GENEMARK PREDICTIONS Sequence: gi|111074074|ref|NC_008273.1| Borrelia afzelii PKo plasmid cp30, complete sequence Sequence file: NC_008273.fna Sequence length: 30017 GC Content: 29.22% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 30 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 -------- -------- ---------- ----- ---- ---- 3 632 direct fr 3 0.86 .... 63 632 direct fr 3 0.86 .... 114 632 direct fr 3 0.85 0.35 1038 1367 complement fr 2 0.64 0.61 1038 1205 complement fr 2 0.64 0.63 1642 2457 complement fr 3 0.74 1.00 1642 2058 complement fr 3 0.71 0.40 1642 1914 complement fr 3 0.72 0.10 2569 3072 complement fr 3 0.63 0.63 3078 3956 complement fr 2 0.67 0.58 3078 3755 complement fr 2 0.72 0.17 3078 3404 complement fr 2 0.52 0.13 3078 3299 complement fr 2 0.71 0.74 3078 3233 complement fr 2 0.62 0.03 3953 4285 complement fr 1 0.57 0.74 5038 5883 complement fr 3 0.78 0.22 5038 5550 complement fr 3 0.82 0.20 5038 5526 complement fr 3 0.81 0.06 5038 5421 complement fr 3 0.78 0.73 5887 6522 complement fr 3 0.54 0.91 5887 6519 complement fr 3 0.54 0.84 5887 6501 complement fr 3 0.56 0.50 5887 6447 complement fr 3 0.56 0.33 5887 6198 complement fr 3 0.58 0.08 5887 6153 complement fr 3 0.56 0.19 5887 6141 complement fr 3 0.57 0.01 6513 7817 complement fr 2 0.87 0.92 6513 7733 complement fr 2 0.89 0.01 6513 7571 complement fr 2 0.87 0.39 6513 7559 complement fr 2 0.87 0.07 8186 8503 complement fr 1 0.62 0.43 8186 8497 complement fr 1 0.62 0.24 8186 8485 complement fr 1 0.64 0.18 8186 8368 complement fr 1 0.52 0.01 8519 8947 complement fr 1 0.77 0.69 8519 8704 complement fr 1 0.73 0.31 8519 8680 complement fr 1 0.69 0.09 8961 9830 complement fr 2 0.85 0.00 8961 9734 complement fr 2 0.86 0.15 8961 9638 complement fr 2 0.84 0.05 10054 10623 complement fr 3 0.55 0.06 10054 10383 complement fr 3 0.61 0.04 10054 10359 complement fr 3 0.58 0.38 10054 10317 complement fr 3 0.53 0.18 10620 11006 complement fr 2 0.79 0.98 10620 10937 complement fr 2 0.77 0.05 10620 10805 complement fr 2 0.65 0.39 10994 11377 complement fr 1 0.62 0.37 10994 11347 complement fr 1 0.63 0.01 10994 11335 complement fr 1 0.62 0.21 11377 11832 complement fr 3 0.71 0.98 11377 11757 complement fr 3 0.75 0.03 11377 11607 complement fr 3 0.68 0.56 11851 12810 complement fr 3 0.81 0.95 11851 12738 complement fr 3 0.82 0.02 11851 12690 complement fr 3 0.81 0.10 11851 12585 complement fr 3 0.80 0.01 12832 13404 complement fr 3 0.83 0.76 12832 13341 complement fr 3 0.87 0.16 13429 14187 complement fr 3 0.76 0.97 13429 13998 complement fr 3 0.77 0.05 13429 13782 complement fr 3 0.71 0.00 14195 14758 complement fr 1 0.86 0.99 14195 14695 complement fr 1 0.87 0.00 14195 14431 complement fr 1 0.78 0.03 14195 14419 complement fr 1 0.78 0.03 14770 15465 complement fr 3 0.83 1.00 14770 15360 complement fr 3 0.85 0.04 14770 15123 complement fr 3 0.77 0.05 14770 14994 complement fr 3 0.66 0.03 15482 16705 complement fr 1 0.75 0.50 15482 15904 complement fr 1 0.81 0.05 15482 15640 complement fr 1 0.56 0.57 16771 18123 complement fr 3 0.78 0.16 16771 17970 complement fr 3 0.79 0.09 16771 17739 complement fr 3 0.78 0.04 16771 17439 complement fr 3 0.74 0.31 16771 17298 complement