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_NSLX010000371.2342.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_NSLX010000371.2342.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_NSLX010000371.2342.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_NSLX010000371.2342.AOI_01 Sequence length = 15251 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 0001 +2 233 242 382 147 138 -0.21 27 - 27 - 72 - - 0002 -1 396 360 208 186 150 0.98 99 - - - 99 - - +2 485 488 610 123 120 -7.10 3 13 3 - - - 83 0003 -3 629 533 366 261 165 -0.84 99 - - - - - 99 0004 +1 463 496 792 327 294 -4.05 99 99 - - - - - 0005 -1 801 678 553 246 123 2.03 92 7 - - 92 - - -1 1125 963 802 321 159 -3.13 0 - 99 - 0 - - +3 996 1038 1172 174 132 -9.70 0 0 99 0 - 0 - +1 943 985 1179 234 192 -12.16 0 0 99 - - 0 - -1 1278 1248 1126 150 120 -2.03 0 - 99 - 0 0 - +1 1180 1192 1335 153 141 -4.43 0 0 99 - - 0 - -1 1413 1407 1279 132 126 2.03 0 - 99 - 0 0 - -1 1611 1605 1474 135 129 -3.90 0 - 99 - 0 0 - -3 1700 1640 1515 183 123 -6.51 0 - 99 - - 0 0 -1 2007 1944 1822 183 120 -4.23 0 0 99 - 0 0 - +1 1984 2011 2187 201 174 -7.42 0 0 99 - - 0 - +3 2214 2256 2402 186 144 -6.40 0 - 99 0 - 0 - 0006 -2 2533 2506 851 1680 1653 0.08 0 - 99 - - 0 - +1 2428 2479 2607 177 126 -6.78 0 0 99 - - - - 0007 +2 629 638 2692 2061 2052 9.61 99 - 99 - - - - 0008 -3 2774 2756 2541 231 213 -3.93 99 - - - - - 99 +1 2608 2731 2877 267 144 -9.26 0 0 99 - - - - -2 2962 2902 2753 207 147 0.13 0 - 99 - - 0 - +3 2991 3009 3134 141 123 -8.65 0 - 99 0 - - 0 -1 3336 3336 3199 135 135 -0.93 0 - 99 - 0 0 - 0009 +2 2729 2777 3403 672 624 9.36 99 - 99 - - - - -2 3469 3334 3152 315 180 2.93 0 - 99 - - 0 - 0010 +1 3304 3340 3480 174 138 -3.18 28 28 - 66 5 - - 0011 +3 3264 3351 3518 252 165 -3.23 99 - - 99 - - - +3 3519 3534 3668 147 132 -4.71 0 - 0 0 - 99 - -1 3813 3771 3619 192 150 -8.92 0 - 0 - 0 99 - +2 3404 3692 3817 411 123 -1.93 0 - 0 - 0 99 - -3 3869 3842 3717 150 123 -11.43 0 - - - - 99 0 0012 -2 3892 3889 3470 420 417 6.45 99 - - - - 99 - +3 3732 3750 3896 162 144 -3.23 0 - - 0 - 99 - 0013 -1 4107 4062 3856 249 204 1.26 99 - - - 99 - - +3 4167 4227 4385 216 156 -3.10 0 0 - 0 99 - - +1 3973 4348 4530 555 180 1.83 0 0 - - 99 - - +3 4386 4440 4619 231 177 -9.20 0 - - 0 99 - - +2 4595 4769 4918 321 147 -0.74 0 - 0 - 99 0 - -2 4924 4870 4649 273 219 -7.51 0 - 0 - 99 0 - -3 5024 5024 4899 123 123 -10.53 0 0 - - 99 - 0 +2 5078 5090 5227 147 135 2.77 0 0 0 0 99 - - +1 5029 5125 5256 225 129 -2.48 0 0 - - 99 - - 0014 -1 5274 5274 4108 1164 1164 8.48 99 - - - 99 - - +2 5228 5321 5455 225 132 -4.11 0 0 0 - 99 0 - -3 5687 5684 5562 123 120 -5.51 0 18 0 - 81 - 0 +2 5456 5573 5857 399 282 -4.53 0 0 0 - 99 - - -2 6055 5926 5603 450 321 -8.42 0 0 - - 99 0 - 0015 -1 6297 6288 5293 1002 993 3.92 99 0 - - 99 - - 0016 +1 5284 5728 6483 1197 753 0.12 99 99 - - - - - +2 6362 6413 6547 183 132 -5.76 0 - 0 - 99 0 - -2 6865 6835 6596 267 237 -9.47 0 0 - - 99 0 - -3 6944 6917 6789 153 126 -6.16 0 0 - - 99 - 0 +2 6875 6881 7009 132 126 -7.49 0 0 0 0 99 - - +3 6804 6840 7025 219 183 -9.50 0 0 - 0 99 - - +1 6484 6574 7068 582 492 -0.00 0 0 - - 99 - - +2 7043 7082 7207 162 123 -5.99 0 2 0 - 97 - - +1 7069 7258 7428 357 168 2.37 0 0 0 - 99 0 - +2 7208 7307 7459 249 150 -6.69 0 - 0 - 99 0 - +3 7323 7323 7475 150 150 -5.72 0 - - 0 99 0 - 0017 -1 7569 7473 6352 