Command: /data/pg-molgen/software/bagel4/tools/glimmer3.02/bin/glimmer3 -C 51.5 -o 12 -g 120 -t 12 -r -l /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_CP0245981.2411.AOI_01.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_CP0245981.2411.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_CP0245981.2411.AOI_01.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/GLIMMER.icm Excluded regions file = none List of orfs file = none Input is NOT separate orfs Independent (non-coding) scores are NOT used Circular genome = false Truncated orfs = false Minimum gene length = 120 bp Maximum overlap bases = 12 Threshold score = 12 Use first start codon = false Start codons = atg,gtg,ttg Start probs = 0.600,0.300,0.100 Stop codons = taa,tag,tga GC percentage = 51.5% >NZ_CP0245981.2411.AOI_01 Sequence length = 21125 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 -1 285 207 85 198 120 -13.43 0 - 0 0 0 99 - -1 486 408 286 198 120 -14.00 0 - 0 0 0 99 - 0001 +2 2 50 916 912 864 13.05 0 - 0 - - 99 - +2 917 923 1330 411 405 2.44 0 - 0 - - 99 - +3 1242 1245 1397 153 150 2.00 0 - - 0 - 99 - +1 1405 1423 1545 138 120 4.13 1 1 - - 98 - - +1 1546 1549 1710 162 159 0.39 0 0 - - 99 - - +1 1711 1756 1890 177 132 -0.52 0 0 0 - 99 - - +2 1751 1778 1906 153 126 -5.01 0 - 0 - 99 - - 0002 -2 2029 2014 1877 150 135 1.61 99 - - - 0 99 - 0003 +2 1913 1925 2059 144 132 -1.16 99 - 99 - 0 - - +2 2060 2063 2185 123 120 -12.42 0 - 0 4 0 - 95 0004 -1 2217 1854 1417 798 435 5.99 99 - - - 99 - - +3 1965 2091 2258 291 165 3.89 0 - - 0 - - 99 +1 2116 2266 2415 297 147 -5.61 0 0 0 - - - 99 +2 2246 2297 2455 207 156 -6.64 0 - 0 - - - 99 -2 2515 2515 2390 123 123 -6.74 0 - - 39 - 0 60 +3 2379 2415 2537 156 120 6.08 4 - - 4 - - 95 +1 2641 2668 2829 186 159 -3.51 0 0 - 0 - - 99 +3 2589 2592 2849 258 255 2.30 0 - - 0 - - 99 -2 3157 3118 2975 180 141 -13.82 0 - - 0 - 0 99 +3 2850 3006 3254 402 246 2.31 0 - - 0 - - 99 0005 -3 3284 3194 1977 1305 1215 4.66 99 - - - - - 99 +1 3562 3583 3726 162 141 -2.14 0 0 - - - - 99 +3 3633 3633 4151 516 516 2.52 0 - - 0 - - 99 +1 4159 4171 4326 165 153 -7.02 0 0 - 0 - - 99 +3 4152 4155 4352 198 195 5.44 0 - - 0 - - 99 0006 -3 4352 4319 3417 933 900 9.75 99 - - - - - 99 +3 4353 4446 4595 240 147 -9.18 0 - - 0 99 - - +2 4733 4763 4891 156 126 -0.59 0 0 0 - 99 0 - 0007 -1 5052 5022 4426 624 594 10.24 99 - - - 99 - - 0008 +1 4471 4543 5064 591 519 2.18 99 99 - - - - - 0009 +2 4892 4907 5089 195 180 0.13 99 - 99 - - - - 0010 +1 5095 5107 5241 144 132 -4.95 69 69 12 18 - - - 0011 +2 5090 5120 5251 159 129 -5.63 57 - 57 42 - - - -3 5384 5375 5238 144 135 -3.61 0 99 - 0 - - 0 0012 +3 5079 5187 5432 351 243 -5.61 99 - - 99 - - - +2 5300 5324 5452 150 126 -7.21 0 99 0 - - - - +2 5453 5540 5698 243 156 -9.71 0 99 0 0 0 - - +3 5433 5517 5720 285 201 -9.24 0 99 - 0 0 - - -3 5813 5681 5553 258 126 -5.06 0 99 0 0 0 - 0 0013 +1 5242 5272 5862 618 588 7.83 99 99 - - - - - -1 5868 5742 5368 498 372 0.48 0 99 - - 0 - - 0014 -1 6063 5994 5869 192 123 -3.27 32 - 67 - 32 - - 0015 +2 5846 5927 6067 219 138 2.88 79 - 79 - 0 19 - 0016 +3 5937 5958 6176 237 216 -2.72 99 - - 99 - 0 - 0017 -2 6199 6070 5918 279 150 0.08 99 - - - - 99 - 0018 -1 6285 6249 