GENEMARK PREDICTIONS Sequence: gi|28373131|ref|NC_004565.1| Clostridium tetani E88 plasmid pE88, complete sequence Sequence file: NC_004565.fna Sequence length: 74082 GC Content: 24.53% 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 -------- -------- ---------- ----- ---- ---- 510 1826 direct fr 3 0.93 0.22 558 1826 direct fr 3 0.93 0.03 864 1826 direct fr 3 0.91 0.05 1944 2228 direct fr 3 0.77 0.79 1959 2228 direct fr 3 0.83 0.60 1986 2228 direct fr 3 0.82 0.43 2013 2228 direct fr 3 0.80 0.16 2876 3286 complement fr 1 0.82 0.81 2876 3169 complement fr 1 0.81 0.07 2876 3139 complement fr 1 0.78 0.25 3428 3646 complement fr 1 0.62 0.60 3671 3886 complement fr 1 0.68 0.99 3671 3826 complement fr 1 0.69 0.02 4065 4406 complement fr 2 0.80 0.38 4065 4238 complement fr 2 0.69 0.04 4870 5223 direct fr 1 0.70 0.87 4930 5223 direct fr 1 0.82 0.10 5274 5738 direct fr 3 0.73 0.03 5316 5738 direct fr 3 0.76 0.07 5415 5738 direct fr 3 0.88 0.52 5454 5738 direct fr 3 0.87 0.02 5771 5950 direct fr 2 0.51 0.23 5780 5950 direct fr 2 0.54 0.14 6534 6860 direct fr 3 0.55 0.26 6618 6860 direct fr 3 0.67 0.74 6663 6860 direct fr 3 0.68 0.03 7873 8292 direct fr 1 0.83 0.89 7948 8292 direct fr 1 0.83 0.60 8251 8292 direct fr 1 0.61 0.00 8469 9008 complement fr 2 0.86 0.61 8469 8696 complement fr 2 0.74 0.02 9010 9507 complement fr 3 0.82 0.01 9010 9438 complement fr 3 0.80 0.76 9010 9246 complement fr 3 0.67 0.01 9833 10255 complement fr 1 0.78 0.04 9833 10138 complement fr 1 0.82 0.07 10398 10553 complement fr 2 0.51 0.80 10828 11817 direct fr 1 0.95 0.99 10855 11817 direct fr 1 0.96 0.05 11377 11817 direct fr 1 0.91 0.02 11545 11817 direct fr 1 0.85 0.01 11832 12173 direct fr 3 0.75 0.91 12024 12173 direct fr 3 0.82 0.02 12293 12478 complement fr 1 0.93 0.38 12293 12442 complement fr 1 0.91 0.11 12873 13541 direct fr 3 0.86 0.81 12879 13541 direct fr 3 0.88 0.83 12987 13541 direct fr 3 0.92 0.28 13029 13541 direct fr 3 0.91 0.03 13203 13541 direct fr 3 0.87 0.29 13558 16011 direct fr 1 0.81 0.53 13588 16011 direct fr 1 0.82 0.08 13822 16011 direct fr 1 0.81 0.11 13840 16011 direct fr 1 0.81 0.09 15798 15929 complement fr 2 0.54 0.18 16369 17493 complement fr 3 0.89 0.00 16369 17490 complement fr 3 0.89 0.00 16369 17424 complement fr 3 0.94 0.29 16369 17391 complement fr 3 0.94 0.27 16369 17316 complement fr 3 0.94 0.30 17429 17836 complement fr 1 0.73 0.21 17429 17671 complement fr 1 0.80 0.18 17429 17662 complement fr 1 0.79 0.06 17429 17644 complement fr 1 0.78 0.16 18829 19047 direct fr 1 0.70 0.05 18847 19047 direct fr 1 0.68 0.01 18859 19047 direct fr 1 0.66 0.08 19636 19860 complement fr 3 0.55 0.61 19636 19851 complement fr 3 0.55 0.45 19636 19788 complement fr 3 0.61 0.45 20220 21941 direct fr 3 0.81 0.22 20256 21941 direct fr 3 0.83 0.72 20376 21941 direct fr 3 0.84 0.58 20448 21941 direct fr 3 0.84 0.30 20469 21941 direct fr 3 0.85 0.70 20502 21941 direct fr 3 0.86 0.34 20541 21941 direct fr 3 0.86 0.44 21961 23022 complement fr 3 0.89 0.08 21961 22989 complement fr 3 0.91 0.19 21961 22881 complement fr 3 0.91 0.10 