GENEMARK PREDICTIONS Sequence: gi|170745005|ref|NC_010509.1| Methylobacterium radiotolerans JCM 2831 plasmid pMRAD02, complete sequence Sequence file: NC_010509.fna Sequence length: 47003 GC Content: 62.48% Window length: 96 Window step: 12 Threshold value: 0.500 --- Matrix: Heuristic, GC = 62 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 -------- -------- ---------- ----- ---- ---- 118 2274 direct fr 1 0.72 0.00 151 2274 direct fr 1 0.74 0.00 229 2274 direct fr 1 0.77 0.69 310 2274 direct fr 1 0.78 0.91 346 2274 direct fr 1 0.77 0.16 352 2274 direct fr 1 0.77 0.05 147 269 direct fr 3 0.55 0.12 2339 3625 direct fr 2 0.72 0.74 2366 3625 direct fr 2 0.74 0.00 2414 3625 direct fr 2 0.75 0.02 2558 3625 direct fr 2 0.78 0.25 2657 3625 direct fr 2 0.79 0.15 3691 4206 direct fr 1 0.68 0.35 3781 4206 direct fr 1 0.79 0.61 3829 4206 direct fr 1 0.80 0.16 3850 4206 direct fr 1 0.80 0.06 3961 4206 direct fr 1 0.75 0.38 5429 5782 complement fr 1 0.65 0.94 5429 5692 complement fr 1 0.68 0.60 5429 5686 complement fr 1 0.67 0.22 5429 5617 complement fr 1 0.57 0.71 6058 7527 complement fr 3 0.63 0.00 6058 7314 complement fr 3 0.73 0.06 6058 7269 complement fr 3 0.75 0.04 6058 7221 complement fr 3 0.75 0.94 6058 7167 complement fr 3 0.74 0.02 6058 7113 complement fr 3 0.73 0.30 7376 8350 complement fr 1 0.72 0.20 7376 8269 complement fr 1 0.72 0.14 7376 8260 complement fr 1 0.72 0.19 7376 8176 complement fr 1 0.69 0.16 8340 8885 complement fr 2 0.51 0.01 8340 8774 complement fr 2 0.63 0.32 8340 8741 complement fr 2 0.66 0.47 8340 8687 complement fr 2 0.63 0.22 8340 8678 complement fr 2 0.63 0.24 8926 9555 direct fr 1 0.67 0.72 9019 9555 direct fr 1 0.71 0.29 9094 9555 direct fr 1 0.66 0.21 9103 9555 direct fr 1 0.66 0.10 9605 9988 complement fr 1 0.50 0.40 10192 10524 complement fr 3 0.50 0.15 10192 10479 complement fr 3 0.55 0.59 10192 10470 complement fr 3 0.55 0.28 10192 10464 complement fr 3 0.56 0.23 10192 10332 complement fr 3 0.51 0.45 10566 10943 complement fr 2 0.58 0.33 10566 10892 complement fr 2 0.52 0.06 10566 10886 complement fr 2 0.52 0.00 11938 12252 complement fr 3 0.67 0.90 11938 12240 complement fr 3 0.70 0.71 11938 12180 complement fr 3 0.73 0.20 11938 12117 complement fr 3 0.65 0.09 11938 12096 complement fr 3 0.61 0.21 12262 12582 complement fr 3 0.52 0.45 12626 12853 complement fr 1 0.62 0.92 12626 12760 complement fr 1 0.55 0.67 12626 12754 complement fr 1 0.51 0.25 13233 13424 complement fr 2 0.67 0.71 13233 13379 complement fr 2 0.59 0.25 13233 13355 complement fr 2 0.52 0.06 13454 13750 complement fr 1 0.53 0.08 13454 13624 complement fr 1 0.57 0.36 13832 14098 complement fr 1 0.73 0.69 13832 14044 complement fr 1 0.68 0.13 13832 14035 complement fr 1 0.66 0.03 14168 14479 complement fr 1 0.69 0.84 14168 14473 complement fr 1 0.69 0.39 14168 14413 complement fr 1 0.68 0.57 14168 14311 complement fr 1 0.57 0.10 14168 14296 complement fr 1 0.54 0.17 14506 14688 complement fr 3 0.65 0.82 14506 14643 complement fr 3 0.61 0.24 14830 15636 complement fr 3 0.53 0.00 14830 15624 complement fr 3 0.54 0.00 14830 15393 complement fr 3 0.73 0.59 14830 15129 complement fr 3 0.61 0.58 14830 15117 complement fr 3 0.60 0.66 15444 15917 complement fr 2 0.61 0.00 15444 15848 complement fr 2 0.71 0.87 15444 15842 complement fr 2 0.71 0.89 15444 15821 complement fr 2 0.72 0.54 15444 15776 complement fr 2 0.69 0.08 15444 15731 complement fr 2 0.64 0.30 15845 16315 complement fr 1 0.54 0.08 15845 16297 complement fr 1 0.55 0.02 15845 16258 complement fr 1 0.59 0.39 15845 16186 complement fr 1 0.63 0.92 15845 16150 complement fr 1 