GENEMARK PREDICTIONS Sequence: gi|29377803|ref|NC_004669.1| Enterococcus faecalis V583 plasmid pTEF1, complete sequence Sequence file: NC_004669.fna Sequence length: 66320 GC Content: 34.41% 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 -------- -------- ---------- ----- ---- ---- 101 1111 direct fr 2 0.79 0.41 197 1111 direct fr 2 0.81 0.35 224 1111 direct fr 2 0.81 0.16 401 1111 direct fr 2 0.77 0.02 1140 2321 direct fr 3 0.72 0.82 1155 2321 direct fr 3 0.73 0.12 1197 2321 direct fr 3 0.74 0.43 1560 2321 direct fr 3 0.70 0.03 1602 2321 direct fr 3 0.69 0.94 2348 3979 direct fr 2 0.89 0.01 2363 3979 direct fr 2 0.90 0.01 2387 3979 direct fr 2 0.91 0.85 2483 3979 direct fr 2 0.93 0.19 2519 3979 direct fr 2 0.93 0.01 2555 3979 direct fr 2 0.93 0.02 3980 4975 complement fr 1 0.62 0.00 3980 4939 complement fr 1 0.64 0.45 3980 4777 complement fr 1 0.62 0.18 3980 4774 complement fr 1 0.61 0.06 3980 4507 complement fr 1 0.59 0.02 5439 6125 direct fr 3 0.85 0.97 5445 6125 direct fr 3 0.85 0.94 5481 6125 direct fr 3 0.90 0.02 5496 6125 direct fr 3 0.89 0.05 5595 6125 direct fr 3 0.87 0.03 6333 7070 direct fr 3 0.69 0.13 6669 7070 direct fr 3 0.72 0.44 7583 8269 complement fr 1 0.85 0.97 7583 8263 complement fr 1 0.87 0.96 7583 8227 complement fr 1 0.88 0.02 7583 8212 complement fr 1 0.88 0.03 7583 8113 complement fr 1 0.86 0.04 9848 10771 complement fr 1 0.81 0.10 9848 10735 complement fr 1 0.83 0.38 9848 10708 complement fr 1 0.83 0.41 9848 10693 complement fr 1 0.84 0.18 9848 10609 complement fr 1 0.86 0.00 9848 10585 complement fr 1 0.87 0.44 9848 10537 complement fr 1 0.89 0.41 10846 11532 complement fr 3 0.85 0.97 10846 11526 complement fr 3 0.85 0.96 10846 11490 complement fr 3 0.88 0.02 10846 11475 complement fr 3 0.88 0.03 10846 11376 complement fr 3 0.86 0.04 12099 12251 complement fr 2 0.63 0.98 12099 12233 complement fr 2 0.60 0.39 12099 12212 complement fr 2 0.53 0.04 12615 13304 complement fr 2 0.80 0.94 12615 13199 complement fr 2 0.78 0.59 12615 13178 complement fr 2 0.78 0.37 12615 13061 complement fr 2 0.81 0.83 13884 14360 complement fr 2 0.80 0.99 13884 14234 complement fr 2 0.86 0.23 13884 14090 complement fr 2 0.85 0.07 13884 13964 complement fr 2 0.61 0.00 14500 15450 complement fr 3 0.84 0.06 14500 15210 complement fr 3 0.85 0.03 14500 15138 complement fr 3 0.83 0.06 15830 16585 complement fr 1 0.87 0.22 15830 16459 complement fr 1 0.90 0.00 15830 16249 complement fr 1 0.89 0.01 15830 16171 complement fr 1 0.86 0.05 16747 17013 complement fr 3 0.77 0.99 17020 17394 complement fr 3 0.77 0.09 17020 17241 complement fr 3 0.84 0.94 17020 17202 complement fr 3 0.83 0.03 17020 17115 complement fr 3 0.70 0.00 17620 18117 complement fr 3 0.58 0.12 17620 18108 complement fr 3 0.59 0.27 18114 18899 complement fr 2 0.74 0.68 18114 18845 complement fr 2 0.77 0.10 18114 18746 complement