GENEMARK PREDICTIONS Sequence: gi|83582730|ref|NC_007641.1| Rhodospirillum rubrum ATCC 11170 plasmid unnamed, complete sequence Sequence file: NC_007641.fna Sequence length: 53732 GC Content: 59.77% 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 -------- -------- ---------- ----- ---- ---- 248 904 direct fr 2 0.80 0.56 254 904 direct fr 2 0.82 0.61 320 904 direct fr 2 0.85 0.34 347 904 direct fr 2 0.85 0.13 500 904 direct fr 2 0.82 0.72 1305 2369 direct fr 3 0.58 0.00 1485 2369 direct fr 3 0.67 0.11 1515 2369 direct fr 3 0.66 0.00 1617 2369 direct fr 3 0.66 0.35 3063 4355 complement fr 2 0.50 0.61 3063 3815 complement fr 2 0.56 0.26 3063 3809 complement fr 2 0.56 0.41 3063 3755 complement fr 2 0.53 0.13 5259 6218 complement fr 2 0.56 0.36 5259 6137 complement fr 2 0.57 0.30 5259 6092 complement fr 2 0.55 0.20 10381 10806 direct fr 1 0.53 0.00 10420 10806 direct fr 1 0.58 0.21 10432 10806 direct fr 1 0.60 0.09 10435 10806 direct fr 1 0.60 0.02 10555 10806 direct fr 1 0.87 0.47 10570 10806 direct fr 1 0.89 0.95 10624 10806 direct fr 1 0.89 0.01 10651 10806 direct fr 1 0.87 0.01 10834 11760 direct fr 1 0.94 0.96 10921 11760 direct fr 1 0.94 0.00 10927 11760 direct fr 1 0.94 0.01 12479 13036 complement fr 1 0.72 0.88 12479 12934 complement fr 1 0.74 0.24 12479 12886 complement fr 1 0.71 0.23 12479 12715 complement fr 1 0.74 0.49 13049 13348 complement fr 1 0.75 0.57 13049 13288 complement fr 1 0.69 0.20 13049 13255 complement fr 1 0.64 0.39 13409 13705 complement fr 1 0.58 0.01 13409 13675 complement fr 1 0.65 0.06 13409 13606 complement fr 1 0.83 0.74 13859 14095 direct fr 2 0.60 0.88 13910 14095 direct fr 2 0.63 0.12 13967 14095 direct fr 2 0.50 0.10 14096 15022 complement fr 1 0.93 0.97 14096 14935 complement fr 1 0.92 0.01 14096 14929 complement fr 1 0.92 0.02 15050 15436 complement fr 1 0.58 0.11 15050 15424 complement fr 1 0.60 0.14 15050 15421 complement fr 1 0.60 0.03 15050 15301 complement fr 1 0.87 0.59 15050 15286 complement fr 1 0.88 0.97 15050 15232 complement fr 1 0.85 0.01 15288 16091 direct fr 3 0.59 0.76 15468 16091 direct fr 3 0.68 0.16 15594 16091 direct fr 3 0.69 0.72 15687 16091 direct fr 3 0.62 0.14 16441 17346 direct fr 1 0.80 0.10 16483 17346 direct fr 1 0.81 0.91 16537 17346 direct fr 1 0.81 0.01 16558 17346 direct fr 1 0.81 0.33 16591 17346 direct fr 1 0.84 0.77 17434 18111 direct fr 1 0.87 0.31 17512 18111 direct fr 1 0.89 0.17 17641 18111 direct fr 1 0.87 0.40 17734 18111 direct fr 1 0.85 0.04 18136 18918 direct fr 1 0.86 0.19 18229 18918 direct fr 1 0.93 0.28 18331 18918 direct fr 1 0.93 0.01 18334 18918 direct fr 1 0.93 0.02 18915 20465 direct fr 3 0.85 0.07 18918 20465 direct fr 3 0.85 0.05 19011 20465 direct fr 3 0.87 0.17 19110 20465 direct fr 3 0.86 0.34 19137 20465 direct fr 3 0.86 0.09 21078 21272 complement fr 2 0.63 0.32 21078 21251 complement fr 2 0.60 0.65 21078 21236 complement fr 2 0.58 0.63 21316 21792 complement fr 3 0.81 0.04 21316 21732 complement fr 3 0.85 0.92 21316 21717 complement fr 3 0.84 0.78 21316 21702 complement fr 3 0.84 0.03 21900 22385 direct fr 3 0.83 0.99 21951 22385 direct