GENEMARK PREDICTIONS Sequence: gi|148244055|ref|NC_009470.1| Acidiphilium cryptum JF-5 plasmid pACRY04, complete sequence Sequence file: NC_009470.fna Sequence length: 37415 GC Content: 59.62% 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 -------- -------- ---------- ----- ---- ---- 838 1398 complement fr 3 0.66 0.62 838 1383 complement fr 3 0.67 0.73 838 1341 complement fr 3 0.66 0.15 838 1326 complement fr 3 0.66 0.29 2519 2698 complement fr 1 0.53 0.06 2934 3410 complement fr 2 0.52 0.70 2934 3404 complement fr 2 0.53 0.61 2934 3248 complement fr 2 0.52 0.18 4269 4682 complement fr 2 0.59 0.96 4269 4664 complement fr 2 0.60 0.68 4269 4412 complement fr 2 0.55 0.29 4269 4397 complement fr 2 0.53 0.67 4667 6574 complement fr 1 0.76 0.30 4667 6505 complement fr 1 0.77 0.54 4667 6445 complement fr 1 0.77 0.61 4667 6421 complement fr 1 0.77 0.18 4667 6415 complement fr 1 0.77 0.05 6185 6295 direct fr 2 0.50 0.73 7113 7466 direct fr 3 0.51 0.23 7483 9297 direct fr 1 0.69 0.06 7525 9297 direct fr 1 0.70 0.90 7531 9297 direct fr 1 0.70 0.92 7543 9297 direct fr 1 0.69 0.90 9281 9850 direct fr 2 0.57 0.63 9287 9850 direct fr 2 0.57 0.74 9536 9850 direct fr 2 0.57 0.43 9593 9850 direct fr 2 0.60 0.41 9635 9850 direct fr 2 0.54 0.05 10734 11108 complement fr 2 0.54 0.39 10734 11048 complement fr 2 0.54 0.09 10734 11009 complement fr 2 0.54 0.50 10734 10976 complement fr 2 0.55 0.18 11540 12913 direct fr 2 0.79 0.45 11717 12913 direct fr 2 0.88 0.84 11801 12913 direct fr 2 0.88 0.05 11840 12913 direct fr 2 0.88 0.07 11885 12913 direct fr 2 0.88 0.75 12941 13237 direct fr 2 0.58 0.27 13007 13237 direct fr 2 0.66 0.56 13115 13237 direct fr 2 0.69 0.21 13157 13237 direct fr 2 0.56 0.62 13258 13974 direct fr 1 0.65 0.09 13327 13974 direct fr 1 0.70 0.17 13468 13974 direct fr 1 0.79 0.55 13672 13974 direct fr 1 0.76 0.41 13997 14206 complement fr 1 0.64 0.83 14102 16660 direct fr 2 0.67 0.15 14252 16660 direct fr 2 0.69 0.44 14324 16660 direct fr 2 0.69 0.90 14396 16660 direct fr 2 0.69 0.23 16679 19669 complement fr 1 0.55 0.45 16679 19558 complement fr 1 0.56 0.03 16679 19510 complement fr 1 0.57 0.08 16679 19384 complement fr 1 0.59 0.01 16679 19312 complement fr 1 0.60 0.74 16679 19237 complement fr 1 0.60 0.04 16679 19003 complement fr 1 0.60 0.82 16934 17641 direct fr 2 0.53 0.40 16979 17641 direct fr 2 0.53 0.17 17228 17641 direct fr 2 0.50 0.41 17384 17641 direct fr 2 0.69 0.50 17411 17641 direct fr 2 0.67 0.28 19361 19693 direct fr 2 0.50 0.71 19769 21016 complement fr 1 0.75 0.63 19769 20977 complement fr 1 0.76 0.64 19769 20908 complement fr 1 0.75 0.66 19769 20893 complement fr 1 0.75 0.55 21120 21713 complement fr 2 0.58 0.79 21120 21698 complement fr 2 0.58 0.27 21120 21668 complement fr 2 0.57 0.03 21120 21527 complement fr 2 0.67 0.26 22119 22343 direct fr 3 0.50 0.37 22433 22942 direct fr 2 0.66 0.97 22457 22942 direct fr 2 0.66 0.52 22556 22942 direct fr 2 0.58 0.67 25913 26179 complement fr 1 0.56 0.54 25913 26176 complement fr 1 0.56 0.26 25913 26107 complement fr 1 0.60 0.06 25913 26086 complement fr 1 0.55 0.35 26368 26568 complement fr 3 0.53 0.83 26565 27185 complement fr 2 0.68 0.13 26565 27131 