0.59 0.25 15845 16138 complement fr 1 0.58 0.07 16601 16696 direct fr 2 0.51 0.92 17980 18345 direct fr 1 0.58 0.37 18076 18345 direct fr 1 0.59 0.52 18175 18345 direct fr 1 0.60 0.94 18370 19188 direct fr 1 0.63 0.36 18400 19188 direct fr 1 0.66 0.97 18415 19188 direct fr 1 0.67 0.65 18460 19188 direct fr 1 0.65 0.08 18472 19188 direct fr 1 0.65 0.16 19214 21580 direct fr 2 0.76 0.80 19223 21580 direct fr 2 0.76 0.54 19226 21580 direct fr 2 0.76 0.27 19229 21580 direct fr 2 0.76 0.29 19286 21580 direct fr 2 0.77 0.04 19388 21580 direct fr 2 0.79 0.13 19424 21580 direct fr 2 0.80 0.63 19556 21580 direct fr 2 0.80 0.67 19622 21580 direct fr 2 0.80 0.22 19631 21580 direct fr 2 0.80 0.03 21750 22064 direct fr 3 0.72 0.20 21810 22064 direct fr 3 0.71 0.26 21921 22064 direct fr 3 0.69 0.50 21942 22064 direct fr 3 0.64 0.68 22077 22418 direct fr 3 0.59 0.08 22161 22418 direct fr 3 0.76 0.75 22167 22418 direct fr 3 0.76 0.63 22179 22418 direct fr 3 0.75 0.72 22415 24913 direct fr 2 0.88 0.77 22424 24913 direct fr 2 0.88 0.74 22520 24913 direct fr 2 0.88 0.65 22541 24913 direct fr 2 0.88 0.12 24926 25636 direct fr 2 0.87 0.76 25043 25636 direct fr 2 0.91 0.08 25073 25636 direct fr 2 0.90 0.02 25094 25636 direct fr 2 0.90 0.04 25686 25961 direct fr 3 0.61 0.89 25758 25961 direct fr 3 0.65 0.33 25806 25961 direct fr 3 0.57 0.08 25962 27059 direct fr 3 0.83 0.99 25968 27059 direct fr 3 0.83 0.98 25971 27059 direct fr 3 0.84 0.96 26097 27059 direct fr 3 0.86 0.25 26100 27059 direct fr 3 0.86 0.14 26106 27059 direct fr 3 0.86 0.24 27194 28114 direct fr 2 0.74 0.02 27233 28114 direct fr 2 0.77 0.01 27353 28114 direct fr 2 0.88 0.44 27359 28114 direct fr 2 0.88 0.19 27386 28114 direct fr 2 0.90 0.37 27398 28114 direct fr 2 0.90 0.64 27464 28114 direct fr 2 0.90 0.06 28111 28989 direct fr 1 0.74 0.65 28135 28989 direct fr 1 0.75 0.18 28168 28989 direct fr 1 0.75 0.13 28234 28989 direct fr 1 0.73 0.06 28986 30131 direct fr 3 0.66 0.55 28989 30131 direct fr 3 0.66 0.41 29043 30131 direct fr 3 0.69 0.65 29052 30131 direct fr 3 0.69 0.71 29079 30131 direct fr 3 0.70 0.83 29109 30131 direct fr 3 0.69 0.18 29118 30131 direct fr 3 0.69 0.09 30115 31188 direct fr 1 0.71 0.12 30148 31188 direct fr 1 0.73 0.18 30172 31188 direct fr 1 0.74 0.29 30184 31188 direct fr 1 0.75 0.50 30205 31188 direct fr 1 0.76 0.43 30412 31188 direct fr 1 0.77 0.35 30421 31188 direct fr 1 0.77 0.11 31391 34084 direct fr 2 0.83 0.84 31430 34084 direct fr 2 0.84 0.09 31478 34084 direct fr 2 0.84 0.59 31571 34084 direct fr 2 0.84 0.46 34177 34803 direct fr 1 0.78 0.13 34495 34803 direct fr 1 0.83 0.58 34582 34803 direct fr 1 0.78 0.20 34654 34803 direct fr 1 0.69 0.01 34816 36495 direct fr 1 0.75 0.50 34861 36495 direct fr 1 0.77 0.58 34876 36495 direct fr 1 0.77 0.72 34879 36495 direct fr 1 0.77 0.57 37354 37887 direct fr 1 0.51 0.01 37483 37887 direct fr 1 0.63 0.22 37486 37887 direct fr 1 0.63 0.08 37489 37887 direct fr 1 0.62 0.06 37884 38519 direct fr 3 0.65 0.33 37917 38519 direct fr 3 0.69 0.09 38175 38519 direct fr 3 0.72 0.30 38187 38519 direct fr 3 0.71 0.08 38244 38519 direct fr 3 0.67 0.17 38570 39673 complement fr 1 0.67 0.91 38570 39490 complement fr 1 0.70 0.83 38570 39481 complement fr 1 0.70 0.45 38570 39478 complement fr 1 0.70 0.47 39670 40152 complement fr 3 0.71 0.10 39670 39939 complement fr 3 0.66 0.31 39670 39774 complement fr 3 0.50 0.32 40669 41868 complement fr 3 0.53 0.00 40669 41805 complement fr 3 0.56 0.67 40669 41763 complement fr 3 0.58 0.15 40669 41679 complement fr 3 0.55 0.29 40669 41580 complement fr 3 0.51 0.31 40669 41574 complement fr 3 0.51 