GENEMARK PREDICTIONS Sequence: gi|116326547|ref|NC_008505.1| Lactococcus lactis subsp. cremoris SK11 plasmid 3, complete sequence Sequence file: NC_008505.fna Sequence length: 74750 GC Content: 35.41% 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 -------- -------- ---------- ----- ---- ---- 242 1645 direct fr 2 0.90 0.51 254 1645 direct fr 2 0.90 0.65 404 1645 direct fr 2 0.96 0.23 503 1645 direct fr 2 0.96 0.15 722 1645 direct fr 2 0.95 0.22 1917 2738 complement fr 2 0.63 0.24 1917 2621 complement fr 2 0.64 0.30 1917 2516 complement fr 2 0.58 0.05 2783 3118 complement fr 1 0.63 0.00 2783 3058 complement fr 1 0.77 0.62 2783 2914 complement fr 1 0.62 0.12 2783 2893 complement fr 1 0.58 0.03 3229 4266 direct fr 1 0.91 0.84 3358 4266 direct fr 1 0.93 0.01 3643 4266 direct fr 1 0.90 0.23 3670 4266 direct fr 1 0.90 0.27 4347 4598 direct fr 3 0.75 0.63 4506 4598 direct fr 3 0.85 0.16 4785 5675 direct fr 3 0.52 0.20 5295 5675 direct fr 3 0.50 0.04 6029 6610 direct fr 2 0.80 0.57 6113 6610 direct fr 2 0.85 0.71 6134 6610 direct fr 2 0.85 0.01 6272 6610 direct fr 2 0.84 0.29 6347 6610 direct fr 2 0.80 0.18 6783 8540 direct fr 3 0.90 0.18 6984 8540 direct fr 3 0.90 0.62 7041 8540 direct fr 3 0.90 0.02 8636 9133 complement fr 1 0.74 0.67 8636 9118 complement fr 1 0.78 0.37 8636 9115 complement fr 1 0.78 0.29 8636 8974 complement fr 1 0.77 0.33 8636 8971 complement fr 1 0.77 0.36 8636 8884 complement fr 1 0.71 0.20 9313 9813 complement fr 3 0.80 0.65 9313 9777 complement fr 3 0.86 0.14 9313 9582 complement fr 3 0.79 0.22 10255 11511 direct fr 1 0.77 0.86 10309 11511 direct fr 1 0.79 0.02 10321 11511 direct fr 1 0.78 0.16 10435 11511 direct fr 1 0.77 0.50 11776 12111 complement fr 3 0.53 0.07 11776 12090 complement fr 3 0.57 0.25 11776 12087 complement fr 3 0.57 0.13 11776 11997 complement fr 3 0.57 0.01 12446 13126 complement fr 1 0.88 0.92 12446 13063 complement fr 1 0.87 0.05 12446 12976 complement fr 1 0.85 0.33 13286 14416 direct fr 2 0.80 0.10 13430 14416 direct fr 2 0.90 0.23 13460 14416 direct fr 2 0.90 0.54 13463 14416 direct fr 2 0.90 0.56 14652 15368 direct fr 3 0.88 0.80 14988 15368 direct fr 3 0.88 0.03 15042 15368 direct fr 3 0.86 0.02 15201 15368 direct fr 3 0.75 0.23 15446 18214 direct fr 2 0.94 0.09 15458 18214 direct fr 2 0.95 0.06 15674 18214 direct fr 2 0.97 0.12 15776 18214 direct fr 2 0.97 0.03 15782 18214 direct fr 2 0.97 0.04 18204 18416 direct fr 3 0.56 0.97 18957 20363 direct fr 3 0.71 0.24 19029 20363 direct fr 3 0.74 0.04 19104 20363 direct fr 3 0.78 0.40 19161 20363 direct fr 3 0.81 0.02 19197 20363 direct fr 3 0.84 0.22 19239 20363 direct fr 3 0.87 0.39 19275 20363 direct fr 3 0.88 0.45 19278 20363 direct fr 3 0.88 0.37 19305 20363 direct fr 3 0.88 0.35 20356 20880 direct fr 1 0.65 0.77 20476 20880 direct fr 1 0.82 0.12 20734 20880 direct fr 1 0.74 0.16 20797 20880 direct fr 1 0.52 0.05 21461 22165 complement fr 1 0.94 0.06 21461 21901 complement fr 1 0.91 0.50 22257 22601 complement fr 2 0.75 0.67 22257 22382 complement fr 2 0.56 0.48 22727 24526 complement fr 1 0.73 0.74 22727 24514 complement fr 1 