fr 3 0.67 0.37 18154 18639 complement fr 3 0.78 0.71 18154 18528 complement fr 3 0.80 0.06 18154 18519 complement fr 3 0.80 0.12 18154 18306 complement fr 3 0.60 0.30 18809 19525 direct fr 2 0.78 0.36 18926 19525 direct fr 2 0.76 0.13 19124 19525 direct fr 2 0.78 0.43 19181 19525 direct fr 2 0.81 0.12 19660 20169 complement fr 3 0.82 0.04 19660 19854 complement fr 3 0.68 0.12 20281 20901 complement fr 3 0.86 0.58 20281 20889 complement fr 3 0.88 0.01 20281 20883 complement fr 3 0.88 0.01 20281 20694 complement fr 3 0.89 0.06 20281 20673 complement fr 3 0.88 0.02 20281 20655 complement fr 3 0.88 0.01 20929 21477 complement fr 3 0.81 0.75 20929 21465 complement fr 3 0.83 0.09 20929 21459 complement fr 3 0.83 0.07 20929 21150 complement fr 3 0.72 0.29 21910 22686 direct fr 1 0.65 0.40 22210 22686 direct fr 1 0.54 0.08 22691 23020 complement fr 1 0.51 0.60 22691 22981 complement fr 1 0.57 0.01 22691 22915 complement fr 1 0.69 0.01 22691 22882 complement fr 1 0.74 0.85 23168 24496 complement fr 1 0.86 0.91 23168 24436 complement fr 1 0.88 0.03 23168 24400 complement fr 1 0.88 0.05 23168 24241 complement fr 1 0.87 0.12 25236 25760 complement fr 2 0.79 0.22 25773 26330 complement fr 2 0.81 0.74 25773 26312 complement fr 2 0.85 0.18 25773 26267 complement fr 2 0.86 0.57 26372 27127 complement fr 1 0.74 0.92 26372 27016 complement fr 1 0.70 0.07 26372 26944 complement fr 1 0.66 0.18 26808 26930 direct fr 3 0.51 0.74 27103 27681 complement fr 3 0.71 0.95 27103 27582 complement fr 3 0.73 0.02 27103 27564 complement fr 3 0.71 0.11 27103 27561 complement fr 3 0.71 0.04 27691 28785 complement fr 3 0.61 0.08 27691 28416 complement fr 3 0.78 0.35 27691 28191 complement fr 3 0.75 0.03 29165 30019 direct fr 2 0.83 0.90 29237 30019 direct fr 2 0.88 0.12 29252 30019 direct fr 2 0.88 0.37 29411 30019 direct fr 2 0.86 0.00 29612 30019 direct fr 2 0.93 0.41 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 632 direct fr 3 671 1078 complement fr 1 1038 1373 complement fr 2 1371 1586 complement fr 2 1642 2469 complement fr 3 2569 3087 complement fr 3 3078 3962 complement fr 2 3953 4321 complement fr 1 4315 4746 complement fr 3 4877 5089 complement fr 1 5038 5889 complement fr 3 5887 6525 complement fr 3 6397 6837 direct fr 1 6513 7835 complement fr 2 7825 8076 complement fr 3 8058 8267 complement fr 2 8186 8521 complement fr 1 8519 8971 complement fr 1 8961 10091 complement fr 2 10054 10626 complement fr 3 10620 11051 complement fr 2 10994 11440 complement fr 1 11377 11835 complement fr 3 11851 12831 complement fr 3 12832 13407 complement fr 3 13429 14193 complement fr 3 14195 14791 complement fr 1 14770 15471 complement fr 3 15482 16813 complement fr 1 16771 18135 complement fr 3 18154 18660 complement fr 3 18734 19525 direct fr 2 19660 20193 complement fr 3 20281 20916 complement fr 3 20929 21483 complement fr 3 21895 22686 direct fr 1 22691 23059 complement fr 1 23168 24508 complement fr 1 25236 25772 complement fr 2 25773 26342 complement fr 2 26372 27172 complement fr 1 26748 26930 direct fr 3 27103 27693 complement fr 3 27691 28806 complement fr 3 29153 30019 direct fr 2 -------------------- 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