GENEMARK PREDICTIONS Sequence: gi|153930562|ref|NC_009704.1| Yersinia pseudotuberculosis IP 31758 plasmid_59kb, complete sequence Sequence file: NC_009704.fna Sequence length: 58679 GC Content: 40.22% 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 -------- -------- ---------- ----- ---- ---- 519 1556 complement fr 2 0.67 0.29 519 1412 complement fr 2 0.68 0.64 519 1376 complement fr 2 0.67 0.03 519 1271 complement fr 2 0.72 0.16 519 1166 complement fr 2 0.72 0.05 1836 2138 complement fr 2 0.57 0.59 2126 2416 complement fr 1 0.67 0.12 2126 2356 complement fr 1 0.74 0.42 2126 2323 complement fr 1 0.70 0.03 2809 2949 direct fr 1 0.62 0.32 2845 2949 direct fr 1 0.61 0.10 3122 3289 complement fr 1 0.68 0.65 3354 3650 complement fr 2 0.64 0.00 3354 3548 complement fr 2 0.68 0.57 3354 3527 complement fr 2 0.63 0.52 3928 4839 complement fr 3 0.70 0.70 3928 4806 complement fr 3 0.72 0.66 3928 4656 complement fr 3 0.71 0.40 3928 4578 complement fr 3 0.67 0.02 4836 5057 complement fr 2 0.61 0.65 4836 5006 complement fr 2 0.74 0.39 4836 4994 complement fr 2 0.72 0.08 4836 4940 complement fr 2 0.57 0.06 5634 6002 direct fr 3 0.74 0.43 5688 6002 direct fr 3 0.85 0.41 5781 6002 direct fr 3 0.83 0.61 5880 6002 direct fr 3 0.73 0.01 6020 7120 direct fr 2 0.77 0.00 6134 7120 direct fr 2 0.85 0.77 6161 7120 direct fr 2 0.85 0.84 6260 7120 direct fr 2 0.83 0.40 7133 7513 direct fr 2 0.64 0.40 7139 7513 direct fr 2 0.64 0.20 7145 7513 direct fr 2 0.66 0.22 7175 7513 direct fr 2 0.71 0.06 7205 7513 direct fr 2 0.76 0.28 7370 7513 direct fr 2 0.66 0.13 7382 7513 direct fr 2 0.64 0.07 7412 7513 direct fr 2 0.62 0.12 7570 7830 direct fr 1 0.51 0.91 7823 10360 direct fr 2 0.88 0.52 7997 10360 direct fr 2 0.90 0.12 8018 10360 direct fr 2 0.90 0.18 10357 11079 direct fr 1 0.87 0.56 10471 11079 direct fr 1 0.91 0.10 10873 11079 direct fr 1 0.82 0.21 10957 11079 direct fr 1 0.70 0.27 11094 11981 direct fr 3 0.82 0.45 11472 11981 direct fr 3 0.82 0.06 11568 11981 direct fr 3 0.83 0.64 11775 11981 direct fr 3 0.73 0.30 11984 12433 direct fr 2 0.65 0.12 12089 12433 direct fr 2 0.76 0.20 12287 12433 direct fr 2 0.66 0.10 12438 13817 direct fr 3 0.87 0.64 12459 13817 direct fr 3 0.87 0.13 12510 13817 direct fr 3 0.87 0.15 12543 13817 direct fr 3 0.88 0.37 13835 14611 direct fr 2 0.82 0.12 13874 14611 direct fr 2 0.87 0.14 13940 14611 direct fr 2 0.89 0.17 13970 14611 direct fr 2 0.90 0.53 13979 14611 direct fr 2 0.90 0.75 14605 14826 direct fr 1 0.58 0.09 14626 14826 direct fr 1 0.62 0.16 14632 14826 direct fr 1 0.65 0.24 14774 16195 direct fr 2 0.73 0.17 14831 16195 direct fr 2 0.75 0.07 14864 16195 direct fr 2 0.76 0.27 14876 16195 direct fr 2 0.76 0.82 15070 15231 complement fr 3 0.53 0.94 16248 16868 direct fr 