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_NSLN010000011.1529.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_NSLN010000011.1529.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_NSLN010000011.1529.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_NSLN010000011.1529.AOI_01 Sequence length = 14565 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 +3 87 216 395 306 177 -3.95 0 0 99 0 - - - 0001 +1 214 331 456 240 123 -4.52 98 98 1 - - - - -3 509 491 357 150 132 -11.74 0 - 99 - - - 0 0002 -1 603 597 457 144 138 -2.75 65 - 34 - 65 - - 0003 +2 2 464 754 750 288 -3.52 99 - 99 - - - - -2 955 862 716 237 144 -6.84 0 - - 99 - 0 - -2 1144 1135 956 186 177 -10.52 0 - - 0 - 0 99 +1 1141 1141 1275 132 132 -2.02 0 0 - 0 - - 99 -2 1345 1267 1145 198 120 -10.65 0 0 - 0 - 0 99 -2 1546 1468 1346 198 120 -10.65 0 0 - 0 - 0 99 0004 +3 669 705 1976 1305 1269 2.23 0 - - 0 - - 99 +3 1977 1983 2390 411 405 -0.11 0 - - 0 - - 99 +1 2302 2305 2457 153 150 2.02 1 1 - - - - 98 0005 -3 2480 2480 726 1752 1752 7.52 99 - - - - - 99 +2 2465 2483 2605 138 120 1.64 0 - 0 - - 99 - +2 2606 2609 2770 162 159 0.98 0 - 0 - - 99 - +2 2771 2816 2950 177 132 -2.73 0 - 0 0 - 99 - +3 2811 2838 2966 153 126 -4.23 1 - - 1 - 98 - 0006 -3 3089 3074 2937 150 135 0.44 99 - - - - 0 99 0007 +3 2973 2985 3119 144 132 -2.00 99 - - 99 - 0 - +3 3120 3123 3245 123 120 -12.57 0 44 - 0 55 0 - 0008 -2 3277 2914 2477 798 435 5.41 99 - - - - 99 - 0009 +1 3025 3064 3318 291 252 2.82 24 24 - - 75 - - +2 3176 3311 3475 297 162 -6.69 0 - 0 0 99 - - +3 3306 3345 3515 207 168 -8.44 0 - - 0 99 - - -3 3575 3575 3450 123 123 -7.54 0 11 - - 88 - 0 +1 3439 3475 3597 156 120 4.61 0 0 - - 99 - - +2 3701 3728 3889 186 159 -2.44 0 1 0 - 98 - - +1 3649 3652 3909 258 255 1.84 0 0 - - 99 - - -3 4217 4178 4035 180 141 -10.65 0 73 - - 26 - 0 +1 3910 3997 4314 402 315 2.03 1 1 - - 98 - - 0010 -1 4344 4290 3037 1305 1251 3.90 99 - - - 99 - - +1 4717 4747 4875 156 126 -0.74 0 0 - 0 0 - 99 0011 -3 5036 5006 4317 717 687 11.94 99 - - 0 - - 99 0012 +3 4266 4527 5048 780 519 0.78 99 - - 99 - - - 0013 +1 4876 4891 5073 195 180 -1.53 99 99 - - - - - +3 5079 5091 5225 144 132 -6.61 0 0 98 0 - - - +1 5074 5104 5235 159 129 -6.34 1 1 98 - - - - 0014 -2 5368 5359 5222 144 135 -1.86 14 - 0 85 - 14 - 0015 +2 5063 5171 5416 351 243 -4.32 99 - 99 - - - - +1 5284 5308 5436 150 126 -5.26 0 0 - 99 - - - +1 5437 5524 5682 243 156 -6.67 0 0 0 99 - - 0 +2 5417 5501 5704 285 201 -9.11 0 - 0 99 - - 0 -2 5797 5665 5537 258 126 -4.24 0 0 0 99 - 0 0 0016 +3 5226 5346 5846 618 498 7.86 99 - - 99 - - - -3 5882 5726 5379 501 345 0.30 0 - - 99 - - 0 0017 +2 5711 5843 5968 255 123 -1.67 48 - 48 51 - - - +3 5847 5970 6158 309 186 -2.23 1 98 - 1 - 0 - 0018 +1 5887 5941 6162 273 219 0.53 99 99 - - - 0 - -2 6181 5977 5852 327 123 -5.20 1 - - 98 - 1 - +2 6104 6113 6253 147 138 0.53 0 - 0 - 99 - - 0019 -1 6267 6231 6079 186 150 5.09 99 - - - 99 - - 0020 -3 6500 6404 6237 261 165 0.69 99 - - - - - 99 0021 +1 6334 6367 6663 327 294 -4.14 99 99 - - - - - 0022 -1 6672 6618 6424 246 192 2.44 99 0 - - 99 - - -1 6996 6834 6673 321 159 -3.06 0 - 99 - 0 - - +3 6867 6909 7043 174 132 -10.70 0 0 99 0 - 0 - +1 6814 6856 7050 234 192 -9.13 0 0 99 - - 0 - -1 7149 7137 6997 150 138 -2.06 0 - 99 - 0 0 - +1 7051 7063 7206 153 141 -3.61 0 0 99 - - 0 - -1 7284 7278 7150 132 126 1.60 0 - 99 - 0 0 - -1 7482 7476 7345 135 129 -2.93 0 - 99 - 0 0 - -3 7571 7511 7386 183 123 -9.76 0 - 99 - - 0 0 -1 7878 7815 7693 183 120 -2.81 0 0 99 - 0 0 - +1 7855 7882 8058 201 174 -8.10 0 0 99 - - 0 - +3 8085 8127 8273 186 144 -7.54 0 - 96 0 - 3 - 0023 -2 8404 8377 6722 1680 1653 0.71 0 - 99 - - 0 - +1 8299 8350 8478 177 126 -7.29 0 0 99 - - - - 0024 +2 6500 6509 8563 2061 2052 9.81 99 - 99 - - - - 0025 -3 8645 8582 8412 231 168 -1.88 99 - - - - - 99 0026 +1 8479 8548 8748 267 198 -6.66 99 99 - - - - - -2 8833 8773 8624 207 147 2.36 0 - 99 - - 0 - +3 8862 8880 9005 141 123 -6.85 0 - 99 0 - - 0 -1 9207 9207 9070 135 135 -3.34 0 - 99 - 0 0 - 0027 +2 8600 8648 9274 672 624 8.04 99 - 99 - - - - -2 9340 9205 9023 315 180 3.00 0 - 99 - - 0 - 0028 +1 9175 9211 9351 174 138 -3.87 18 18 - 66 14 - - 0029 +3 9135 9222 9389 252 165 -3.83 99 - - 99 - - - +3 9390 9405 9539 147 132 -6.33 0 - 0 0 - 99 - -1 9684 9642 9490 192 150 -7.91 0 - 0 - 0 99 - +2 9275 9356 9688 411 330 -0.11 0 - 0 - - 99 - -3 9740 9713 9588 150 123 -10.18 0 - - - - 99 0 0030 -2 9763 9760 9341 420 417 6.16 99 - - - - 99 - +3 9603 9621 9767 162 144 -1.77 0 - - 0 - 99 - 0031 -1 9978 9933 9727 249 204 0.44 99 - - - 99 - - +3 10038 10098 10259 219 159 -5.50 0 0 - 0 99 - - +1 9844 10096 10311 465 213 2.03 0 0 - - 99 - - +2 10469 10643 10792 321 147 -0.96 0 - 0 - 99 0 - -2 10798 10744 10523 273 219 -5.81 0 - 0 - 99 0 - -3 10898 10898 10773 123 123 -10.15 0 0 - - 99 - 0 +2 10952 10976 11101 147 123 0.87 0 0 0 0 99 0 - +1 10903 10999 11130 225 129 -0.14 0 0 - - 99 - - 0032 -1 11148 11148 9979 1167 1167 8.62 99 - - - 99 - - +2 11102 11195 11329 225 132 -2.53 0 0 0 - 99 0 - -3 11561 11558 11436 123 120 -8.66 0 2 0 - 97 - 0 +2 11330 11447 11731 399 282 -3.41 0 0 0 - 99 - - -2 11836 11800 11477 357 321 -7.06 0 0 - - 99 0 - 0033 -1 12171 12159 11167 1002 990 4.65 99 0 - - 99 - - 0034 +1 11158 11170 12357 1197 1185 0.71 99 99 - - - - - +2 12236 12287 12421 183 132 -3.77 0 - 0 - 99 0 - -2 12739 12709 12470 267 237 -9.40 0 0 - - 99 0 - -3 12818 12791 12663 153 126 -7.16 0 0 - - 99 - 0 +2 12749 12755 12883 132 126 -5.30 0 0 0 0 99 - - +3 12678 12714 12899 219 183 -9.10 0 0 - 0 99 - - +1 12358 12448 12942 582 492 0.70 0 0 - - 99 - - +2 12917 12956 13081 162 123 -5.71 0 0 0 - 99 - - +1 12943 13132 13302 357 168 3.89 0 0 0 - 99 0 - +2 13082 13157 13333 249 174 -5.21 0 - 0 - 99 0 - +3 13197 13197 13349 150 150 -7.81 0 - - 0 99 0 - 0035 -1 13443 13347 12226 1215 1119 4.69 99 - - - 99 - - +3 13476 13632 13796 318 162 -0.02 0 - 0 0 - 99 - +1 13735 13750 13890 153 138 -11.05 0 0 2 - - 97 - +2 13589 13607 13951 360 342 2.00 0 - 0 - - 99 - 0036 -2 14050 13936 13361 687 573 3.27 99 - - - - 99 - +3 14001 14016 14159 156 141 -3.70 0 - 64 0 34 - - 0037 -1 14265 14187 14008 255 177 -1.94 26 - 73 - 26 - - 0038 +2 14012 14192 14326 312 132 2.99 99 - 99 - - - 0 0039 -2 14377 14377 14252 123 123 -2.06 99 - - - - 99 - 0040 -1 14412 14403 14266 144 135 -7.87 99 - - - 99 - -