GENEMARK PREDICTIONS Sequence: gi|119709757|ref|NC_008696.1| Thermofilum pendens Hrk 5 plasmid pTPEN01, complete sequence Sequence file: NC_008696.fna Sequence length: 31504 GC Content: 56.54% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 57 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 -------- -------- ---------- ----- ---- ---- 47 1714 complement fr 1 0.92 0.96 47 1618 complement fr 1 0.93 0.11 47 1594 complement fr 1 0.93 0.07 47 1528 complement fr 1 0.93 0.05 1778 2146 complement fr 1 0.53 0.00 1778 2074 complement fr 1 0.64 0.61 1778 1999 complement fr 1 0.55 0.07 2071 3015 complement fr 3 0.83 0.74 2071 2940 complement fr 3 0.87 0.25 2071 2889 complement fr 3 0.86 0.16 2071 2862 complement fr 3 0.86 0.35 3012 3581 complement fr 2 0.72 0.93 3012 3578 complement fr 2 0.72 0.93 3012 3572 complement fr 2 0.73 0.90 3012 3545 complement fr 2 0.77 0.82 3012 3536 complement fr 2 0.78 0.06 3012 3527 complement fr 2 0.78 0.06 3012 3515 complement fr 2 0.77 0.09 3585 3803 complement fr 2 0.61 0.25 3585 3764 complement fr 2 0.67 0.78 3585 3740 complement fr 2 0.63 0.28 3585 3719 complement fr 2 0.60 0.11 3846 4226 complement fr 2 0.68 0.28 3846 4214 complement fr 2 0.70 0.49 3846 4187 complement fr 2 0.78 0.28 3846 4157 complement fr 2 0.77 0.32 3846 4133 complement fr 2 0.76 0.49 4306 4677 complement fr 3 0.62 0.19 4306 4653 complement fr 3 0.66 0.13 4306 4632 complement fr 3 0.69 0.16 4306 4623 complement fr 3 0.69 0.31 4306 4581 complement fr 3 0.72 0.36 4677 5198 complement fr 2 0.64 0.00 4677 5147 complement fr 2 0.72 0.72 4677 5108 complement fr 2 0.75 0.34 4677 5009 complement fr 2 0.79 0.52 4677 4847 complement fr 2 0.64 0.46 5211 5609 complement fr 2 0.61 0.41 5211 5588 complement fr 2 0.65 0.72 5211 5474 complement fr 2 0.77 0.92 5211 5471 complement fr 2 0.77 0.90 5211 5453 complement fr 2 0.75 0.55 6000 6362 complement fr 2 0.52 0.51 6000 6356 complement fr 2 0.51 0.26 6000 6134 complement fr 2 0.65 0.91 6500 6706 complement fr 1 0.68 0.29 6500 6697 complement fr 1 0.68 0.58 6500 6658 complement fr 1 0.61 0.44 6813 7586 complement fr 2 0.82 0.11 6813 7550 complement fr 2 0.86 0.59 6813 7430 complement fr 2 0.89 0.08 6813 7409 complement fr 2 0.88 0.05 6813 7355 complement fr 2 0.87 0.11 8070 8855 complement fr 2 0.79 0.05 8070 8840 complement fr 2 0.80 0.04 8070 8822 complement fr 2 0.81 0.15 8070 8768 complement fr 2 0.86 0.66 8070 8708 complement fr 2 0.85 0.15 8070 8681 complement fr 2 0.85 0.01 8952 9350 direct fr 3 0.58 0.92 8982 9350 direct fr 3 0.64 0.66 9027 9350 direct fr 3 0.62 0.24 9503 9862 direct fr 2 0.70 0.75 9527 9862 direct fr 2 0.72 0.22 9581 9862 direct fr 2 0.73 0.17 9599 9862 direct fr 2 0.76 0.35 9626 9862 direct fr 2 0.77 0.75 9925 10311 direct fr 1 0.54 0.29 10445 10888 complement fr 1 0.82 0.30 10445 10840 complement fr 1 0.84 0.60 10445 10825 complement fr 1 0.84 0.23 10445 10819 complement fr 1 0.83 0.39 10818 12032 direct fr 3 0.66 0.31 10824 12032 direct fr 3 0.66 0.15 10842 12032 direct fr 3 0.67 