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_FUFD010000331.2774.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_FUFD010000331.2774.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_FUFD010000331.2774.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_FUFD010000331.2774.AOI_01 Sequence length = 19838 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 -1 219 216 67 150 147 -3.66 0 99 0 - 0 - - +2 2 74 355 351 279 -10.07 0 99 0 - - - - 0001 +1 1 4 429 426 423 5.18 99 99 - - - - - -1 450 363 220 228 141 -1.44 0 99 - - 0 - 0 -3 491 398 192 297 204 -0.40 0 99 - - - - 0 0002 -1 666 660 451 213 207 -5.26 98 - 1 - 98 - - 0003 +2 356 560 697 339 135 -6.00 99 - 99 - - - - 0004 +3 840 858 989 147 129 -5.40 17 - - 17 - 82 - 0005 +3 1023 1038 1175 150 135 -7.20 99 - - 99 - - - +2 1346 1349 1477 129 126 -3.96 0 - 0 - 99 - - +3 1467 1563 1694 225 129 -10.38 0 0 - 0 99 0 - -2 1840 1627 1505 333 120 -4.32 0 - - 0 99 0 0 -3 1862 1805 1683 177 120 -3.52 0 3 - - 96 0 0 +1 1558 1639 1878 318 237 -1.74 0 0 - - 99 - - 0006 -1 1980 1818 1297 681 519 2.66 99 - - - 99 - - -1 2214 2133 1981 231 150 -7.60 0 - 0 - 0 99 - -3 2342 2291 2058 282 231 -8.01 0 - 0 - - 99 0 -1 2466 2394 2272 192 120 -2.30 0 - 96 - 0 3 - -1 2649 2634 2467 180 165 -4.42 0 - 99 - 0 0 0 -3 2786 2645 2367 417 276 -11.10 0 - 99 - - 0 0 0007 -2 2815 2764 1841 972 921 3.35 99 - 0 - - 99 - 0008 +1 2746 2746 2880 132 132 -1.46 99 99 0 - - - - 0009 +2 1823 2165 2887 1062 720 1.17 99 - 99 - - - - +2 2888 2915 3046 156 129 -8.69 0 0 0 1 0 - 98 +1 2899 2905 3066 165 159 -4.10 0 0 - 0 0 - 99 +3 2775 2940 3083 306 141 -3.06 0 - - 0 0 - 99 -1 3162 2967 2809 351 156 -8.94 0 - - 0 0 - 99 0010 +1 3205 3217 3345 138 126 -3.77 88 88 - 4 - - 6 +3 3084 3099 3359 273 258 -2.15 0 - - 0 - - 99 +2 3284 3287 3472 186 183 -0.96 0 - 0 - - 99 0 0011 -3 3488 3239 2787 699 450 3.98 99 - - - - - 99 +3 3402 3402 3590 186 186 -3.53 0 - - 0 - 99 - -1 3633 3615 3466 165 147 -7.59 0 - - - 0 99 - 0012 -2 3637 3526 3236 399 288 3.48 99 - - - - 99 - +2 3572 3587 3841 267 252 -5.68 0 - 0 - - - 99 +1 3736 3808 3930 192 120 -3.60 0 0 - 0 0 - 99 -1 3957 3891 3634 321 255 -6.13 0 - - - 0 - 99 +3 3801 3816 3992 189 174 1.78 0 - - 0 - - 99 0013 -3 4115 4094 3489 624 603 7.63 99 - - - - - 99 0014 +1 4081 4093 4221 138 126 2.49 99 99 - - - 0 - +2 4298 4298 4450 150 150 -2.64 0 0 0 - 99 - - +3 4353 4635 4784 429 147 -9.04 0 92 - 0 7 - - +1 4222 4234 4845 621 609 3.13 0 0 - - 99 - - -2 4978 4936 4646 330 288 -8.89 0 - - - 99 0 - +2 4754 4799 5089 333 288 -3.13 0 - 0 - 99 - - +1 4846 4954 5205 357 249 2.55 0 0 - - 99 - - 0015 -1 5325 5319 4105 1218 1212 5.79 99 - - - 99 - - +3 5451 5457 5612 159 153 0.89 0 - 0 0 - 99 0 +2 5309 5393 5671 360 276 3.94 0 - 0 - - 99 0 0016 -2 5989 5929 5378 609 549 8.31 99 - - - - 99 - -3 6059 5966 5736 