GENEMARK PREDICTIONS Sequence: gi|98152871|ref|NC_008036.1| Sphingopyxis alaskensis RB2256 F plasmid, complete sequence Sequence file: NC_008036.fna Sequence length: 28543 GC Content: 60.37% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 60 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 -------- -------- ---------- ----- ---- ---- 1028 1795 complement fr 1 0.63 0.56 1028 1792 complement fr 1 0.63 0.31 1028 1750 complement fr 1 0.67 0.21 1028 1654 complement fr 1 0.68 0.81 1028 1648 complement fr 1 0.68 0.55 1028 1645 complement fr 1 0.68 0.37 1803 4727 complement fr 2 0.75 0.09 1803 4688 complement fr 2 0.76 0.39 1803 4631 complement fr 2 0.76 0.51 1803 4532 complement fr 2 0.76 0.42 1803 4529 complement fr 2 0.76 0.26 4829 5167 direct fr 2 0.62 0.00 4862 5167 direct fr 2 0.70 0.52 4922 5167 direct fr 2 0.71 0.13 4937 5167 direct fr 2 0.70 0.05 4994 5167 direct fr 2 0.60 0.25 5726 6991 direct fr 2 0.58 0.15 5741 6991 direct fr 2 0.59 0.06 5765 6991 direct fr 2 0.60 0.22 5807 6991 direct fr 2 0.61 0.74 5819 6991 direct fr 2 0.61 0.41 5981 6991 direct fr 2 0.67 0.09 6038 6991 direct fr 2 0.69 0.77 6068 6991 direct fr 2 0.68 0.13 7141 8589 direct fr 1 0.60 0.40 7324 8589 direct fr 1 0.58 0.29 7495 8589 direct fr 1 0.61 0.05 7516 8589 direct fr 1 0.61 0.02 7597 8589 direct fr 1 0.62 0.31 9243 10043 direct fr 3 0.51 0.86 9246 10043 direct fr 3 0.51 0.68 9924 10043 direct fr 3 0.61 0.23 9927 10043 direct fr 3 0.57 0.23 9933 10043 direct fr 3 0.57 0.13 10057 11700 direct fr 1 0.60 0.13 10105 11700 direct fr 1 0.62 0.51 10147 11700 direct fr 1 0.61 0.43 10219 11700 direct fr 1 0.60 0.11 11790 12170 direct fr 3 0.57 0.72 11850 12170 direct fr 3 0.61 0.52 11853 12170 direct fr 3 0.61 0.40 11889 12170 direct fr 3 0.62 0.59 12472 12972 direct fr 1 0.54 0.20 12478 12972 direct fr 1 0.54 0.18 12487 12972 direct fr 1 0.55 0.17 12637 12972 direct fr 1 0.67 0.84 12643 12972 direct fr 1 0.67 0.43 12646 12972 direct fr 1 0.67 0.40 12976 13287 direct fr 1 0.55 0.55 13066 13287 direct fr 1 0.59 0.45 13385 14383 direct fr 2 0.71 0.61 13433 14383 direct fr 2 0.71 0.09 13436 14383 direct fr 2 0.71 0.17 13475 14383 direct fr 2 0.70 0.10 14390 14602 direct fr 2 0.55 0.92 14396 14602 direct fr 2 0.55 0.66 14429 14602 direct fr 2 0.66 0.48 14614 14835 direct fr 1 0.62 0.82 14623 14835 direct fr 1 0.64 0.55 16351 16881 direct fr 1 0.50 0.53 16576 16881 direct fr 1 0.59 0.36 16606 16881 direct fr 1 0.62 0.79 16612 16881 direct fr 1 0.64 0.70 16651 16881 direct fr 1 0.61 0.16 17319 19244 direct fr 3 0.51 0.10 17334 19244 direct fr 3 0.51 0.02 17475 19244 direct fr 3 0.54 0.87 17478 19244 direct fr 3 0.54 0.74 17487 19244 direct fr 3 0.54 0.41 19235 19531 direct fr 2 0.59 0.86 19262 19531 direct fr 2 0.63 0.70 19295 19531 direct fr 2 0.61 0.01 19313 19531 direct fr 2 0.58 0.03 19382 19531 direct fr 2 0.67 0.54 19525 20211 direct fr 1 