fr 3 0.84 0.00 21990 22385 direct fr 3 0.83 0.35 22095 22385 direct fr 3 0.78 0.01 22802 23734 complement fr 1 0.63 0.73 22802 23581 complement fr 1 0.60 0.03 22802 23575 complement fr 1 0.59 0.02 22802 23569 complement fr 1 0.59 0.01 23871 24092 complement fr 2 0.52 0.02 23871 24062 complement fr 2 0.58 0.56 23871 24008 complement fr 2 0.62 0.77 24461 25255 direct fr 2 0.67 0.35 24554 25255 direct fr 2 0.70 0.05 24650 25255 direct fr 2 0.68 0.71 24653 25255 direct fr 2 0.68 0.63 25803 26258 direct fr 3 0.51 0.00 25935 26258 direct fr 3 0.67 0.08 26001 26258 direct fr 3 0.68 0.42 26025 26258 direct fr 3 0.72 0.28 26058 26258 direct fr 3 0.73 0.07 26130 26258 direct fr 3 0.68 0.05 26140 27666 direct fr 1 0.78 0.10 26194 27666 direct fr 1 0.81 0.00 26248 27666 direct fr 1 0.84 0.06 26476 27666 direct fr 1 0.86 0.01 26530 27666 direct fr 1 0.87 0.67 26596 27666 direct fr 1 0.88 0.19 26644 27666 direct fr 1 0.88 0.01 27680 28666 complement fr 1 0.77 0.87 27680 28453 complement fr 1 0.76 0.15 27680 28420 complement fr 1 0.75 0.09 27680 28378 complement fr 1 0.73 0.12 28989 30377 complement fr 2 0.93 0.75 28989 30254 complement fr 2 0.94 0.52 28989 30188 complement fr 2 0.93 0.04 28989 30179 complement fr 2 0.93 0.01 30461 31993 complement fr 1 0.93 0.97 30461 31828 complement fr 1 0.95 0.25 30461 31813 complement fr 1 0.95 0.07 30461 31597 complement fr 1 0.94 0.03 32076 32378 complement fr 2 0.95 0.95 32076 32282 complement fr 2 0.94 0.58 32481 33188 complement fr 2 0.82 0.23 32481 33113 complement fr 2 0.89 0.79 32481 33020 complement fr 2 0.88 0.01 32481 32963 complement fr 2 0.86 0.01 33307 33534 direct fr 1 0.78 0.84 33531 33917 direct fr 3 0.75 0.98 33573 33917 direct fr 3 0.76 0.00 33633 33917 direct fr 3 0.74 0.82 33768 33917 direct fr 3 0.57 0.06 33946 35163 complement fr 3 0.82 0.63 33946 35031 complement fr 3 0.82 0.03 33946 35010 complement fr 3 0.82 0.00 33946 34968 complement fr 3 0.81 0.11 35373 37865 complement fr 2 0.88 0.99 35373 37805 complement fr 2 0.88 0.00 35373 37676 complement fr 2 0.88 0.01 35373 37538 complement fr 2 0.87 0.00 38320 38886 direct fr 1 0.96 0.74 38497 38886 direct fr 1 0.94 0.16 38554 38886 direct fr 1 0.94 0.11 39009 40766 direct fr 3 0.97 0.70 39096 40766 direct fr 3 0.98 0.05 39105 40766 direct fr 3 0.98 0.01 39156 40766 direct fr 3 0.98 0.49 40763 41086 complement fr 1 0.54 0.83 40763 41083 complement fr 1 0.54 0.64 40763 41008 complement fr 1 0.69 0.94 40763 40954 complement fr 1 0.82 0.05 40763 40921 complement fr 1 0.81 0.33 40763 40918 complement fr 1 0.80 0.50 40773 42251 direct fr 3 0.77 0.32 40905 42251 direct fr 3 0.83 0.34 40944 42251 direct fr 3 0.85 0.16 40965 42251 direct fr 3 0.87 0.27 41067 42251 direct fr 3 0.87 0.40 41169 42251 direct fr 3 0.87 0.29 42399 42710 direct fr 3 0.62 0.09 42477 42710 direct fr 3 0.79 0.36 42576 42710 direct fr 3 0.74 0.13 42645 42710 direct fr 3 0.63 0.77 42745 43599 direct fr 1 0.68 0.34 42871 43599 direct fr 1 0.68 0.02 42877 43599 direct fr 1 0.67 0.01 42889 43599 direct fr 1 0.67 0.01 43586 44356 direct fr 2 0.96 0.15 43703 44356 direct fr 2 0.96 