21961 22866 complement fr 3 0.91 0.20 23357 23458 direct fr 2 0.68 0.07 23390 23458 direct fr 2 0.53 0.22 23519 23737 complement fr 1 0.60 0.44 23519 23734 complement fr 1 0.64 0.43 23809 24495 direct fr 1 0.90 0.86 23953 24495 direct fr 1 0.90 0.09 23959 24495 direct fr 1 0.90 0.12 24061 24495 direct fr 1 0.89 0.58 24499 25473 direct fr 1 0.83 0.36 24529 25473 direct fr 1 0.86 0.26 24604 25473 direct fr 1 0.88 0.00 24640 25473 direct fr 1 0.90 0.12 24712 25473 direct fr 1 0.92 0.25 24721 25473 direct fr 1 0.92 0.05 25671 26078 direct fr 3 0.83 0.15 25920 26078 direct fr 3 0.85 0.01 25935 26078 direct fr 3 0.82 0.10 26108 26866 direct fr 2 0.86 0.90 26219 26866 direct fr 2 0.92 0.01 26462 26866 direct fr 2 0.88 0.71 26651 26866 direct fr 2 0.82 0.01 26844 28781 direct fr 3 0.68 0.90 26853 28781 direct fr 3 0.68 0.90 26967 28781 direct fr 3 0.71 0.72 27015 28781 direct fr 3 0.71 0.05 27021 28781 direct fr 3 0.71 0.08 27024 28781 direct fr 3 0.71 0.07 29536 30111 direct fr 1 0.88 0.80 29542 30111 direct fr 1 0.88 0.93 29575 30111 direct fr 1 0.91 0.51 29650 30111 direct fr 1 0.90 0.02 29758 30111 direct fr 1 0.87 0.11 30338 31174 direct fr 2 0.86 0.86 30401 31174 direct fr 2 0.89 0.36 30635 31174 direct fr 2 0.86 0.36 30794 31174 direct fr 2 0.81 0.03 31328 31504 direct fr 2 0.68 0.92 31346 31504 direct fr 2 0.64 0.05 31355 31504 direct fr 2 0.64 0.20 31639 31890 direct fr 1 0.84 0.21 32157 32252 direct fr 3 0.53 0.26 32303 32668 direct fr 2 0.84 0.46 33162 35102 complement fr 2 0.66 0.01 33162 35063 complement fr 2 0.67 0.04 33162 34943 complement fr 2 0.70 0.03 33162 34586 complement fr 2 0.76 0.00 33162 34475 complement fr 2 0.78 0.01 33162 34181 complement fr 2 0.83 0.29 33162 33995 complement fr 2 0.82 0.13 35102 35482 complement fr 1 0.62 0.25 35102 35428 complement fr 1 0.69 0.04 35102 35323 complement fr 1 0.60 0.32 35102 35308 complement fr 1 0.58 0.17 35521 36054 complement fr 3 0.80 0.31 35521 36036 complement fr 3 0.79 0.03 35521 36027 complement fr 3 0.79 0.16 36699 37001 direct fr 3 0.77 0.97 36708 37001 direct fr 3 0.77 0.98 37332 37562 complement fr 2 0.65 0.11 37332 37532 complement fr 2 0.76 0.47 37559 37705 complement fr 1 0.68 0.67 37559 37690 complement fr 1 0.62 0.11 37990 38466 complement fr 3 0.81 0.29 37990 38367 complement fr 3 0.85 0.35 38919 39119 complement fr 2 0.51 0.11 39438 42413 complement fr 2 0.95 0.34 39438 42392 complement fr 2 0.96 0.46 39438 42365 complement fr 2 0.96 0.58 39438 41936 complement fr 2 0.96 0.25 39438 41732 complement fr 2 0.96 0.22 42761 43603 direct fr 2 0.69 0.92 42788 43603 direct fr 2 0.71 0.60 42881 43603 direct fr 2 0.70 0.25 42887 43603 direct fr 2 0.70 0.53 42956 43603 direct fr 2 0.68 0.16 43698 44405 direct fr 3 0.54 0.59 44443 45192 direct fr 1 0.51 0.11 45324 45830 direct fr 3 0.93 0.35 45339 45830 direct fr 3 0.92 0.13 45525 45830 direct fr 3 0.88 0.06 46073 46369 complement fr 1 0.84 0.28 46073 46309 complement fr 1 0.81 0.04 46073 46276 complement fr 1 0.77 0.33 46386 46895 complement fr 2 0.55 0.06 46386 46790 complement fr 2 0.62 0.81 47307 