0.08 10899 12032 direct fr 3 0.69 0.78 10905 12032 direct fr 3 0.69 0.79 10998 12032 direct fr 3 0.67 0.08 11678 11824 complement fr 1 0.52 0.61 12044 12730 direct fr 2 0.62 0.25 12104 12730 direct fr 2 0.66 0.06 12143 12730 direct fr 2 0.68 0.55 12164 12730 direct fr 2 0.68 0.51 12185 12730 direct fr 2 0.67 0.37 12776 13279 direct fr 2 0.86 0.74 12803 13279 direct fr 2 0.88 0.55 12824 13279 direct fr 2 0.88 0.19 12917 13279 direct fr 2 0.86 0.71 13276 13575 direct fr 1 0.76 0.91 13297 13575 direct fr 1 0.82 0.52 13300 13575 direct fr 1 0.82 0.50 13363 13575 direct fr 1 0.79 0.20 13556 13774 direct fr 2 0.52 0.30 13568 13774 direct fr 2 0.55 0.12 13607 13774 direct fr 2 0.63 0.30 13646 13774 direct fr 2 0.63 0.63 13806 14255 direct fr 3 0.62 0.00 13971 14255 direct fr 3 0.83 0.62 14305 14574 direct fr 1 0.68 0.28 14413 14574 direct fr 1 0.71 0.62 14431 14574 direct fr 1 0.69 0.51 14571 14876 direct fr 3 0.76 0.97 14580 14876 direct fr 3 0.76 0.97 14664 14876 direct fr 3 0.72 0.03 14736 14876 direct fr 3 0.68 0.66 14742 14876 direct fr 3 0.66 0.71 14866 15402 direct fr 1 0.51 0.01 14920 15402 direct fr 1 0.57 0.10 15052 15402 direct fr 1 0.78 0.59 15064 15402 direct fr 1 0.80 0.66 15109 15402 direct fr 1 0.82 0.24 15166 15402 direct fr 1 0.79 0.07 15187 15402 direct fr 1 0.76 0.13 14936 15067 direct fr 2 0.66 0.07 15432 17306 direct fr 3 0.84 0.53 15438 17306 direct fr 3 0.85 0.38 15546 17306 direct fr 3 0.86 0.17 15627 17306 direct fr 3 0.86 0.25 15672 17306 direct fr 3 0.86 0.18 17355 17555 direct fr 3 0.51 0.15 17552 17845 direct fr 2 0.68 0.86 17555 17845 direct fr 2 0.68 0.87 17585 17845 direct fr 2 0.77 0.73 17687 17845 direct fr 2 0.78 0.05 17690 17845 direct fr 2 0.77 0.04 18301 18462 direct fr 1 0.55 0.89 18367 18462 direct fr 1 0.55 0.19 18459 18707 complement fr 2 0.70 0.54 18459 18683 complement fr 2 0.74 0.49 18459 18572 complement fr 2 0.52 0.17 18892 19323 complement fr 3 0.62 0.34 18892 19152 complement fr 3 0.68 0.08 19362 19472 complement fr 2 0.50 0.07 19986 20183 complement fr 2 0.58 0.67 19986 20171 complement fr 2 0.55 0.20 20180 22081 complement fr 1 0.78 0.47 20180 21703 complement fr 1 0.83 0.26 20180 21481 complement fr 1 0.81 0.04 20180 21337 complement fr 1 0.79 0.79 23125 23532 complement fr 3 0.83 0.83 23125 23460 complement fr 3 0.80 0.02 23125 23454 complement fr 3 0.80 0.02 23724 24191 complement fr 2 0.89 0.68 23724 24185 complement fr 2 0.89 0.43 23724 24086 complement fr 2 0.87 0.27 24413 25006 complement fr 1 0.59 0.19 24413 24997 complement fr 1 0.59 0.29 24413 24904 complement fr 1 0.62 0.07 24413 24814 complement fr 1 0.71 0.32 24413 24760 complement fr 1 0.70 0.20 24413 24727 complement fr 1 0.71 0.18 25066 25848 complement fr 3 0.68 0.20 25066 25824 complement fr 3 0.71 0.06 25066 25800 complement fr 3 0.73 0.08 25066 25767 complement fr 3 0.74 0.78 25066 25692 complement fr 3 0.73 0.54 25066 25584 complement fr 3 0.68 0.15 25066 25551 complement fr 3 0.66 0.16 25827 26120 complement fr 2 0.58 0.33 25827 