6097 186 150 7.37 99 - - - 99 - - 0019 -3 6518 6422 6255 261 165 1.40 99 - - - - - 99 0020 +1 6352 6355 6681 327 324 -2.44 99 99 - - - - - 0021 -1 6690 6636 6442 246 192 3.98 99 0 - - 99 - - -1 7014 6852 6691 321 159 -2.77 0 - 99 - 0 - - +3 6885 6927 7061 174 132 -11.76 0 0 99 0 - 0 - +1 6832 6874 7068 234 192 -8.92 0 0 99 - - 0 - -1 7167 7146 7015 150 129 -2.28 0 - 99 - 0 0 - +1 7069 7081 7224 153 141 -4.05 0 0 99 - - 0 - -1 7302 7296 7168 132 126 -0.27 0 - 99 - 0 0 - -1 7500 7494 7363 135 129 -3.68 0 - 99 - 0 0 - -3 7589 7529 7404 183 123 -10.40 0 - 99 - - 0 0 0022 -2 7753 7687 6740 1011 945 0.51 0 - 99 - - 0 - -1 7896 7833 7711 183 120 -2.26 0 0 99 - 0 - - +1 7873 7900 8076 201 174 -8.16 0 0 99 - - - - +3 8103 8145 8291 186 144 -7.45 0 - 99 0 - 0 - -2 8422 8353 7940 480 411 1.70 0 - 99 - - 0 - +1 8317 8368 8496 177 126 -3.97 0 0 99 - - - - 0023 +2 6518 6527 8581 2061 2052 9.88 99 - 99 - - - - 0024 +1 8497 8566 8766 267 198 -7.15 99 99 - - - - - -2 8851 8791 8642 207 147 5.32 0 - 99 - - 0 - +3 8880 8898 9023 141 123 -7.66 0 - 99 0 - - 0 -1 9225 9225 9088 135 135 -2.24 0 - 99 - 0 0 - 0025 +2 8582 8666 9292 708 624 9.98 99 - 99 - - - - -2 9358 9223 9041 315 180 1.92 0 - 99 - - 0 - +1 9193 9229 9369 174 138 -4.28 10 10 - 65 23 - - 0026 +3 9153 9240 9407 252 165 -2.43 99 - - 99 - - - +3 9408 9423 9557 147 132 -6.33 0 - 0 0 - 99 - -1 9702 9660 9508 192 150 -7.93 0 - 0 - 0 99 - +2 9293 9374 9706 411 330 0.39 0 - 0 - - 99 - -3 9758 9731 9606 150 123 -9.04 0 - - - - 99 0 0027 -2 9781 9655 9359 420 294 6.46 99 - 0 - - 99 - 0028 +3 9621 9639 9785 162 144 -1.56 72 - - 72 - 27 - +1 10042 10102 10260 216 156 -6.47 0 0 0 - - 99 - 0029 +2 9902 9974 10312 408 336 2.09 99 - 99 - - - - +1 10261 10315 10494 231 177 -7.92 0 0 - - - 99 - +3 10470 10611 10793 321 180 -3.18 0 - - 0 - 99 0 -3 10799 10745 10524 273 219 -5.94 0 - - 0 - 99 0 -1 10899 10899 10774 123 123 -10.29 0 - 0 - 0 99 - +3 10953 10977 11102 147 123 3.38 0 0 0 0 - 99 0 +2 10904 10961 11131 225 168 1.18 0 - 0 - - 99 - 0030 -2 11149 11149 9983 1164 1164 9.18 99 - - - - 99 - +3 11103 11196 11330 225 132 -2.09 0 - 0 0 - 99 0 -1 11562 11559 11437 123 120 -11.74 0 - 0 0 0 99 - +3 11331 11448 11732 399 282 -3.54 0 - 0 0 - 99 - -3 11837 11801 11478 357 321 -6.51 0 - 0 - - 99 0 0031 -2 12172 12163 11168 1002 993 8.83 99 - 0 - - 99 - 0032 +2 11159 11171 12358 1197 1185 0.80 99 - 99 - - - - +3 12237 12288 12422 183 132 -2.57 0 - - 0 - 99 0 -3 12740 12710 12471 267 237 -10.22 0 - 0 - - 99 0 -1 12819 12792 12664 153 126 -9.16 0 - 0 - 0 99 - +3 12750 12756 12884 132 126 -8.85 0 0 0 0 - 99 - +1 12679 12715 12900 219 183 -8.30 0 0 0 - - 99 - +2 12359 12449 12943 582 492 -0.18 0 - 0 - - 99 - +3 12918 12957 13082 162 123 -6.03 0 - 0 0 - 99 - +2 12944 13136 13303 357 165 1.47 0 - 0 0 - 99 0 +3 13083 13158 13334 249 174 -6.59 0 - - 0 - 99 0 +1 13198 13198 13350 150 150 -7.23 0 0 - - - 99 0 0033 -2 13444 13348 12227 1215 1119 4.69 99 - - - - 99 - +1 13477 13633 13797 318 162 -0.19 0 0 - 0 - - 99 +2 13736 13751 13891 153 138 -10.41 0 - 0 0 - - 99 +3 13590 13608 13952 360 342 0.76 0 - - 0 - - 99 0034 -3 14051 13937 13362 687 573 3.65 99 - - - - - 99 +1 14002 14035 14160 156 123 -4.44 1 1 - 28 - 69 - 0035 +1 14167 