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_NSLU010000091.1837.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_NSLU010000091.1837.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_NSLU010000091.1837.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_NSLU010000091.1837.AOI_01 Sequence length = 14604 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 +2 86 215 394 306 177 -4.50 4 29 4 65 - - - 0001 +3 213 330 455 240 123 -2.97 99 0 - 99 - - - -2 508 490 356 150 132 -6.04 1 98 - - - 1 - 0002 -3 602 596 456 144 138 2.15 98 1 - - - - 98 0003 +1 1 463 753 750 288 -2.43 99 99 - - - - - -1 954 861 715 237 144 -3.76 0 - 99 - 0 - - -1 1143 1134 955 186 177 -8.06 0 - 0 - 0 99 - -1 1344 1266 1144 198 120 -7.41 0 - 0 0 0 99 - -1 1545 1467 1345 198 120 -7.41 0 - 0 0 0 99 - 0004 +2 668 704 1975 1305 1269 1.41 0 - 0 - - 99 - +2 1976 2201 2389 411 186 -2.80 0 - 0 - - 99 - +3 2301 2304 2456 153 150 3.62 0 - - 0 - 99 - 0005 -2 2479 2479 725 1752 1752 6.41 99 - - - - 99 - 0006 +1 2464 2473 2604 138 129 2.56 99 99 - - - - - +1 2605 2608 2769 162 159 1.84 0 0 - - 99 - - +1 2770 2815 2949 177 132 -1.24 0 0 1 - 98 - - 0007 +2 2810 2837 2965 153 126 0.96 24 - 24 - 75 - - 0008 -2 3088 3073 2936 150 135 0.94 99 - - - 0 99 - +2 2972 2984 3118 144 132 -1.08 4 - 4 95 0 - - +2 3119 3122 3244 123 120 -7.64 0 - 0 14 0 - 85 0009 -1 3276 2913 2476 798 435 3.89 99 - - - 99 - - 0010 +3 2988 2997 3317 327 318 0.94 99 - - 99 - - - +1 3175 3310 3474 297 162 -2.33 0 0 0 - - - 99 +2 3305 3344 3514 207 168 -7.70 0 - 0 - - - 99 -2 3574 3574 3449 123 123 -4.48 0 - - 97 - 0 2 0011 +3 3438 3471 3596 156 123 7.25 50 - - 50 - - 49 +1 3700 3727 3888 186 159 -3.33 0 0 - 2 - - 96 +3 3648 3651 3908 258 255 1.52 1 - - 1 - - 98 -2 4216 4177 4034 180 141 -8.21 0 - - 2 - 0 97 +3 3909 4065 4313 402 246 0.66 0 - - 0 - - 99 0012 -3 4343 4253 3036 1305 1215 3.74 99 - - - - - 99 +3 4716 4746 4874 156 126 0.11 0 - 0 0 - 99 0 0013 -2 5035 5005 4316 717 687 11.63 99 - 0 - - 99 - 0014 +2 4265 4526 5047 780 519 -0.22 99 - 99 - - - - 0015 +3 4875 4929 5072 195 141 0.47 99 - - 99 - - - 0016 +2 5078 5090 5224 144 132 -4.14 18 - 18 81 - - - 0017 +3 5073 5103 5234 159 129 -3.36 99 - - 99 - - - -1 5367 5361 5221 144 138 -3.08 0 0 99 - 0 - - 0018 +1 5155 5170 5415 258 243 -4.48 99 99 - - - - - +3 5283 5307 5435 150 126 -4.19 0 - 99 0 - - - +3 5436 5523 5681 243 156 -5.28 0 0 99 0 - 0 - +1 5416 5500 5703 285 201 -8.04 0 0 99 - - 0 - -1 5796 5664 5536 258 126 -3.34 0 0 99 0 0 0 - 0019 +2 5225 5255 5845 618 588 5.78 99 - 99 - - - - -2 5851 5725 5378 471 345 -0.44 0 - 99 - - 0 - +3 5829 5970 6128 297 156 0.18 0 98 - 0 - 0 - 0020 +1 5887 5941 6162 273 219 3.72 99 99 - - - 0 - 0021 -2 6181 6052 5852 327 198 -2.05 52 - - 47 - 52 - +2 6104 6113 6253 147 138 3.20 9 - 9 - 90 - - 0022 -1 6267 6231 6079 186 150 4.79 99 - - - 99 - - 0023 -3 6500 6404 6237 261 165 1.06 99 - - - - - 99 0024 +1 6334 6337 6663 327 324 -1.69 99 99 - - - - - 0025 -1 6672 6549 6424 246 123 3.60 96 3 - - 96 - - -1 6996 6834 6673 321 159 -1.78 0 - 99 - 0 - - +3 6867 6909 7043 174 132 -5.44 0 0 99 0 - 0 - +1 6814 6856 7050 234 192 -10.24 0 0 99 - - 0 - -1 7149 7137 