3 0.83 0.13 16539 16868 direct fr 3 0.76 0.32 16987 17466 direct fr 1 0.75 0.30 17089 17466 direct fr 1 0.80 0.33 17140 17466 direct fr 1 0.78 0.23 17281 17466 direct fr 1 0.73 0.84 17489 18421 direct fr 2 0.78 0.43 17516 18421 direct fr 2 0.78 0.21 17531 18421 direct fr 2 0.78 0.17 18434 20140 direct fr 2 0.89 0.12 18464 20140 direct fr 2 0.90 0.24 18551 20140 direct fr 2 0.92 0.13 18656 20140 direct fr 2 0.92 0.19 18668 20140 direct fr 2 0.92 0.45 20150 21484 direct fr 2 0.79 0.47 20258 21484 direct fr 2 0.82 0.89 20522 21484 direct fr 2 0.82 0.47 20774 21484 direct fr 2 0.81 0.79 21471 21914 direct fr 3 0.76 0.06 21663 21914 direct fr 3 0.82 0.01 21738 21914 direct fr 3 0.76 0.28 21762 21914 direct fr 3 0.73 0.11 21911 23443 direct fr 2 0.76 0.98 21983 23443 direct fr 2 0.78 0.00 22025 23443 direct fr 2 0.77 0.18 22058 23443 direct fr 2 0.76 0.16 23436 24500 direct fr 3 0.66 0.66 23466 24500 direct fr 3 0.68 0.51 23604 24500 direct fr 3 0.68 0.78 23823 24500 direct fr 3 0.67 0.00 23892 24500 direct fr 3 0.73 0.07 24084 24500 direct fr 3 0.80 0.30 24120 24500 direct fr 3 0.79 0.04 24171 24500 direct fr 3 0.79 0.52 24201 24500 direct fr 3 0.82 0.47 24517 25023 direct fr 1 0.81 0.95 24598 25023 direct fr 1 0.87 0.04 24646 25023 direct fr 1 0.85 0.13 24649 25023 direct fr 1 0.85 0.13 25039 25992 direct fr 1 0.73 0.58 25114 25992 direct fr 1 0.75 0.01 25414 25992 direct fr 1 0.75 0.14 25447 25992 direct fr 1 0.77 0.06 25999 27261 direct fr 1 0.70 0.63 26005 27261 direct fr 1 0.71 0.60 26101 27261 direct fr 1 0.72 0.11 26134 27261 direct fr 1 0.72 0.28 26359 27261 direct fr 1 0.70 0.53 26392 27261 direct fr 1 0.72 0.66 27495 27896 direct fr 3 0.66 0.80 27901 28332 direct fr 1 0.74 0.42 27919 28332 direct fr 1 0.77 0.43 27922 28332 direct fr 1 0.77 0.28 28141 28332 direct fr 1 0.63 0.19 28144 28332 direct fr 1 0.63 0.17 28177 28332 direct fr 1 0.55 0.04 28616 28774 direct fr 2 0.50 0.25 28986 29492 direct fr 3 0.69 0.18 29031 29492 direct fr 3 0.74 0.62 29130 29492 direct fr 3 0.68 0.17 29172 29492 direct fr 3 0.65 0.07 29517 30002 direct fr 3 0.72 0.65 29589 30002 direct fr 3 0.78 0.09 29811 30002 direct fr 3 0.81 0.63 30129 30335 direct fr 3 0.70 0.70 30468 30716 direct fr 3 0.56 0.80 30797 31144 direct fr 2 0.85 0.63 30845 31144 direct fr 2 0.83 0.09 31067 31144 direct fr 2 0.57 0.40 31794 31967 complement fr 2 0.56 0.15 31794 31955 complement fr 2 0.56 0.12 32134 32811 complement fr 3 0.68 0.18 32134 32799 complement fr 3 0.69 0.36 32134 32685 complement fr 3 0.70 0.00 32134 32649 complement fr 3 0.68 0.19 32134 32553 complement fr 3 0.65 0.06 32134 32541 complement fr 3 0.67 0.01 32134 32328 complement fr 3 0.75 0.20 32812 32982 complement fr 3 0.65 0.95 32812 32940 complement fr 3 