14176 14316 147 138 -0.72 75 75 - 24 - 0 - 0036 -2 14392 14188 14009 381 177 -0.67 56 - - 43 - 56 - 0037 +3 14013 14193 14417 402 222 -0.13 99 - - 99 0 - - 0038 -3 14456 14414 14253 201 159 1.39 98 - - 0 0 - 98 0039 -3 14579 14579 14457 120 120 2.30 50 - - 48 1 - 50 0040 -1 14643 14589 14188 453 399 -3.99 99 - - - 99 - - +1 14695 14914 15135 438 219 -7.76 0 0 99 - - 0 - 0041 +2 14561 14597 15199 636 600 7.14 99 - 99 - - 0 - -2 15292 15196 14576 714 618 3.12 0 - 99 - - 0 - +3 15066 15159 15389 321 228 -9.20 0 99 - 0 - - - -3 15674 15668 15513 159 153 -1.60 0 99 - 0 0 - 0 0042 +1 15136 15196 15747 609 549 8.81 99 99 - - - - - -1 15816 15732 15454 360 276 3.79 0 99 - 0 0 - - -2 16279 16171 15920 357 249 2.29 0 - 99 - - 0 - -1 16371 16344 16036 333 306 -2.31 0 - 99 - 0 - - +1 16147 16189 16479 330 288 -8.89 0 0 99 - - - - -3 16772 16490 16341 429 147 -10.52 0 - 8 - - 91 0 -1 16827 16827 16675 150 150 -4.33 0 - 99 - 0 0 - 0043 +2 15800 15806 17020 1218 1212 5.86 99 - 99 - - - - -2 17044 16990 16280 762 708 2.41 0 - 99 - - 0 - -2 17389 17317 17195 192 120 -2.38 0 - 0 99 - 0 0 +2 17168 17234 17455 285 219 -6.97 0 - 0 99 - - 0 -3 17534 17396 17133 399 261 2.35 0 - - 99 - - 0 0044 +3 17010 17031 17636 624 603 7.40 99 - - 99 - - - +2 17492 17510 17659 165 147 -8.24 6 93 6 - - - - 0045 -3 17723 17723 17535 186 186 -2.51 17 82 - - - - 17 -1 17841 17838 17653 186 183 2.72 0 99 - 0 0 - - 0046 +1 17488 17662 17889 399 225 3.60 99 99 - 0 - - - -2 17920 17908 17780 138 126 -5.85 0 - - 99 - 0 0 -3 18041 18026 17766 273 258 0.34 0 - - 99 - - 0 -2 18226 18220 18059 165 159 -1.68 0 - 0 99 - 0 0 -1 18237 18210 18079 156 129 -11.46 0 - 0 99 0 0 0 +2 17963 18158 18316 351 156 -9.91 0 - 0 99 - - 0 0047 +3 17637 17802 18338 699 534 6.75 99 - - 99 - - - -3 18350 18185 18042 306 141 -1.59 0 - 0 99 - - 0 0048 -2 18379 18379 18245 132 132 -2.40 99 - - - 0 99 - 0049 -1 18582 18573 18238 342 333 -0.67 99 - - - 99 - - +2 18476 18482 18658 180 174 -5.45 0 99 0 0 - - - +3 18339 18480 18758 417 276 -11.37 0 99 - 0 - - - +2 18659 18731 18853 192 120 -3.14 0 0 0 - 99 - - +3 18783 18834 19067 282 231 -9.40 0 99 - 0 0 - - +2 18929 18992 19144 213 150 -9.23 0 99 0 - 0 - - 0050 +1 18310 18361 19284 972 921 3.37 99 99 - - - - - 0051 -1 19380 18960 18583 795 375 3.20 13 86 - - 13 - - +1 19285 19303 19437 150 132 -2.34 7 7 58 0 - 34 - +3 19263 19320 19442 177 120 -4.98 1 - 50 1 - 47 - 0052 -2 19567 19387 19247 318 138 -1.95 60 - 39 - - 60 - +1 19438 19498 19641 201 141 -8.52 0 0 99 0 - - 0 -3 19658 19577 19431 225 144 -8.06 0 - 99 - - - 0 -1 19779 19776 19648 129 126 -4.63 0 - 99 - 0 - - 0053 +2 19145 19505 19828 681 321 3.65 99 - 99 - - - - 0054 -1 20274 20256 20125 147 129 -9.13 16 - 83 - 16 - - 0055 -2 20575 20572 20417 156 153 -3.29 99 - - - - 99 0 0056 -3 20627 20516 20352 273 162 -5.90 99 - - - - - 99 0057 +2 20477 20534 20662 183 126 -5.13 99 - 99 - - - - 0058 -1 20757 20727 20563 192 162 -7.54 99 - - - 99 - - +2 20663 20750 20893 228 141 -2.86 0 - 0 17 - 82 - +3 20622 20736 20921 297 183 -0.14 1 - - 1 - 98 - +2 20894 20897 21046 150 147 -4.16 0 - 0 - - 99 - 0059 -2 21124 21007 20684 438 321 1.84 99 - - - - 99 - 0060 -1 21123 21111 20986 135 123 -3.04 16 - - - 16 83 0