 0.01 22986 23291 complement fr 2 0.63 0.10 24916 25080 direct fr 1 0.51 0.38 25077 25424 direct fr 3 0.53 0.09 25158 25424 direct fr 3 0.59 0.08 25221 25424 direct fr 3 0.51 0.14 25599 27131 direct fr 3 0.60 0.21 25728 27131 direct fr 3 0.62 0.15 25782 27131 direct fr 3 0.63 0.06 25824 27131 direct fr 3 0.64 0.46 25965 27131 direct fr 3 0.63 0.41 26019 27131 direct fr 3 0.61 0.09 27698 28660 direct fr 2 0.55 0.21 27716 28660 direct fr 2 0.55 0.42 27887 28660 direct fr 2 0.58 0.11 27923 28660 direct fr 2 0.58 0.34 27962 28660 direct fr 2 0.57 0.07 28049 28660 direct fr 2 0.62 0.02 28175 28660 direct fr 2 0.69 0.28 29020 29262 direct fr 1 0.61 0.31 29161 29262 direct fr 1 0.52 0.25 29308 29931 direct fr 1 0.61 0.62 29356 29931 direct fr 1 0.61 0.04 29554 29931 direct fr 1 0.64 0.11 29569 29931 direct fr 1 0.62 0.07 29976 30110 direct fr 3 0.54 0.49 30195 30479 complement fr 2 0.58 0.26 30195 30434 complement fr 2 0.65 0.56 30195 30338 complement fr 2 0.52 0.30 31571 31855 direct fr 2 0.54 0.45 31628 31855 direct fr 2 0.55 0.31 32397 33929 direct fr 3 0.82 0.76 32493 33929 direct fr 3 0.85 0.09 32871 33929 direct fr 3 0.83 0.91 32892 33929 direct fr 3 0.83 0.27 34124 34366 direct fr 2 0.60 0.24 34265 34366 direct fr 2 0.53 0.19 34412 35215 direct fr 2 0.60 0.62 34460 35215 direct fr 2 0.60 0.04 34658 35215 direct fr 2 0.62 0.11 34673 35215 direct fr 2 0.61 0.07 34700 35215 direct fr 2 0.61 0.43 35367 35693 direct fr 3 0.72 0.89 35472 35693 direct fr 3 0.77 0.62 35475 35693 direct fr 3 0.76 0.71 35704 37347 direct fr 1 0.83 0.87 35719 37347 direct fr 1 0.83 0.70 35740 37347 direct fr 1 0.85 0.16 35881 37347 direct fr 1 0.87 0.56 35941 37347 direct fr 1 0.88 0.24 35968 37347 direct fr 1 0.88 0.27 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 1 258 direct fr 1 537 734 direct fr 3 644 1561 direct fr 2 1323 1514 complement fr 2 1865 3730 direct fr 2 1876 2046 complement fr 3 3728 4030 direct fr 2 4014 4583 direct fr 3 4585 5292 direct fr 1 5268 5651 direct fr 3 5471 5731 direct fr 2 5735 5917 direct fr 2 6035 6523 direct fr 2 7084 7227 direct fr 1 7334 7930 complement fr 1 8001 8393 complement fr 2 8451 9275 complement fr 2 8944 9111 complement fr 3 9203 9913 complement fr 1 9850 10116 complement fr 3 10343 10780 complement fr 1 11211 12311 complement fr 2 12362 13051 complement fr 1 13131 13451 direct fr 3 13573 13761 direct fr 1 14092 14733 complement fr 3 14192 14386 direct fr 2 14826 15029 direct fr 3 15259 15573 complement fr 3 15278 15841 direct fr 2 15372 15587 direct fr 3 16125 16394 complement fr 2 16304 16975 complement fr 1 16973 17236 complement fr 1 17357 17701 complement fr 1 17699 18541 complement fr 1 19643 19924 complement fr 1 20106 20267 direct fr 3 20249 20905 direct fr 2 20880 21470 direct fr 3 21672 22118 complement fr 2 22151 22525 complement fr 1 22523 22783 complement fr 1 22986 23633 complement fr 2 24128 24418 complement fr 1 24646 25080 direct fr 1 25008 25424 direct fr 3 25587 27131 direct fr 3 26147 26335 complement fr 1 27680 28660 direct fr 2 27679 28329 complement fr 3 28741 28965 complement fr 3 28999 29262 direct fr 1 29260 29931 direct fr 1 29841 30110 direct fr 3 30195 30518 complement fr 2 31194 31379 direct fr 3 31532 31855 direct fr 2 32382 33929 direct fr 3 34103 34366 direct fr 2 34364 35215 direct fr 2 35343 35693 direct fr 3 35677 37347 direct fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 2 5496 +/- 11 bp (direct) 2 3 9060 +/- 11 bp (complement) -------------------- 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