0.79 0.00 32812 32922 complement fr 3 0.77 0.09 33378 33923 direct fr 3 0.68 0.30 33459 33923 direct fr 3 0.69 0.53 33477 33923 direct fr 3 0.68 0.02 33543 33923 direct fr 3 0.62 0.15 34388 34684 direct fr 2 0.70 0.81 34505 34684 direct fr 2 0.73 0.43 34580 34684 direct fr 2 0.58 0.03 35377 35859 direct fr 1 0.51 0.02 35407 35859 direct fr 1 0.54 0.59 35557 35859 direct fr 1 0.65 0.08 35614 35859 direct fr 1 0.58 0.09 35641 35859 direct fr 1 0.52 0.20 36756 37538 complement fr 2 0.77 0.92 36756 37391 complement fr 2 0.77 0.22 36756 37382 complement fr 2 0.77 0.20 36756 37247 complement fr 2 0.73 0.00 37549 38265 complement fr 3 0.65 0.03 37549 38238 complement fr 3 0.67 0.15 37549 38232 complement fr 3 0.68 0.06 37549 37887 complement fr 3 0.64 0.02 37549 37800 complement fr 3 0.52 0.15 39224 39370 direct fr 2 0.50 0.29 39227 39370 direct fr 2 0.50 0.33 39239 39370 direct fr 2 0.52 0.10 39675 42635 complement fr 2 0.93 0.85 39675 42431 complement fr 2 0.94 0.66 39675 41939 complement fr 2 0.94 0.06 39675 41900 complement fr 2 0.94 0.04 42628 42861 complement fr 3 0.71 0.89 42867 44906 complement fr 2 0.83 0.88 42867 44768 complement fr 2 0.83 0.88 42867 44618 complement fr 2 0.82 0.02 42867 44369 complement fr 2 0.79 0.10 44942 45466 complement fr 1 0.67 0.20 44942 45346 complement fr 1 0.67 0.04 44942 45220 complement fr 1 0.66 0.61 44942 45217 complement fr 1 0.66 0.31 44942 45163 complement fr 1 0.57 0.07 45463 47400 complement fr 3 0.82 0.90 45463 47325 complement fr 3 0.83 0.21 45463 47133 complement fr 3 0.84 0.16 45463 47091 complement fr 3 0.85 0.30 47397 50018 complement fr 2 0.84 0.07 47397 49997 complement fr 2 0.85 0.17 47397 49502 complement fr 2 0.83 0.11 47397 49079 complement fr 2 0.81 0.32 47397 48503 complement fr 2 0.73 0.26 50056 50412 complement fr 3 0.66 0.03 50056 50358 complement fr 3 0.75 0.79 50056 50352 complement fr 3 0.76 0.90 50056 50229 complement fr 3 0.65 0.02 51001 51123 direct fr 1 0.63 0.93 51135 51863 direct fr 3 0.86 1.00 51150 51863 direct fr 3 0.87 0.69 51213 51863 direct fr 3 0.86 0.06 51312 51863 direct fr 3 0.88 0.86 51860 52300 direct fr 2 0.85 0.96 51938 52300 direct fr 2 0.86 0.02 51953 52300 direct fr 2 0.85 0.11 51998 52300 direct fr 2 0.83 0.14 52464 53075 complement fr 2 0.87 0.70 52464 52910 complement fr 2 0.88 0.09 52464 52847 complement fr 2 0.86 0.01 52464 52676 complement fr 2 0.77 0.14 53106 53483 complement fr 2 0.77 0.03 53106 53456 complement fr 2 0.77 0.85 53106 53435 complement fr 2 0.76 0.91 54111 54257 direct fr 3 0.55 0.01 54138 54257 direct fr 3 0.59 0.14 54309 54728 direct fr 3 0.82 0.81 54348 54728 direct fr 3 0.85 0.06 54761 55000 direct fr 2 0.58 0.28 54881 55000 direct fr 2 0.54 0.31 55088 55408 complement fr 1 0.62 0.51 