GENEMARK PREDICTIONS Sequence: gi|11497372|ref|NC_000956.1| Borrelia burgdorferi B31 plasmid lp56, complete sequence Sequence file: NC_000956.fna Sequence length: 52971 GC Content: 27.29% 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 -------- -------- ---------- ----- ---- ---- 856 1407 direct fr 1 0.76 0.01 973 1407 direct fr 1 0.86 0.25 1108 1407 direct fr 1 0.80 0.11 1324 1407 direct fr 1 0.51 0.01 1404 1814 direct fr 3 0.63 0.00 2110 2268 direct fr 1 0.58 0.84 2744 3496 direct fr 2 0.87 0.01 2762 3496 direct fr 2 0.90 0.05 2861 3496 direct fr 2 0.92 0.02 2978 3496 direct fr 2 0.91 0.06 3332 3496 direct fr 2 0.78 0.58 3623 4108 direct fr 2 0.84 1.00 3680 4108 direct fr 2 0.87 0.00 3806 4108 direct fr 2 0.85 0.00 3827 4108 direct fr 2 0.85 0.00 4249 4986 complement fr 3 0.76 0.63 4249 4929 complement fr 3 0.78 0.36 4249 4899 complement fr 3 0.77 0.27 4249 4809 complement fr 3 0.74 0.06 5069 5830 complement fr 1 0.81 0.92 5069 5335 complement fr 1 0.75 0.16 6336 6479 complement fr 2 0.65 0.90 6800 7411 direct fr 2 0.85 0.96 6836 7411 direct fr 2 0.90 0.66 6899 7411 direct fr 2 0.91 0.08 7283 7411 direct fr 2 0.67 0.00 7433 8392 direct fr 2 0.89 0.95 7469 8392 direct fr 2 0.93 0.03 7505 8392 direct fr 2 0.92 0.01 7553 8392 direct fr 2 0.92 0.27 8406 8867 direct fr 3 0.83 1.00 8412 8867 direct fr 3 0.83 1.00 8487 8867 direct fr 3 0.83 0.00 8637 8867 direct fr 3 0.74 0.17 8867 9250 direct fr 2 0.80 0.72 8897 9250 direct fr 2 0.82 0.09 8909 9250 direct fr 2 0.83 0.29 9083 9250 direct fr 2 0.69 0.01 9238 9435 direct fr 1 0.78 0.96 9259 9435 direct fr 1 0.88 0.20 9307 9435 direct fr 1 0.84 0.03 9439 9627 direct fr 1 0.70 0.93 9624 10190 direct fr 3 0.79 0.16 9642 10190 direct fr 3 0.82 0.40 9894 10190 direct fr 3 0.83 0.64 9930 10190 direct fr 3 0.81 0.23 9936 10190 direct fr 3 0.81 0.37 10414 11283 direct fr 1 0.94 0.00 10795 11283 direct fr 1 0.89 0.31 10900 11283 direct fr 1 0.86 0.01 11276 11725 direct fr 2 0.80 0.81 11297 11725 direct fr 2 0.84 0.79 11420 11725 direct fr 2 0.89 0.01 11477 11725 direct fr 2 0.86 0.43 11540 11725 direct fr 2 0.82 0.05 11741 12196 direct fr 2 0.86 0.17 11747 12196 direct fr 2 0.86 0.37 11759 12196 direct fr 2 0.88 0.65 11831 12196 direct fr 2 0.92 0.10 11906 12196 direct fr 2 0.90 0.14 11939 12196 direct fr 2 0.89 0.07 12193 12429 direct fr 1 0.76 0.98 12310 12429 direct fr 1 0.85 0.12 12437 13732 direct fr 2 0.92 0.85 12521 13732 direct fr 2 0.95 0.01 12695 13732 direct fr 2 0.94 0.07 12740 13732 direct fr 2 0.93 0.29 13755 14438 direct fr 3 0.79 0.94 13959 14438 direct fr 3 0.83 0.32 13974 14438 direct fr 3 0.84 0.20 14127 14438 direct fr 3 0.87 0.11 14184 14438 direct fr 3 0.85 0.34 14442 15392 direct fr 3 0.90 0.81 14592 15392 direct fr 3 0.93 0.11 14742 15392 direct fr 3 0.93 0.78 14766 15392 direct fr 3 0.92 0.07 15410 15964 direct fr 2 0.82 0.98 15437 15964 direct fr 2 0.85 0.05 15994 16326 direct fr 1 0.69 0.49 16323 17198 direct fr 3 0.91 0.57 16524 17198 direct fr 3 0.95 0.21 16875 17198 direct fr 3 0.91 0.67 16980 17198 direct fr 3 0.96 0.79 17208 17813 direct fr 3 0.77 0.11 17511 17813 