fr 2 0.75 0.16 18114 18563 complement fr 2 0.78 0.02 18114 18377 complement fr 2 0.75 0.00 19757 21970 complement fr 1 0.85 0.73 19757 21895 complement fr 1 0.86 0.05 19757 21757 complement fr 1 0.86 0.00 19757 21700 complement fr 1 0.86 0.02 19757 21550 complement fr 1 0.93 0.13 19757 21517 complement fr 1 0.94 0.08 21957 24245 complement fr 2 0.88 0.88 21957 24119 complement fr 2 0.87 0.20 21957 24029 complement fr 2 0.87 0.50 24320 24715 complement fr 1 0.69 0.74 24320 24661 complement fr 1 0.75 0.05 24320 24655 complement fr 1 0.74 0.07 24320 24589 complement fr 1 0.69 0.12 24672 27236 complement fr 2 0.89 0.00 24672 27191 complement fr 2 0.90 0.75 24672 27164 complement fr 2 0.91 0.82 24672 27080 complement fr 2 0.91 0.06 24672 26960 complement fr 2 0.91 0.20 28273 28548 complement fr 3 0.58 0.20 28273 28533 complement fr 3 0.61 0.38 28273 28491 complement fr 3 0.70 0.20 28273 28476 complement fr 3 0.70 0.81 28538 29572 complement fr 1 0.79 0.88 28538 29512 complement fr 1 0.82 0.00 28538 29383 complement fr 1 0.85 0.00 28538 29380 complement fr 1 0.85 0.00 28538 29338 complement fr 1 0.90 0.09 28538 29299 complement fr 1 0.92 0.84 28538 29260 complement fr 1 0.92 0.06 29565 29879 complement fr 2 0.72 0.96 29565 29864 complement fr 2 0.75 0.99 29565 29762 complement fr 2 0.71 0.03 29879 30295 complement fr 1 0.59 0.12 29879 30247 complement fr 1 0.67 0.01 29879 30211 complement fr 1 0.73 0.63 29879 30187 complement fr 1 0.76 0.86 29879 30079 complement fr 1 0.65 0.22 30279 30896 complement fr 2 0.85 0.04 30279 30863 complement fr 2 0.89 0.03 30279 30644 complement fr 2 0.84 0.00 30279 30623 complement fr 2 0.83 0.13 30899 32170 complement fr 1 0.83 0.00 30899 31903 complement fr 1 0.89 0.00 30899 31840 complement fr 1 0.89 0.86 30899 31663 complement fr 1 0.88 0.01 32196 33068 complement fr 2 0.90 0.12 32196 33056 complement fr 2 0.91 0.10 32196 33053 complement fr 2 0.91 0.10 32196 32645 complement fr 2 0.87 0.01 32196 32477 complement fr 2 0.80 0.07 32196 32312 complement fr 2 0.51 0.10 33076 33954 complement fr 3 0.86 0.92 33076 33729 complement fr 3 0.87 0.10 33076 33567 complement fr 3 0.84 0.00 33076 33507 complement fr 3 0.87 0.82 33965 34225 complement fr 1 0.66 0.33 33965 34141 complement fr 1 0.69 0.04 34294 34680 complement fr 3 0.70 0.03 34294 34599 complement fr 3 0.82 0.94 34294 34470 complement fr 3 0.82 0.07 34294 34383 complement fr 3 0.75 0.06 34702 35022 complement fr 3 0.82 0.27 34702 34926 complement fr 3 0.75 0.14 34702 34920 complement fr 3 0.74 0.07 35117 39082 complement fr 1 0.98 0.02 35117 39007 complement fr 1 0.99 0.75 35117 38971 complement fr 1 0.99 0.00 35117 38947 complement fr 1 0.99 0.25 39314 39649 complement fr 1 0.75 0.79 39314 39496 complement fr 1 0.74 0.00 39314 39424 complement fr 1 0.59 0.04 40246 42966 complement fr 3 0.97 0.30 40246 42918 complement