1215 1119 4.40 99 - - - 99 - - +3 7602 7758 7922 318 162 -0.11 0 - 2 0 - 96 - +1 7861 7876 8016 153 138 -9.99 0 0 4 - - 95 - +2 7715 7733 8077 360 342 1.07 0 - 0 - - 99 - +1 8071 8161 8286 213 123 -3.91 2 2 - 21 - 75 - 0018 -2 8533 8092 7487 1044 603 3.01 99 - - - - 99 - 0019 +3 8127 8268 8558 429 288 0.23 99 - - 99 - - - 0020 -1 8697 8679 8314 381 363 -3.28 99 - - - 99 - - 0021 +1 8575 8620 8760 183 138 0.07 99 99 - - - - - 0022 -1 8829 8829 8704 123 123 -3.86 99 - - - 99 - - +2 8945 9164 9385 438 219 -8.25 0 - 0 99 - - 0 0023 +3 8811 8847 9449 636 600 5.71 99 - - 99 - - 0 -3 9542 9197 8826 714 369 2.14 0 - - 99 - - 0 +1 9316 9409 9639 321 228 -6.84 0 0 99 - - - - -1 9924 9918 9763 159 153 0.70 0 0 99 - 0 0 - 0024 +2 9386 9446 9997 609 549 8.21 99 - 99 - - - - 0025 -2 10051 10036 9704 345 330 3.25 99 0 - - - 99 - -3 10067 10055 9915 150 138 -7.50 0 - - 0 - 99 0 -1 10530 10446 10171 357 273 2.16 0 99 - - 0 - - -3 10622 10577 10287 333 288 -3.54 0 99 - - - - 0 +3 10398 10440 10730 330 288 -9.81 0 99 - 0 - - - -2 11023 10741 10592 429 147 -9.81 0 1 - - 98 0 - -3 11078 11078 10926 150 150 -1.94 0 99 - - 0 - 0 -1 11154 11142 10531 621 609 2.66 0 99 - - 0 - - 0026 +1 10051 10057 11271 1218 1212 5.41 99 99 - - - - - 0027 -1 11295 11283 11155 138 126 1.91 99 - - 0 99 - - -2 11575 11560 11384 189 174 1.07 0 - 99 - - 0 - -1 11640 11568 11446 192 120 -3.61 0 0 99 - 0 0 - +1 11419 11485 11742 321 255 -6.96 0 0 99 - - - - -3 11804 11789 11535 267 252 -4.93 0 - 99 - - - 0 0028 +2 11261 11282 11887 624 603 7.23 99 - 99 - - - - +1 11743 11761 11910 165 147 -7.97 1 1 - 98 - - - -2 11974 11974 11786 186 186 -4.74 0 - - 99 - 0 - -3 12092 12089 11904 186 183 -0.05 0 - 0 99 - - 0 0029 +3 11739 11955 12140 399 183 5.42 99 - 0 99 - - - 0030 -1 12171 12159 12031 138 126 -3.91 97 - 1 - 97 0 - 0031 -2 12292 12277 12017 273 258 -1.46 32 - 67 - - 32 - -1 12477 12471 12310 165 159 -3.16 0 0 99 - 0 0 - -3 12488 12461 12330 156 129 -8.54 0 0 97 - 0 2 0 +1 12283 12409 12567 282 156 -9.86 0 0 99 - - 0 - 0032 +2 11888 12137 12589 699 450 2.97 99 - 99 - - - - -2 12601 12436 12293 306 141 -2.68 0 0 99 - - 0 - 0033 -1 12630 12630 12496 132 132 -2.50 99 - - - 99 - 0 +1 12727 12742 12909 180 165 -4.79 0 0 0 1 - - 98 +2 12590 12731 13009 417 276 -10.95 0 - 0 0 - - 99 +1 12910 12982 13104 192 120 -3.56 0 0 - 22 - - 76 +2 13034 13085 13318 282 231 -8.62 0 - 0 99 - - 0 +1 13162 13243 13395 231 150 -8.50 0 0 - 99 - - 0 0034 +3 12561 12612 13535 972 921 2.68 99 - - 99 - - 0 0035 -3 13631 13211 12489 1140 720 0.14 99 - - - - - 99 +2 13514 13571 13693 177 120 -2.64 0 82 0 0 16 - - -1 13818 13737 13498 318 237 -2.22 0 99 - - 0 - - +3 13536 13749 13871 333 120 -4.08 0 99 0 0 - 0 - -2 13909 13813 13682 225 129 -10.09 0 99 - 0 0 0 - -3 14030 14027 13899 129 126 -4.39 0 99 - - - - 0 0036 +1 13396 13558 14079 681 519 2.42 99 99 - - - - - 0037 -2 14353 14338 14201 150 135 -7.27 99 - - - - 99 - 0038 -2 14536 14518 14387 147 129 -5.30 40 - - 59 - 40 - 0039 +1 14710 14716 14856 144 138 -0.41 99 99 0 - - - 0 0040 -3 14891 14816 14679 210 135 -6.47 99 - - - - - 99 0041 +2 14717 14798 14926 207 126 -6.37 99 - 99 - - - - 0042 -1 15021 14991 14827 192 162 -8.02 99 - - - 99 - - +2 14927 15014 15157 228 141 -2.21 0 - 0 27 - 72 - +3 14886 15000 15185 297 183 0.64 11 - - 11 - 88 - 0043 -2 15250 15142 14948 300 192 2.26 76 - 0 22 - 76 -