complement fr 2 0.72 0.21 26565 26837 complement fr 2 0.77 0.71 26565 26813 complement fr 2 0.75 0.25 27154 28509 complement fr 3 0.63 0.41 27154 28428 complement fr 3 0.64 0.69 27154 28308 complement fr 3 0.62 0.19 27154 28305 complement fr 3 0.62 0.27 30195 30350 direct fr 3 0.51 0.45 30231 30350 direct fr 3 0.66 0.81 30665 30916 complement fr 1 0.50 0.43 31098 32363 complement fr 2 0.57 0.71 31098 32336 complement fr 2 0.58 0.90 31098 32318 complement fr 2 0.59 0.19 31098 32309 complement fr 2 0.58 0.46 31098 31982 complement fr 2 0.54 0.22 31098 31946 complement fr 2 0.55 0.03 31098 31859 complement fr 2 0.57 0.85 32780 34243 complement fr 1 0.55 0.05 32780 34207 complement fr 1 0.56 0.03 32780 34123 complement fr 1 0.59 0.01 32780 34048 complement fr 1 0.61 0.54 32780 34042 complement fr 1 0.60 0.59 32780 33997 complement fr 1 0.59 0.11 35674 36117 complement fr 3 0.52 0.71 35674 36075 complement fr 3 0.50 0.01 35674 36021 complement fr 3 0.51 0.00 35674 35949 complement fr 3 0.62 0.48 35674 35940 complement fr 3 0.62 0.64 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 838 1434 complement fr 3 2315 2488 complement fr 1 2387 2728 direct fr 2 2519 2797 complement fr 1 2934 3599 complement fr 2 3810 4247 complement fr 2 3900 4094 direct fr 3 4269 4781 complement fr 2 4466 5725 direct fr 2 4667 6691 complement fr 1 5954 6295 direct fr 2 6571 6885 complement fr 3 6601 6939 direct fr 1 6990 7205 complement fr 2 7041 7466 direct fr 3 7441 9297 direct fr 1 7783 8262 complement fr 3 9260 9940 complement fr 1 9275 9850 direct fr 2 10059 10709 complement fr 2 10068 10706 direct fr 3 10725 11054 direct fr 3 10734 11291 complement fr 2 11468 12913 direct fr 2 11567 12478 complement fr 1 12815 13297 complement fr 1 12911 13237 direct fr 2 13255 13974 direct fr 1 13267 13830 complement fr 3 13803 14120 complement fr 2 13997 14413 complement fr 1 14024 16660 direct fr 2 15458 16021 complement fr 1 16679 19720 complement fr 1 16853 17641 direct fr 2 17639 18376 direct fr 2 18303 18464 direct fr 3 18374 19204 direct fr 2 19202 19693 direct fr 2 19769 21085 complement fr 1 20117 20962 direct fr 2 21120 21764 complement fr 2 21150 22343 direct fr 3 22373 22942 direct fr 2 22873 23115 complement fr 3 23055 23243 complement fr 2 23119 23403 complement fr 3 23183 24100 direct fr 2 23401 23616 complement fr 3 23844 24302 direct fr 3 24107 25762 direct fr 2 24704 25261 complement fr 1 25461 25724 direct fr 3 25913 26185 complement fr 1 26210 26419 complement fr 1 26368 26652 complement fr 3 26565 27224 complement fr 2 26697 27284 direct fr 3 27154 28641 complement fr 3 27670 28056 direct fr 1 29068 29994 direct fr 1 29710 30042 complement fr 3 29832 30350 direct fr 3 30419 31087 direct fr 2 30665 30964 complement fr 1 31098 32375 complement fr 2 31527 32021 direct fr 3 32215 32940 direct fr 1 32323 32853 complement fr 3 32672 32926 direct fr 2 32780 34279 complement fr 1 33062 33379 direct fr 2 33377 34066 direct fr 2 34156 35343 direct fr 1 34231 34848 complement fr 3 35674 36147 complement fr 3 36449 37156 direct fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 2 23220 +/- 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