0.74 0.44 22727 24415 complement fr 1 0.74 0.40 22727 24268 complement fr 1 0.72 0.07 25064 25471 complement fr 1 0.77 0.30 25064 25456 complement fr 1 0.80 0.35 25064 25336 complement fr 1 0.78 0.24 25064 25312 complement fr 1 0.76 0.28 25064 25294 complement fr 1 0.74 0.28 25476 25844 complement fr 2 0.53 0.13 25476 25760 complement fr 2 0.62 0.04 25476 25688 complement fr 2 0.75 0.65 25476 25661 complement fr 2 0.74 0.39 26139 26405 complement fr 2 0.69 0.45 26424 26675 complement fr 2 0.77 0.59 26424 26516 complement fr 2 0.77 0.20 26756 27004 complement fr 1 0.63 0.84 26756 26977 complement fr 1 0.68 0.05 26756 26920 complement fr 1 0.65 0.83 26756 26902 complement fr 1 0.60 0.11 27663 28109 complement fr 2 0.71 0.62 27663 28082 complement fr 2 0.70 0.54 27663 28070 complement fr 2 0.69 0.49 29938 30402 complement fr 3 0.87 0.75 29938 30399 complement fr 3 0.87 0.58 29938 30303 complement fr 3 0.84 0.46 30431 30727 complement fr 1 0.68 0.80 30431 30694 complement fr 1 0.73 0.18 30431 30670 complement fr 1 0.71 0.26 30431 30562 complement fr 1 0.62 0.43 31440 32087 complement fr 2 0.85 0.80 31440 32021 complement fr 2 0.85 0.03 31440 31901 complement fr 2 0.81 0.00 31440 31733 complement fr 2 0.70 0.00 32461 33066 complement fr 3 0.80 0.17 32461 32919 complement fr 3 0.83 0.02 32461 32865 complement fr 3 0.80 0.00 32461 32730 complement fr 3 0.77 0.14 34197 35147 complement fr 2 0.62 0.11 34197 35066 complement fr 2 0.64 0.75 34197 34964 complement fr 2 0.60 0.02 34197 34790 complement fr 2 0.65 0.59 35678 36358 complement fr 1 0.86 0.72 35678 36208 complement fr 1 0.83 0.33 35678 36136 complement fr 1 0.82 0.61 36638 38317 direct fr 2 0.91 0.97 36776 38317 direct fr 2 0.94 0.27 36782 38317 direct fr 2 0.94 0.07 36791 38317 direct fr 2 0.94 0.60 38405 39133 complement fr 1 0.77 0.55 38405 39088 complement fr 1 0.75 0.01 38405 39028 complement fr 1 0.73 0.09 39220 39591 complement fr 3 0.79 0.17 39220 39573 complement fr 3 0.78 0.34 39220 39531 complement fr 3 0.75 0.03 40077 41426 complement fr 2 0.89 0.60 40077 41309 complement fr 2 0.92 0.01 40077 41204 complement fr 2 0.92 0.03 40077 41168 complement fr 2 0.92 0.55 41564 42187 complement fr 1 0.88 0.71 41564 41953 complement fr 1 0.87 0.10 41564 41950 complement fr 1 0.87 0.01 41564 41935 complement fr 1 0.86 0.04 42453 43043 complement fr 2 0.78 0.03 42453 43037 complement fr 2 0.78 0.16 42453 42779 complement fr 2 0.72 0.14 42453 42599 complement fr 2 0.59 0.33 43173 43430 complement fr 2 0.60 0.03 43173 43403 complement fr 2 0.69 0.69 43173 43379 complement fr 2 0.67 0.84 43629 43991 complement fr 2 0.73 0.20 43629 43817 complement fr 2 0.69 0.43 43629 43769 complement fr 2 0.60 0.22 44001 44288 complement fr 2 0.80 0.64 44001 44231 complement fr 2 0.79 0.33 44001 44195 complement fr 2 0.75 0.58 44401 45081 direct fr 1 0.86 0.56 44551 45081 direct fr 1 0.85 0.39 44623 45081 direct fr 1 0.84 0.61 44791 45081 direct fr 1 0.75 0.29 45329 51247 complement fr 1 0.97 0.31 45329 51217 complement fr 1 0.97 0.11 45329 51076 complement fr 1 0.97 0.31 45329 50923 complement fr 