0.09 41798 42658 complement fr 1 0.85 0.24 41798 42391 complement fr 1 0.88 0.65 41798 42181 complement fr 1 0.83 0.10 42655 43050 complement fr 3 0.62 0.39 42655 43005 complement fr 3 0.70 0.01 42655 42939 complement fr 3 0.76 0.52 42655 42885 complement fr 3 0.70 0.25 42655 42879 complement fr 3 0.70 0.33 43054 43455 complement fr 3 0.58 0.10 43054 43419 complement fr 3 0.62 0.25 43054 43407 complement fr 3 0.62 0.15 43054 43221 complement fr 3 0.64 0.53 43054 43200 complement fr 3 0.59 0.12 44157 44384 complement fr 2 0.61 0.94 44395 44709 complement fr 3 0.78 0.93 44395 44706 complement fr 3 0.78 0.89 44395 44703 complement fr 3 0.78 0.84 44703 45110 complement fr 2 0.50 0.32 45112 45303 complement fr 3 0.68 0.94 45112 45267 complement fr 3 0.62 0.05 45112 45231 complement fr 3 0.52 0.25 45388 46377 complement fr 3 0.71 0.08 45388 46359 complement fr 3 0.72 0.02 45388 46320 complement fr 3 0.75 0.39 45388 46248 complement fr 3 0.80 0.67 45388 46197 complement fr 3 0.80 0.03 45388 46092 complement fr 3 0.83 0.26 46663 46758 direct fr 1 0.51 0.92 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 19 2274 direct fr 1 39 269 direct fr 3 166 2355 complement fr 3 2306 3625 direct fr 2 3643 4206 direct fr 1 4189 4521 complement fr 3 4912 5130 complement fr 3 5100 5450 complement fr 2 5429 5794 complement fr 1 6058 7548 complement fr 3 7376 8440 complement fr 1 7397 7969 direct fr 2 8298 8849 direct fr 3 8340 8912 complement fr 2 8911 9555 direct fr 1 9605 10408 complement fr 1 10192 10590 complement fr 3 10515 11060 direct fr 3 10566 11279 complement fr 2 11215 11649 complement fr 3 11473 12597 direct fr 1 11647 11913 complement fr 3 11938 12264 complement fr 3 12262 12669 complement fr 3 12626 12883 complement fr 1 12839 13261 direct fr 2 12881 13207 complement fr 1 13233 13469 complement fr 2 13454 13834 complement fr 1 13526 14716 direct fr 2 13832 14170 complement fr 1 14168 14620 complement fr 1 14506 14832 complement fr 3 14740 15207 direct fr 1 14830 15642 complement fr 3 15444 16154 complement fr 2 15830 16333 direct fr 2 15845 16456 complement fr 1 16331 16696 direct fr 2 16544 17275 complement fr 1 16980 17363 direct fr 3 17842 18345 direct fr 1 18352 19188 direct fr 1 19193 20722 complement fr 1 19208 21580 direct fr 2 21439 21726 complement fr 3 21687 22064 direct fr 3 21956 22120 complement fr 1 22062 22418 direct fr 3 22364 24913 direct fr 2 24721 25032 complement fr 3 24911 25636 direct fr 2 25629 27266 complement fr 2 25662 25961 direct fr 3 25959 27059 direct fr 3 27179 28114 direct fr 2 28045 28989 direct fr 1 28726 29097 complement fr 3 28977 30131 direct fr 3 29063 29722 complement fr 1 30082 31188 direct fr 1 30541 31203 complement fr 3 31038 31376 complement fr 2 31253 34084 direct fr 2 31307 32119 complement fr 1 32245 32688 complement fr 3 34098 34334 complement fr 2 34141 34803 direct fr 1 34801 36495 direct fr 1 35095 35739 complement fr 3 36519 37028 complement fr 2 36654 37139 direct fr 3 37026 37256 complement fr 2 37147 37887 direct fr 1 37854 38519 direct fr 3 38570 39922 complement fr 1 39041 39814 direct fr 2 39670 40374 complement fr 3 40651 41331 direct fr 1 40669 41946 complement fr 3 40884 41156 complement fr 2 41798 42778 complement fr 1 42655 43056 complement fr 3 43054 43623 complement fr 3 44157 44576 complement fr 2 44395 44859 complement fr 3 44697 44978 direct fr 3 44703 45185 complement fr 2 45112 45390 complement fr 3 45388 46518 complement fr 3 46393 46758 direct fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 2 41100 +/- 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