0.52 0.13 19528 20211 direct fr 1 0.52 0.05 19567 20211 direct fr 1 0.55 0.13 19651 20211 direct fr 1 0.61 0.79 19747 20211 direct fr 1 0.56 0.15 19789 20211 direct fr 1 0.59 0.23 19807 20211 direct fr 1 0.60 0.69 19861 20211 direct fr 1 0.57 0.14 19900 20211 direct fr 1 0.54 0.11 19906 20211 direct fr 1 0.54 0.05 20208 21341 direct fr 3 0.60 0.26 20289 21341 direct fr 3 0.63 0.17 20319 21341 direct fr 3 0.62 0.11 20325 21341 direct fr 3 0.62 0.09 21284 22387 direct fr 2 0.64 0.00 21338 22387 direct fr 2 0.67 0.07 21386 22387 direct fr 2 0.70 0.69 21419 22387 direct fr 2 0.70 0.48 21440 22387 direct fr 2 0.69 0.38 23197 23364 direct fr 1 0.53 0.22 23260 23364 direct fr 1 0.57 0.50 23628 24275 direct fr 3 0.59 0.22 23892 24275 direct fr 3 0.60 0.18 23979 24275 direct fr 3 0.68 0.70 24000 24275 direct fr 3 0.68 0.82 25020 25157 direct fr 3 0.58 0.77 25814 26143 direct fr 2 0.54 0.67 25850 26143 direct fr 2 0.51 0.26 26638 28125 complement fr 3 0.70 0.19 26638 28092 complement fr 3 0.71 0.37 26638 28011 complement fr 3 0.70 0.26 26638 27972 complement fr 3 0.70 0.12 28202 28543 direct fr 2 0.87 0.90 28445 28543 direct fr 2 0.99 0.59 28460 28543 direct fr 2 0.99 .... 28463 28543 direct fr 2 0.99 .... List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 290 1030 complement fr 1 1028 1798 complement fr 1 1779 2600 direct fr 3 1803 4772 complement fr 2 3645 4736 direct fr 3 4808 5167 direct fr 2 5040 5642 complement fr 2 5043 5417 direct fr 3 5684 6991 direct fr 2 7111 8589 direct fr 1 7606 7947 complement fr 3 8011 8535 complement fr 3 8904 9953 complement fr 2 9075 10043 direct fr 3 10045 11133 complement fr 3 10048 11700 direct fr 1 11131 11907 complement fr 3 11757 12170 direct fr 3 12107 12499 direct fr 2 12206 12520 complement fr 1 12463 12972 direct fr 1 12496 13239 complement fr 3 12970 13287 direct fr 1 13334 14383 direct fr 2 14054 14416 complement fr 1 14335 14835 direct fr 1 14381 14602 direct fr 2 14762 15706 direct fr 2 14843 15424 complement fr 1 15422 15739 complement fr 1 15619 16881 direct fr 1 15835 16326 complement fr 3 16839 19244 direct fr 3 16965 17873 complement fr 2 17871 18518 complement fr 2 18560 18844 complement fr 1 18705 19271 complement fr 2 19148 19531 direct fr 2 19241 19840 complement fr 1 19417 20211 direct fr 1 19426 20172 complement fr 3 20139 20537 complement fr 2 20178 21341 direct fr 3 20769 21446 complement fr 2 21275 22387 direct fr 2 21692 22249 complement fr 1 22385 23122 direct fr 2 22544 22951 complement fr 1 22903 23364 direct fr 1 23166 24275 direct fr 3 23410 23946 direct fr 1 23613 24245 complement fr 2 24748 24966 direct fr 1 24960 25157 direct fr 3 25105 25455 complement fr 3 25572 25853 direct fr 3 25634 26173 complement fr 1 25667 26143 direct fr 2 26638 28152 complement fr 3 26788 28179 direct fr 1 28169 28543 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