6997 150 138 -1.25 0 - 99 - 0 0 - +1 7051 7063 7206 153 141 -6.34 0 0 99 - - 0 - 0026 -1 7284 7278 7150 132 126 2.55 53 - 46 - 53 0 - -1 7482 7476 7345 135 129 -1.61 0 - 99 - 0 0 - -3 7571 7511 7386 183 123 -6.46 0 - 98 - - 1 0 0027 -2 7735 7669 6722 1011 945 -0.07 0 - 99 - - 0 - -1 7878 7815 7693 183 120 -3.40 0 0 99 - 0 - - +1 7855 7882 8058 201 174 -6.95 0 0 99 - - - - +3 8085 8139 8273 186 132 -5.75 0 - 1 0 - 98 - -2 8404 8377 7922 480 453 0.92 0 - 99 - - 0 - +1 8299 8350 8478 177 126 -8.15 0 0 99 - - - - 0028 +2 6500 6509 8563 2061 2052 4.34 99 - 99 - - - - 0029 +1 8479 8548 8748 267 198 -7.58 99 99 - - - - - -2 8833 8773 8624 207 147 0.12 0 - 99 - - 0 - +3 8862 8880 9005 141 123 -6.60 0 - 99 0 - - 0 -1 9207 9207 9070 135 135 -1.95 0 - 99 - 0 0 - 0030 +2 8564 8648 9274 708 624 8.88 99 - 99 - - - - -2 9340 9205 9023 315 180 1.76 0 - 99 - - 0 - 0031 +1 9175 9211 9351 174 138 -2.65 29 29 - 45 24 - - 0032 +3 9135 9222 9389 252 165 -3.04 99 - - 99 - - - +3 9390 9405 9539 147 132 -5.80 0 - 0 0 - 99 - -1 9684 9669 9490 192 177 -6.87 0 - 0 - 0 99 - +2 9275 9563 9688 411 123 -3.24 0 - 0 - 0 99 - -3 9740 9713 9588 150 123 -10.17 0 - - - - 99 0 0033 -2 9763 9760 9341 420 417 5.79 99 - - - - 99 - +3 9603 9621 9767 162 144 -2.56 0 - - 0 - 99 - 0034 -1 9978 9933 9727 249 204 2.40 99 - - - 99 - - +3 10038 10098 10256 216 156 -3.60 0 0 - 0 99 - - 0035 +1 9844 9970 10401 555 429 0.29 99 99 - - - - - +3 10257 10311 10490 231 177 -8.09 0 - - 0 99 - - +2 10466 10640 10789 321 147 -1.33 0 - 0 - 99 0 - -2 10795 10741 10520 273 219 -7.01 0 - 0 - 99 0 - -3 10895 10895 10770 123 123 -9.91 0 0 - - 99 - 0 +2 10949 10961 11098 147 135 1.25 0 0 0 0 99 - - -2 11119 11104 10967 150 135 -5.06 0 0 - 0 99 0 - +1 10900 10996 11127 225 129 -0.46 0 0 - - 99 - - 0036 -1 11145 11145 9979 1164 1164 7.81 99 - - - 99 - - +2 11099 11192 11326 225 132 -5.58 0 0 0 - 99 0 - -3 11558 11555 11433 123 120 -3.95 0 1 0 - 98 - 0 +2 11327 11366 11728 399 360 -4.11 0 0 0 - 99 - - -2 11833 11797 11474 357 321 -8.33 0 0 - - 99 0 - 0037 -1 12168 12159 11164 1002 993 3.75 99 0 - - 99 - - 0038 +1 11155 12202 12354 1197 150 2.37 99 99 - - - - 0 +2 12233 12284 12418 183 132 -6.30 0 - 0 - 99 0 - -2 12736 12706 12467 267 237 -8.78 0 0 - - 99 0 - -3 12815 12791 12660 153 129 -5.97 0 0 - - 99 - 0 +2 12746 12752 12880 132 126 -5.37 0 0 0 0 99 - - +3 12675 12711 12896 219 183 -9.39 0 0 - 0 99 - - +1 12355 12727 12939 582 210 -1.50 0 0 - - 99 - - +2 12914 12953 13078 162 123 -5.65 0 0 0 - 99 - - +1 12940 13129 13299 357 168 2.51 0 0 0 - 99 0 - +2 13079 13154 13330 249 174 -4.96 0 - 0 - 99 0 - +3 13194 13194 13346 150 150 -6.75 0 - - 0 99 0 - 0039 -1 13440 13344 12223 1215 1119 3.57 99 - - - 99 - - +3 13473 13629 13793 318 162 -0.03 0 - 0 0 - 99 - +1 13732 13747 13887 153 138 -7.86 0 0 0 - - 99 - +2 13586 13604 13948 360 342 0.93 0 - 0 - - 99 - 0040 -2 14047 14014 13358 687 654 7.17 99 - - - - 99 - +3 13998 14013 14156 156 141 -1.15 0 - 93 0 5 - - +3 14163 14172 14312 147 138 0.96 2 - 97 2 0 - - -1 14364 14184 14005 357 177 0.97 0 - 99 - 0 - - 0041 +2 14009 14009 14425 414 414 4.76 99 - 99 - - - - -3 14435 14387 14184 249 201 -1.90 0 - 99 - - - 0