1 0.97 0.04 51542 52441 direct fr 2 0.90 0.27 51554 52441 direct fr 2 0.90 0.11 51662 52441 direct fr 2 0.92 0.02 52591 53271 direct fr 1 0.83 0.83 52654 53271 direct fr 1 0.86 0.04 52741 53271 direct fr 1 0.83 0.39 52813 53271 direct fr 1 0.82 0.61 53910 54032 direct fr 3 0.53 0.50 53931 54032 direct fr 3 0.54 0.01 54491 54676 complement fr 1 0.54 0.15 54743 55633 direct fr 2 0.52 0.20 55058 55633 direct fr 2 0.60 0.00 55253 55633 direct fr 2 0.52 0.03 55268 55633 direct fr 2 0.50 0.04 55779 56075 complement fr 2 0.63 0.21 55779 56030 complement fr 2 0.72 0.49 55779 55970 complement fr 2 0.66 0.02 56387 56758 direct fr 2 0.83 0.12 56447 56758 direct fr 2 0.80 0.02 56579 56758 direct fr 2 0.70 0.64 56845 57354 direct fr 1 0.83 0.41 56890 57354 direct fr 1 0.82 0.01 56950 57354 direct fr 1 0.79 0.10 57394 57573 direct fr 1 0.52 0.45 57994 58194 complement fr 3 0.82 0.93 58471 58680 complement fr 3 0.57 0.65 58471 58671 complement fr 3 0.57 0.86 58471 58617 complement fr 3 0.62 0.17 58471 58605 complement fr 3 0.59 0.02 58471 58596 complement fr 3 0.55 0.00 58802 59002 complement fr 1 0.61 0.99 59980 60660 direct fr 1 0.84 0.73 60130 60660 direct fr 1 0.84 0.39 60202 60660 direct fr 1 0.83 0.61 60370 60660 direct fr 1 0.75 0.28 61058 61390 complement fr 1 0.82 0.95 61058 61273 complement fr 1 0.76 0.55 61058 61207 complement fr 1 0.65 0.02 62032 63030 direct fr 1 0.87 0.36 62176 63030 direct fr 1 0.86 0.93 62245 63030 direct fr 1 0.85 0.20 63027 63497 direct fr 3 0.82 0.32 63039 63497 direct fr 3 0.82 0.01 63304 63837 direct fr 1 0.56 0.00 63358 63837 direct fr 1 0.62 0.04 63424 63837 direct fr 1 0.72 0.04 63457 63837 direct fr 1 0.79 0.42 63487 63837 direct fr 1 0.84 0.70 63547 63837 direct fr 1 0.82 0.51 63550 63837 direct fr 1 0.82 0.46 64050 64892 direct fr 3 0.67 0.55 64158 64892 direct fr 3 0.67 0.16 64197 64892 direct fr 3 0.67 0.15 64266 64892 direct fr 3 0.68 0.71 64969 65172 direct fr 1 0.56 0.92 65023 65172 direct fr 1 0.66 0.14 65569 66561 direct fr 1 0.86 0.93 65785 66561 direct fr 1 0.84 0.14 65791 66561 direct fr 1 0.84 0.21 65869 66561 direct fr 1 0.84 0.31 66598 66717 direct fr 1 0.56 0.93 66776 66928 complement fr 1 0.65 0.64 67032 67265 direct fr 3 0.59 0.59 67125 67265 direct fr 3 0.65 0.30 67552 68136 direct fr 1 0.78 0.18 67732 68136 direct fr 1 0.86 0.09 67780 68136 direct fr 1 0.84 0.03 68247 69293 complement fr 2 0.72 0.50 68247 69188 complement fr 2 0.70 0.03 68247 69173 complement fr 2 0.70 0.00 68247 69074 complement fr 2 0.73 0.11 68247 68927 complement fr 2 0.79 0.03 68247 68552 complement fr 2 0.76 0.02 69455 69730 complement fr 1 0.76 0.70 69850 70518 direct fr 1 0.82 0.80 69886 70518 direct fr 1 0.85 0.02 70006 70518 direct fr 1 0.83 0.07 70009 70518 direct fr 1 0.82 0.12 70506 71900 direct fr 3 0.85 0.32 70731 71900 direct fr 3 0.88 0.58 70818 71900 direct fr 3 0.87 0.45 70956 71900 direct fr 3 0.89 0.01 70986 71900 direct fr 3 0.90 0.24 71025 71900 direct fr 3 0.92 0.24 72084 72890 direct fr 3 0.69 0.08 72132 72890 direct fr 3 0.73 0.91 72255 72890 direct fr 3 0.69 0.08 72420 72890 direct fr 