48431 complement fr 2 0.87 0.00 47307 48428 complement fr 2 0.87 0.00 47307 48362 complement fr 2 0.91 0.29 47307 48329 complement fr 2 0.92 0.12 47307 48254 complement fr 2 0.92 0.31 48367 48801 complement fr 3 0.68 0.15 48367 48609 complement fr 3 0.77 0.18 48367 48600 complement fr 3 0.76 0.06 48367 48582 complement fr 3 0.75 0.16 48826 49356 complement fr 3 0.50 0.09 48826 49347 complement fr 3 0.50 0.31 48826 49173 complement fr 3 0.54 0.03 49310 50122 complement fr 1 0.54 0.40 49310 50113 complement fr 1 0.54 0.50 49310 49945 complement fr 1 0.59 0.06 49310 49918 complement fr 1 0.57 0.61 49310 49702 complement fr 1 0.57 0.24 50975 51895 direct fr 2 0.92 0.99 51005 51895 direct fr 2 0.95 0.03 51017 51895 direct fr 2 0.95 0.02 51041 51895 direct fr 2 0.95 0.01 52413 53732 direct fr 3 0.94 0.22 52461 53732 direct fr 3 0.94 0.03 52767 53732 direct fr 3 0.92 0.04 54773 55213 complement fr 1 0.79 0.34 54773 54904 complement fr 1 0.76 0.12 54773 54844 complement fr 1 0.59 0.00 56391 56750 direct fr 3 0.76 0.92 56701 57186 direct fr 1 0.81 0.12 56734 57186 direct fr 1 0.85 0.02 56761 57186 direct fr 1 0.87 0.13 56878 57186 direct fr 1 0.85 0.00 56965 57186 direct fr 1 0.79 0.08 58025 58633 complement fr 1 0.84 0.91 58025 58588 complement fr 1 0.88 0.01 58025 58462 complement fr 1 0.85 0.07 58025 58333 complement fr 1 0.80 0.06 58890 59366 direct fr 3 0.57 0.85 58962 59366 direct fr 3 0.59 0.36 59088 59366 direct fr 3 0.59 0.06 59451 60056 complement fr 2 0.89 0.02 59451 59738 complement fr 2 0.80 0.26 59451 59681 complement fr 2 0.75 0.05 60161 61354 complement fr 1 0.73 0.70 60161 61339 complement fr 1 0.73 0.27 60161 61177 complement fr 1 0.77 0.41 60161 61093 complement fr 1 0.76 0.03 60161 60991 complement fr 1 0.73 0.05 61356 62486 complement fr 2 0.82 0.26 61356 62360 complement fr 2 0.86 0.39 61356 62285 complement fr 2 0.85 0.01 61356 61910 complement fr 2 0.79 0.28 62491 62670 complement fr 3 0.65 0.18 62882 63565 complement fr 1 0.83 0.78 62882 63295 complement fr 1 0.80 0.02 62882 63292 complement fr 1 0.80 0.04 62882 63283 complement fr 1 0.80 0.04 63985 65337 direct fr 1 0.96 0.05 64009 65337 direct fr 1 0.96 0.04 64303 65337 direct fr 1 0.95 0.03 66192 66410 complement fr 2 0.71 0.96 66192 66392 complement fr 2 0.79 0.98 66192 66356 complement fr 2 0.82 0.05 66192 66302 complement fr 2 0.75 0.00 66434 66655 complement fr 1 0.58 0.82 66434 66619 complement fr 1 0.65 0.99 66743 66922 complement fr 1 0.66 0.82 66743 66904 complement fr 1 0.71 0.11 66743 66871 complement fr 1 0.64 0.13 67415 68161 direct fr 2 0.87 0.28 67580 68161 direct fr 2 0.91 0.10 67619 68161 direct fr 2 0.90 0.48 67769 68161 direct fr 2 0.86 0.01 68165 68461 direct fr 2 0.53 0.80 68252 68461 direct fr 2 0.66 0.12 68640 72596 complement fr 2 0.92 0.51 68640 72587 complement fr 2 0.92 0.66 68640 72527 complement fr 2 0.93 0.03 68640 72524 complement fr 2 0.93 0.02 68640 72452 complement fr 2 0.93 0.21 72818 73363 complement fr 1 0.79 0.65 72818 73360 complement fr 1 0.79 0.67 72818 73354 complement fr 1 0.81 0.78 72818 73039 complement