direct fr 3 0.91 0.11 17823 18638 direct fr 3 0.89 0.99 18222 18638 direct fr 3 0.87 0.52 18363 18638 direct fr 3 0.81 0.06 18776 18916 direct fr 2 0.55 0.00 18791 18916 direct fr 2 0.55 0.03 18920 19267 direct fr 2 0.84 0.87 19082 19267 direct fr 2 0.74 0.83 19257 19592 direct fr 3 0.84 0.78 19410 19592 direct fr 3 0.81 0.67 19579 19938 direct fr 1 0.58 0.03 19585 19938 direct fr 1 0.60 0.00 19729 19938 direct fr 1 0.77 0.13 20022 20738 direct fr 3 0.88 0.58 20043 20738 direct fr 3 0.91 0.94 20052 20738 direct fr 3 0.91 0.47 20115 20738 direct fr 3 0.91 0.02 20397 20738 direct fr 3 0.85 0.01 20640 20738 direct fr 3 0.51 0.01 20844 21455 direct fr 3 0.83 0.00 21024 21455 direct fr 3 0.94 0.00 21045 21455 direct fr 3 0.94 0.07 21093 21455 direct fr 3 0.94 0.40 21532 22479 complement fr 3 0.86 0.73 21532 22404 complement fr 3 0.88 0.03 21532 22389 complement fr 3 0.88 0.03 21532 22251 complement fr 3 0.87 0.72 22869 23966 direct fr 3 0.77 0.35 23058 23966 direct fr 3 0.86 0.13 23121 23966 direct fr 3 0.86 0.44 23289 23966 direct fr 3 0.84 0.05 23976 24542 direct fr 3 0.77 0.99 24084 24542 direct fr 3 0.72 0.00 24102 24542 direct fr 3 0.71 0.07 24518 25273 direct fr 2 0.81 0.67 24596 25273 direct fr 2 0.80 0.09 24641 25273 direct fr 2 0.79 0.16 24707 25273 direct fr 2 0.77 0.32 25317 25877 direct fr 3 0.89 0.94 25800 25877 direct fr 3 0.94 0.23 25848 25877 direct fr 3 0.88 0.00 25890 26426 direct fr 3 0.82 0.40 26268 26426 direct fr 3 0.61 0.13 26921 28246 direct fr 2 0.88 0.98 26978 28246 direct fr 2 0.89 0.01 27137 28246 direct fr 2 0.87 0.55 27218 28246 direct fr 2 0.86 0.00 28299 28724 direct fr 3 0.65 0.97 28500 28724 direct fr 3 0.73 0.77 28533 28724 direct fr 3 0.76 0.58 28730 29506 complement fr 1 0.64 0.70 28730 29500 complement fr 1 0.64 0.49 28730 29458 complement fr 1 0.65 0.23 28730 29206 complement fr 1 0.58 0.50 28730 29143 complement fr 1 0.53 0.10 29907 30974 direct fr 3 0.92 0.64 29925 30974 direct fr 3 0.93 0.30 29937 30974 direct fr 3 0.94 0.07 29949 30974 direct fr 3 0.95 0.00 29979 30974 direct fr 3 0.98 0.74 30423 30974 direct fr 3 0.97 0.00 31117 31710 direct fr 1 0.81 0.01 31138 31710 direct fr 1 0.82 0.23 31168 31710 direct fr 1 0.88 0.92 31315 31710 direct fr 1 0.89 0.31 31453 31710 direct fr 1 0.84 0.33 31928 32458 direct fr 2 0.94 0.13 31997 32458 direct fr 2 0.93 0.09 32006 32458 direct fr 2 0.93 0.23 32455 33807 direct fr 1 0.88 0.07 32608 33807 direct fr 1 0.90 0.01 33352 33807 direct fr 1 0.83 0.06 33424 33807 direct fr 1 0.80 0.10 33873 34358 direct fr 3 0.81 0.36 34119 34358 direct fr 3 0.78 0.37 34940 35098 direct fr 2 0.74 0.33 34961 35098 direct fr 2 0.69 0.38 34982 35098 direct fr 2 0.63 0.03 35115 35807 direct fr 3 0.89 1.00 35220 35807 direct fr 3 0.89 0.00 35418 35807 direct fr 3 0.83 0.04 35454 35807 direct fr 3 0.81 0.01 35819 36385 direct fr 2 0.92 0.99 35885 36385 direct fr 2 0.96 0.01 36143 36385 direct fr 2 0.92 0.00 36215 36385 direct fr 2 0.88 0.08 36389 37135 direct fr 2 0.71 0.98 36593 37135 direct fr 2 0.62 0.01 37816 38196 complement fr 3 0.85 0.11 37816 38058 complement fr 3 0.80 