fr 3 0.98 0.57 40246 42783 complement fr 3 0.98 0.00 40246 42630 complement fr 3 0.97 0.00 42929 43234 complement fr 1 0.71 0.88 42929 43198 complement fr 1 0.75 0.68 42929 43186 complement fr 1 0.74 0.12 42929 43042 complement fr 1 0.52 0.23 43816 44172 complement fr 3 0.53 0.63 43816 44028 complement fr 3 0.51 0.06 44622 45308 complement fr 2 0.85 0.97 44622 45302 complement fr 2 0.85 0.96 44622 45266 complement fr 2 0.87 0.02 44622 45251 complement fr 2 0.87 0.03 44622 45152 complement fr 2 0.85 0.04 45922 47412 direct fr 1 0.84 0.81 45949 47412 direct fr 1 0.86 0.41 46063 47412 direct fr 1 0.88 0.69 46315 47412 direct fr 1 0.85 0.04 46384 47412 direct fr 1 0.84 0.02 47519 48691 direct fr 2 0.80 0.31 47630 48691 direct fr 2 0.81 0.13 47792 48691 direct fr 2 0.78 0.48 47828 48691 direct fr 2 0.77 0.05 48694 49140 direct fr 1 0.62 0.01 48748 49140 direct fr 1 0.71 0.98 48775 49140 direct fr 1 0.70 0.02 48907 49140 direct fr 1 0.68 0.33 48931 49140 direct fr 1 0.70 0.80 49141 50580 direct fr 1 0.83 0.14 49201 50580 direct fr 1 0.86 0.82 49372 50580 direct fr 1 0.84 0.18 49432 50580 direct fr 1 0.83 0.13 50710 51882 complement fr 3 0.80 0.32 50710 51771 complement fr 3 0.79 0.15 50710 51609 complement fr 3 0.75 0.27 50710 51573 complement fr 3 0.74 0.03 52023 52709 complement fr 2 0.85 0.97 52023 52703 complement fr 2 0.86 0.96 52023 52667 complement fr 2 0.88 0.02 52023 52652 complement fr 2 0.87 0.03 52023 52553 complement fr 2 0.85 0.04 52964 53308 direct fr 2 0.65 0.07 53042 53308 direct fr 2 0.80 0.80 53075 53308 direct fr 2 0.80 0.32 53126 53308 direct fr 2 0.75 0.13 53298 53567 direct fr 3 0.53 0.90 53319 53567 direct fr 3 0.58 0.87 53349 53567 direct fr 3 0.64 0.02 53800 55752 complement fr 3 0.70 0.82 53800 55731 complement fr 3 0.70 0.94 53800 55422 complement fr 3 0.65 0.04 53800 55350 complement fr 3 0.67 0.03 53800 55290 complement fr 3 0.68 0.48 54887 55009 direct fr 2 0.59 0.56 54914 55009 direct fr 2 0.75 0.75 54929 55009 direct fr 2 0.73 0.88 54971 55009 direct fr 2 0.56 0.00 55922 57361 direct fr 2 0.86 0.61 56150 57361 direct fr 2 0.92 0.67 56342 57361 direct fr 2 0.90 0.06 56582 57361 direct fr 2 0.89 0.02 57363 58325 direct fr 3 0.87 0.98 57483 58325 direct fr 3 0.86 0.07 57693 58325 direct fr 3 0.85 0.03 57894 58325 direct fr 3 0.79 0.78 58390 58752 complement fr 3 0.72 0.55 58390 58551 complement fr 3 0.65 0.57 58746 59018 complement fr 2 0.65 0.26 58746 59009 complement fr 2 0.68 0.11 58746 59003 complement fr 2 0.71 0.05 58746 58949 complement fr 2 0.78 0.77 58746 58946 complement fr 2 0.78 0.65 58746 58913 complement fr 2 0.74 0.02 59186 59806 direct fr 2 0.87 0.66 59234 59806 direct fr 2 0.89 0.28 59393 59806 direct fr 2 0.85 0.01 59468 59806 direct fr 2 0.83 0.71 59796 60110 direct fr 3 0.72 0.10 59823 60110 direct fr 3 0.81 0.33 59892 60110 direct fr 3 0.87 0.04 