fr 1 0.74 0.32 72818 72952 complement fr 1 0.60 0.31 72818 72934 complement fr 1 0.52 0.16 73932 74084 direct fr 3 0.53 0.23 73941 74084 direct fr 3 0.59 0.08 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 3 140 direct fr 3 258 1826 direct fr 3 1905 2228 direct fr 3 2459 2668 direct fr 2 2876 3304 complement fr 1 3428 3667 complement fr 1 3671 3910 complement fr 1 4065 4466 complement fr 2 4454 4618 complement fr 1 4867 5223 direct fr 1 5214 5738 direct fr 3 5729 5950 direct fr 2 5995 6195 direct fr 1 6183 6398 direct fr 3 6392 6679 complement fr 1 6486 6860 direct fr 3 6858 7124 direct fr 3 7786 8292 direct fr 1 8469 9038 complement fr 2 9010 9588 complement fr 3 9833 10267 complement fr 1 10398 10565 complement fr 2 10780 11817 direct fr 1 11829 12173 direct fr 3 12293 12580 complement fr 1 12864 13541 direct fr 3 13531 16011 direct fr 1 15798 16094 complement fr 2 16061 16285 direct fr 2 16369 17568 complement fr 3 17429 17851 complement fr 1 18171 18539 direct fr 3 18170 18460 complement fr 1 18724 19047 direct fr 1 19200 19427 direct fr 3 19636 19872 complement fr 3 20217 21941 direct fr 3 21961 23052 complement fr 3 23118 23306 complement fr 2 23246 23458 direct fr 2 23519 23755 complement fr 1 23767 24495 direct fr 1 24493 25473 direct fr 1 25635 26078 direct fr 3 26102 26866 direct fr 2 26838 28781 direct fr 3 27071 27502 complement fr 1 28457 28696 complement fr 1 29178 29399 complement fr 2 29479 30111 direct fr 1 30302 31174 direct fr 2 31172 31504 direct fr 2 31486 31890 direct fr 1 32106 32252 direct fr 3 32222 32668 direct fr 2 32658 32948 direct fr 3 33162 35168 complement fr 2 33556 33951 direct fr 1 34591 34791 direct fr 1 35102 35485 complement fr 1 35521 36237 complement fr 3 36669 37001 direct fr 3 37332 37574 complement fr 2 37559 37786 complement fr 1 37990 38490 complement fr 3 38488 38682 complement fr 3 38919 39212 complement fr 2 39438 42425 complement fr 2 42737 43603 direct fr 2 43572 44405 direct fr 3 44377 45192 direct fr 1 45183 45830 direct fr 3 46073 46420 complement fr 1 46386 46931 complement fr 2 47307 48485 complement fr 2 48367 48828 complement fr 3 48826 49428 complement fr 3 49079 49306 direct fr 2 49310 50128 complement fr 1 49647 49847 direct fr 3 50544 50834 complement fr 2 50945 51895 direct fr 2 52224 53732 direct fr 3 54166 54525 direct fr 1 54773 55222 complement fr 1 55239 55469 complement fr 2 56379 56750 direct fr 3 56683 57186 direct fr 1 57241 57984 complement fr 3 57773 57937 direct fr 2 58025 58651 complement fr 1 58854 59366 direct fr 3 59451 60182 complement fr 2 60161 61369 complement fr 1 61146 61370 direct fr 3 61356 62501 complement fr 2 62491 62754 complement fr 3 62882 63595 complement fr 1 63925 65337 direct fr 1 65527 65838 complement fr 3 66192 66416 complement fr 2 66434 66658 complement fr 1 66743 66955 complement fr 1 67370 68161 direct fr 2 68162 68461 direct fr 2 68640 72602 complement fr 2 72818 73381 complement fr 1 73575 73802 direct fr 3 73920 74084 direct fr 3 -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 15:31:13 2007