3 0.60 0.57 72432 72890 direct fr 3 0.59 0.39 72952 73110 direct fr 1 0.62 0.71 72955 73110 direct fr 1 0.62 0.60 72964 73110 direct fr 1 0.64 0.76 72967 73110 direct fr 1 0.64 0.78 72976 73110 direct fr 1 0.65 0.96 73366 74670 direct fr 1 0.87 0.02 73417 74670 direct fr 1 0.91 0.98 73420 74670 direct fr 1 0.91 0.98 73477 74670 direct fr 1 0.91 0.00 List of Regions of interest (regions from stop to stop codon w/ a signal in between) LEnd REnd Strand Frame -------- -------- ----------- ----- 18 221 direct fr 3 239 1645 direct fr 2 1752 1904 direct fr 3 1917 2882 complement fr 2 2783 3148 complement fr 1 3205 4266 direct fr 1 4344 4598 direct fr 3 4710 5675 direct fr 3 6008 6610 direct fr 2 6597 8540 direct fr 3 8636 9151 complement fr 1 9313 9825 complement fr 3 9823 10128 complement fr 3 10219 11511 direct fr 1 11776 12360 complement fr 3 12446 13165 complement fr 1 13241 14416 direct fr 2 14604 15368 direct fr 3 15425 18214 direct fr 2 18198 18416 direct fr 3 18909 20363 direct fr 3 20350 20880 direct fr 1 20883 21119 direct fr 3 21461 22288 complement fr 1 22257 22640 complement fr 2 22727 24556 complement fr 1 25064 25489 complement fr 1 25476 25865 complement fr 2 26139 26426 complement fr 2 26424 26678 complement fr 2 26756 27013 complement fr 1 27663 28301 complement fr 2 29862 30035 complement fr 2 29938 30459 complement fr 3 30431 30748 complement fr 1 31440 32105 complement fr 2 32461 33078 complement fr 3 33333 33695 complement fr 2 34197 35165 complement fr 2 34291 34464 complement fr 3 35449 35649 complement fr 3 35678 36397 complement fr 1 36620 38317 direct fr 2 38405 39331 complement fr 1 39220 39672 complement fr 3 40077 41429 complement fr 2 41564 42241 complement fr 1 42214 42474 complement fr 3 42453 43064 complement fr 2 43173 43448 complement fr 2 43629 44003 complement fr 2 44001 44363 complement fr 2 44362 45081 direct fr 1 45329 51343 complement fr 1 51491 52441 direct fr 2 52552 53271 direct fr 1 53868 54032 direct fr 3 54491 54718 complement fr 1 54668 55633 direct fr 2 55779 56078 complement fr 2 56306 56758 direct fr 2 56647 57354 direct fr 1 57352 57573 direct fr 1 57498 57650 direct fr 3 57994 58230 complement fr 3 58471 58692 complement fr 3 58802 59008 complement fr 1 59941 60660 direct fr 1 60658 61026 direct fr 1 61058 61414 complement fr 1 61936 63030 direct fr 1 62967 63497 direct fr 3 63250 63837 direct fr 1 64017 64892 direct fr 3 64948 65172 direct fr 1 65527 66561 direct fr 1 66559 66717 direct fr 1 66776 66994 complement fr 1 67014 67265 direct fr 3 67369 68136 direct fr 1 68077 68292 complement fr 3 68247 69554 complement fr 2 69076 69237 direct fr 1 69455 69832 complement fr 1 69811 70518 direct fr 1 70503 71900 direct fr 3 72078 72890 direct fr 3 72850 73110 direct fr 1 73345 74670 direct fr 1 73992 74309 complement fr 2 POSSIBLE SEQUENCE FRAMESHIFTS DETECTED From To Frame Frame At base... ----- ----- ---------- 2 3 34452 +/- 11 bp (complement) 3 1 39276 +/- 11 bp (complement) -------------------- ABOUT THE MATRIX USED: Training set derived by GeneMarkS, 4.6a Fri Apr 20 16:59:58 2007