59982 60110 direct fr 3 0.85 0.46 60069 60110 direct fr 3 0.60 0.00 60610 60912 direct fr 1 0.70 0.25 60694 60912 direct fr 1 0.79 0.11 61339 62667 direct fr 1 0.82 0.93 61381 62667 direct fr 1 0.84 0.01 61417 62667 direct fr 1 0.84 0.56 61456 62667 direct fr 1 0.84 0.06 63714 64175 direct fr 3 0.67 0.36 63747 64175 direct fr 3 0.72 0.66 63765 64175 direct fr 3 0.72 0.35 63966 64175 direct fr 3 0.67 0.03 64041 64175 direct fr 3 0.65 0.15 64740 65111 complement fr 2 0.76 0.81 64740 64841 complement fr 2 0.68 0.07 65104 65964 complement fr 3 0.88 0.03 65104 65949 complement fr 3 0.89 0.65 65104 65886 complement fr 3 0.91 0.36 65104 65751 complement fr 3 0.89 0.08 65104 65748 complement fr 3 0.89 0.05 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 77 1111 direct fr 2 1122 2321 direct fr 3 1808 2215 complement fr 1 2342 3979 direct fr 2 3980 5002 complement fr 1 5418 6125 direct fr 3 6261 7070 direct fr 3 7583 8290 complement fr 1 8666 8842 complement fr 1 8682 9035 direct fr 3 9848 10879 complement fr 1 10846 11553 complement fr 3 11564 12106 complement fr 1 12099 12296 complement fr 2 12615 13334 complement fr 2 13414 13665 direct fr 1 13884 14387 complement fr 2 14500 15828 complement fr 3 15830 16597 complement fr 1 16747 17022 complement fr 3 17020 17484 complement fr 3 17526 17723 direct fr 3 17620 18126 complement fr 3 18114 18905 complement fr 2 18896 19069 complement fr 1 19757 21982 complement fr 1 21957 24317 complement fr 2 24320 24745 complement fr 1 24672 27257 complement fr 2 27269 27742 complement fr 1 27884 28357 complement fr 1 28273 28551 complement fr 3 28538 29578 complement fr 1 29565 29888 complement fr 2 29879 30298 complement fr 1 30279 30926 complement fr 2 30899 32182 complement fr 1 32196 33119 complement fr 2 33076 33978 complement fr 3 33965 34258 complement fr 1 34294 34704 complement fr 3 34702 35115 complement fr 3 35117 39136 complement fr 1 39314 39691 complement fr 1 40246 43002 complement fr 3 42929 43249 complement fr 1 43816 44175 complement fr 3 44622 45329 complement fr 2 45357 45527 direct fr 3 45919 47412 direct fr 1 47486 48691 direct fr 2 48685 49140 direct fr 1 49138 50580 direct fr 1 50710 51915 complement fr 3 52023 52730 complement fr 2 52958 53308 direct fr 2 53295 53567 direct fr 3 53800 55782 complement fr 3 54419 54691 direct fr 2 54794 55009 direct fr 2 55253 55516 direct fr 2 55916 57361 direct fr 2 57315 58325 direct fr 3 58390 58758 complement fr 3 58746 59024 complement fr 2 59099 59806 direct fr 2 59694 60110 direct fr 3 60098 60328 direct fr 2 60347 60598 direct fr 2 60586 60912 direct fr 1 61059 61244 complement fr 2 61309 62667 direct fr 1 62556 63014 direct fr 3 63089 63229 direct fr 2 63693 64175 direct fr 3 64740 65141 complement fr 2 65104 65982 complement fr 3 -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 16:03:07 2007