0.23 43706 44356 direct fr 2 0.96 0.20 44416 46656 direct fr 1 0.84 0.02 44677 46656 direct fr 1 0.86 0.86 44743 46656 direct fr 1 0.85 0.01 46714 48117 direct fr 1 0.92 0.13 46822 48117 direct fr 1 0.94 0.00 46825 48117 direct fr 1 0.94 0.01 46858 48117 direct fr 1 0.94 0.07 46903 48117 direct fr 1 0.95 0.95 48119 49639 direct fr 2 0.82 0.45 48122 49639 direct fr 2 0.82 0.36 48155 49639 direct fr 2 0.83 0.02 48191 49639 direct fr 2 0.84 0.11 48284 49639 direct fr 2 0.85 0.09 48368 49639 direct fr 2 0.84 0.12 50066 50716 direct fr 2 0.50 0.78 50369 50716 direct fr 2 0.53 0.13 50378 50716 direct fr 2 0.51 0.35 51594 52616 complement fr 2 0.71 0.00 51594 52595 complement fr 2 0.73 0.00 51594 52592 complement fr 2 0.73 0.00 51594 52526 complement fr 2 0.78 0.79 51594 52475 complement fr 2 0.79 0.52 51594 52382 complement fr 2 0.78 0.45 51594 52280 complement fr 2 0.76 0.00 52529 53584 complement fr 1 0.84 0.22 52529 53536 complement fr 1 0.88 0.30 52529 53524 complement fr 1 0.89 0.92 52529 53494 complement fr 1 0.88 0.80 52529 53353 complement fr 1 0.90 0.31 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 239 904 direct fr 2 1009 1239 complement fr 3 1254 2369 direct fr 3 2379 3020 complement fr 2 3063 5195 complement fr 2 5259 6227 complement fr 2 6225 9968 complement fr 2 8496 9938 direct fr 3 10224 10709 complement fr 2 10303 10806 direct fr 1 10804 11760 direct fr 1 12261 12482 direct fr 3 12287 12883 direct fr 2 12479 13051 complement fr 1 13049 13411 complement fr 1 13337 13750 direct fr 2 13409 13714 complement fr 1 13712 14098 complement fr 1 13748 14095 direct fr 2 14096 15052 complement fr 1 15050 15574 complement fr 1 15147 16091 direct fr 3 16230 17372 direct fr 3 16393 17346 direct fr 1 17374 18111 direct fr 1 18109 18918 direct fr 1 18804 20465 direct fr 3 20348 20632 complement fr 1 20976 21485 direct fr 3 21078 21344 complement fr 2 21316 21858 complement fr 3 21864 22385 direct fr 3 22802 23887 complement fr 1 22943 23323 direct fr 2 23871 24209 complement fr 2 24452 25255 direct fr 2 25329 26258 direct fr 3 26101 27666 direct fr 1 27680 28678 complement fr 1 28920 29318 direct fr 3 28989 30419 complement fr 2 30461 32002 complement fr 1 32076 32471 complement fr 2 32460 33233 direct fr 3 32481 33242 complement fr 2 33247 33534 direct fr 1 33396 33917 direct fr 3 33937 34878 direct fr 1 33946 35190 complement fr 3 35358 37955 direct fr 3 35373 37898 complement fr 2 38260 38886 direct fr 1 38976 40766 direct fr 3 40764 42251 direct fr 3 40763 41116 complement fr 1 41058 41912 complement fr 2 42072 42620 complement fr 2 42390 42710 direct fr 3 42667 43410 complement fr 3 42727 43599 direct fr 1 43409 44356 direct fr 2 44332 46656 direct fr 1 44353 45408 complement fr 3 46654 48117 direct fr 1 48092 49639 direct fr 2 48260 49621 complement fr 1 49640 50716 direct fr 2 50713 51903 complement fr 3 51594 52643 complement fr 2 52493 53734 direct fr 2 52529 53590 complement fr 1 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 1 2 43440 +/- 11 bp (direct) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 19:57:07 2007