55088 55381 complement fr 1 0.59 0.23 55088 55309 complement fr 1 0.52 0.14 55522 56574 complement fr 3 0.91 0.66 55522 56466 complement fr 3 0.93 0.14 55522 56286 complement fr 3 0.92 0.32 55522 56121 complement fr 3 0.90 0.45 56571 57656 complement fr 2 0.77 0.35 56571 57380 complement fr 2 0.93 0.21 56571 57341 complement fr 2 0.93 0.61 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 519 1559 complement fr 2 1836 2141 complement fr 2 2126 2431 complement fr 1 2638 2949 direct fr 1 3122 3340 complement fr 1 3354 3710 complement fr 2 3928 4869 complement fr 3 4836 5063 complement fr 2 5628 6002 direct fr 3 5963 7120 direct fr 2 7118 7513 direct fr 2 7486 7830 direct fr 1 7700 10360 direct fr 2 10339 11079 direct fr 1 11088 11981 direct fr 3 11912 12433 direct fr 2 12366 13817 direct fr 3 13808 14611 direct fr 2 14587 14826 direct fr 1 14744 16195 direct fr 2 15070 15399 complement fr 3 16167 16868 direct fr 3 16966 17466 direct fr 1 17417 18421 direct fr 2 18419 20140 direct fr 2 20138 21484 direct fr 2 21453 21914 direct fr 3 21899 23443 direct fr 2 23433 24500 direct fr 3 24514 25023 direct fr 1 25021 25992 direct fr 1 25990 27261 direct fr 1 27346 27555 complement fr 3 27471 27896 direct fr 3 27886 28332 direct fr 1 28287 28967 direct fr 3 28286 28537 complement fr 1 28550 28774 direct fr 2 28965 29492 direct fr 3 29502 30002 direct fr 3 30021 30335 direct fr 3 30020 30301 complement fr 1 30465 30716 direct fr 3 30683 31144 direct fr 2 31389 31736 direct fr 3 31794 32012 complement fr 2 32134 32814 complement fr 3 32812 32988 complement fr 3 33342 33923 direct fr 3 34367 34684 direct fr 2 34845 35048 direct fr 3 35029 35337 direct fr 1 35335 35859 direct fr 1 36026 36715 complement fr 1 36756 37541 complement fr 2 37549 38301 complement fr 3 38576 39370 direct fr 2 39440 39577 direct fr 2 39675 42662 complement fr 2 42628 42876 complement fr 3 42821 43057 complement fr 1 42867 44936 complement fr 2 44942 45508 complement fr 1 45463 47406 complement fr 3 47397 50039 complement fr 2 48008 48385 complement fr 1 50056 50415 complement fr 3 50737 51123 direct fr 1 51096 51863 direct fr 3 51839 52300 direct fr 2 52464 53093 complement fr 2 53106 53543 complement fr 2 53722 54021 direct fr 1 53994 54257 direct fr 3 54255 54728 direct fr 3 54749 55000 direct fr 2 55088 55459 complement fr 1 55522 56595 complement fr 3 56571 57734 complement fr 2 57338 57679 complement fr 1 57838 58185 complement fr 3 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 3 2 28608 +/- 11 bp (direct) 2 1 42996 +/- 11 bp (complement) 1 2 48180 +/- 11 bp (complement) 2 1 48312 +/- 11 bp (complement) 1 2 57480 +/- 11 bp (complement) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Jul 27 17:11:51 2007