26111 complement fr 2 0.60 0.12 25827 26048 complement fr 2 0.70 0.87 25827 26045 complement fr 2 0.70 0.76 26218 26727 direct fr 1 0.84 0.77 26257 26727 direct fr 1 0.88 0.10 26362 26727 direct fr 1 0.85 0.18 26407 26727 direct fr 1 0.84 0.47 26746 26943 complement fr 3 0.60 0.24 26940 27542 complement fr 2 0.77 0.39 26940 27464 complement fr 2 0.80 0.15 26940 27413 complement fr 2 0.85 0.30 26940 27308 complement fr 2 0.85 0.14 26940 27125 complement fr 2 0.75 0.43 26940 27089 complement fr 2 0.69 0.10 28094 28309 complement fr 1 0.52 0.54 28094 28258 complement fr 1 0.58 0.29 28378 28872 direct fr 1 0.78 0.58 28435 28872 direct fr 1 0.89 0.48 28441 28872 direct fr 1 0.88 0.28 28720 28872 direct fr 1 0.69 0.04 28869 29591 complement fr 2 0.66 0.23 28869 29537 complement fr 2 0.64 0.20 28869 29519 complement fr 2 0.63 0.05 29696 30157 complement fr 1 0.72 0.24 29696 30124 complement fr 1 0.78 0.07 29696 30121 complement fr 1 0.78 0.16 29696 29932 complement fr 1 0.72 0.23 29696 29902 complement fr 1 0.69 0.23 29696 29896 complement fr 1 0.69 0.59 30135 30653 complement fr 2 0.80 0.99 30135 30626 complement fr 2 0.79 0.30 30135 30605 complement fr 2 0.78 0.00 30662 31498 complement fr 1 0.72 .... 30662 31486 complement fr 1 0.72 .... 30662 31456 complement fr 1 0.72 .... List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 47 1732 complement fr 1 1778 2398 complement fr 1 2071 3018 complement fr 3 3012 3587 complement fr 2 3585 3827 complement fr 2 3846 4235 complement fr 2 4306 4686 complement fr 3 4677 5213 complement fr 2 5211 5615 complement fr 2 5503 5727 direct fr 1 5762 6046 complement fr 1 6000 6413 complement fr 2 6500 6793 complement fr 1 6813 7595 complement fr 2 8070 8879 complement fr 2 8937 9350 direct fr 3 9440 9862 direct fr 2 9853 10311 direct fr 1 10445 10966 complement fr 1 10797 12032 direct fr 3 11678 11881 complement fr 1 11978 12730 direct fr 2 12728 13279 direct fr 2 13168 13782 complement fr 3 13243 13575 direct fr 1 13517 13774 direct fr 2 13749 14255 direct fr 3 14224 14574 direct fr 1 14502 14876 direct fr 3 14806 15402 direct fr 1 14846 15067 direct fr 2 15341 15523 complement fr 1 15405 17306 direct fr 3 17313 17555 direct fr 3 17549 17845 direct fr 2 17856 18299 direct fr 3 18151 18462 direct fr 1 18459 18905 complement fr 2 18892 19374 complement fr 3 19362 19538 complement fr 2 19986 20333 complement fr 2 20180 22093 complement fr 1 22272 22496 direct fr 3 22626 22991 direct fr 3 23125 23586 complement fr 3 23724 24236 complement fr 2 24413 25045 complement fr 1 25066 25866 complement fr 3 25827 26147 complement fr 2 26149 26727 direct fr 1 26746 26973 complement fr 3 26940 27584 complement fr 2 27627 27824 complement fr 2 27844 28050 complement fr 3 28094 28324 complement fr 1 28372 28872 direct fr 1 28692 29429 direct fr 3 28869 29738 complement fr 2 29696 30172 complement fr 1 30135 30785 complement fr 2 30662 31504 complement fr 1 -------------------- 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