0.40 37816 37890 complement fr 3 0.58 0.08 38416 38514 complement fr 3 0.71 0.88 38565 39077 complement fr 2 0.86 0.97 38565 39035 complement fr 2 0.85 0.01 38565 39014 complement fr 2 0.84 0.00 39740 39805 complement fr 1 0.58 1.00 39802 39933 complement fr 3 0.76 0.93 39959 40186 complement fr 1 0.65 0.01 40436 43696 complement fr 1 0.95 0.60 40436 42583 complement fr 1 0.95 0.34 40436 42379 complement fr 1 0.94 0.64 40436 42289 complement fr 1 0.94 0.07 46001 46129 complement fr 1 0.63 0.78 47784 48131 complement fr 2 0.85 0.14 47784 47948 complement fr 2 0.71 0.09 48432 48626 complement fr 2 0.56 0.01 48432 48545 complement fr 2 0.68 0.22 51172 51498 complement fr 3 0.59 0.06 52135 52608 complement fr 3 0.80 0.19 52135 52431 complement fr 3 0.81 0.04 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 231 548 direct fr 3 844 1407 direct fr 1 1389 1814 direct fr 3 1723 2268 direct fr 1 2714 3496 direct fr 2 3578 4108 direct fr 2 4249 4998 complement fr 3 5069 5863 complement fr 1 5803 6354 complement fr 3 6336 6698 complement fr 2 6580 6807 direct fr 1 6785 7411 direct fr 2 7412 8392 direct fr 2 8403 8867 direct fr 3 8804 9250 direct fr 2 9193 9435 direct fr 1 9433 9627 direct fr 1 9621 10190 direct fr 3 10153 11283 direct fr 1 11273 11725 direct fr 2 11723 12196 direct fr 2 12190 12429 direct fr 1 12419 13732 direct fr 2 13746 14438 direct fr 3 14436 15392 direct fr 3 15383 15964 direct fr 2 15958 16326 direct fr 1 16317 17198 direct fr 3 17196 17813 direct fr 3 17811 18638 direct fr 3 18707 18916 direct fr 2 18914 19267 direct fr 2 19209 19592 direct fr 3 19521 19784 complement fr 2 19549 19938 direct fr 1 20001 20738 direct fr 3 20814 21455 direct fr 3 21532 22500 complement fr 3 22848 23966 direct fr 3 23964 24542 direct fr 3 24473 25273 direct fr 2 25302 25877 direct fr 3 25875 26426 direct fr 3 26873 28246 direct fr 2 28293 28724 direct fr 3 28730 29521 complement fr 1 29892 30974 direct fr 3 31111 31710 direct fr 1 31853 32458 direct fr 2 32440 33807 direct fr 1 33765 34358 direct fr 3 34356 34751 direct fr 3 34727 35098 direct fr 2 35109 35807 direct fr 3 35786 36385 direct fr 2 36383 37135 direct fr 2 36715 37536 complement fr 3 37816 38418 complement fr 3 38416 38556 complement fr 3 38565 39086 complement fr 2 39043 39375 complement fr 3 39357 39554 complement fr 2 39527 39742 complement fr 1 39802 39981 complement fr 3 39959 40204 complement fr 1 40436 43735 complement fr 1 43767 43910 complement fr 2 43883 44110 complement fr 1 43915 44280 complement fr 3 44211 44387 complement fr 2 44543 44983 direct fr 2 45058 45282 complement fr 3 45801 46007 complement fr 2 46001 46348 complement fr 1 47784 48254 complement fr 2 48252 48434 complement fr 2 48432 48644 complement fr 2 49344 49562 complement fr 2 49535 49696 complement fr 1 50395 50598 complement fr 3 51172 51549 complement fr 3 51918 52124 complement fr 2 52135 52611 complement fr 3 52532 52765 complement fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 1 44052 +/- 11 bp (complement) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Thu Jun 14 14:51:50 2007