321 228 -6.06 0 - - - - 99 0 -2 6430 6211 5990 438 219 -6.90 0 0 - - 99 0 - +1 5833 5935 6549 714 612 2.14 0 0 - - 99 - - 0017 -1 6564 6528 5926 636 600 6.40 99 0 - - 99 - - 0018 +3 6546 6546 6668 120 120 -0.64 65 - 0 65 - - 34 0019 +3 6669 6711 6872 201 159 -0.05 20 - 0 20 - - 78 0020 +2 6482 6596 6937 453 339 -6.06 99 - 99 - - - - 0021 -2 6958 6949 6809 147 138 1.60 90 0 - - - 90 9 0022 -3 7124 7022 6708 414 312 1.28 99 - - - - - 99 -2 7180 7090 6965 213 123 -3.82 1 75 - - - 1 23 -2 7390 7375 7235 153 138 -11.13 0 98 - - 1 0 - -1 7536 7518 7174 360 342 1.59 0 99 - - 0 - - -3 7649 7493 7329 318 162 1.64 0 99 - - 0 - 0 0023 +1 6733 7108 7764 1029 654 3.96 99 99 - - - - - -3 7928 7928 7776 150 150 -5.54 0 0 99 - - - 0 -1 8043 7944 7792 249 150 -6.50 0 0 99 - 0 - - -2 8182 7993 7823 357 168 2.67 0 0 99 - 0 0 - -1 8208 8169 8044 162 123 -5.60 0 - 99 - 0 0 - -1 8376 8370 8242 132 126 -5.89 0 - 99 - 0 0 0 -3 8447 8411 8226 219 183 -9.86 0 - 99 - - 0 0 +3 8307 8331 8462 153 129 -5.81 0 - 99 0 - 0 - +1 8386 8416 8655 267 237 -10.26 0 0 99 - - 0 - -2 8767 8677 8183 582 492 -0.13 0 - 99 - - 0 - -1 8889 8838 8704 183 132 -4.97 0 0 99 - 0 - - 0024 +2 7682 7778 8899 1215 1119 5.23 99 - 99 - - - - +1 9289 9325 9648 357 321 -7.65 0 0 99 - - 0 - +3 9564 9567 9689 123 120 -6.33 0 - 93 0 0 6 - -1 9795 9744 9394 399 348 -2.92 0 - 99 - 0 0 - 0025 +2 8954 8963 9958 1002 993 4.28 99 - 99 - - 0 - 0026 -2 9967 8920 8768 1197 150 1.71 99 - - 0 - 99 - -1 10023 9930 9796 225 132 -3.42 0 0 99 - 0 0 - -1 10173 10161 10024 147 135 4.37 0 - 99 - 0 0 0 -2 10222 10126 9995 225 129 -0.19 0 - 99 - - 0 - +3 10227 10227 10352 123 123 -10.79 0 - 99 0 - 0 - +1 10327 10381 10602 273 219 -8.39 0 0 99 - 0 - - -1 10656 10482 10333 321 147 -0.92 0 0 99 - 0 - - -3 11084 11024 10866 216 156 -5.05 0 - 99 - - 0 0 0027 +2 9977 9977 11143 1164 1164 8.69 99 - 99 - - - - 0028 -2 11278 11152 10814 462 336 0.88 99 - - - - 99 - 0029 +2 11144 11189 11368 222 177 2.99 99 - 99 - - - - 0030 +1 11380 11458 11604 222 144 -6.05 99 99 - - - - - -3 11765 11747 11601 162 144 -3.05 0 99 - - - - 0 +3 11628 11655 11780 150 123 -10.45 0 99 - 0 - - - +2 11684 11726 11878 192 150 -9.27 0 99 0 - 0 - - -3 11978 11963 11829 147 132 -4.90 0 99 - - 0 - 0 0031 +1 11605 11608 12027 420 417 7.34 99 99 - - - - - -1 12093 11805 11680 411 123 -1.82 0 99 0 - 0 - - 0032 -2 12193 12157 12017 174 138 -3.07 21 - 19 - - 21 59 0033 -3 12233 12146 11979 252 165 -2.91 99 - - - - - 99 +2 12161 12161 12298 135 135 0.26 0 0 0 - 99 - - +1 12028 12163 12345 315 180 3.31 0 0 - - 99 - - -3 12506 12488 12363 141 123 -9.50 0 - - 0 99 - 0 +1 12535 12595 12744 207 147 0.36 0 0 - - 99 - - 0034 -1 12804 12720 12094 708 624 9.91 99 - - - 99 - - 0035 -2 12889 12820 12620 267 198 -8.55 99 - - - - 99 - -2 13069 13018 12890 177 126 -6.04 0 - - - 99 0 - -3 13283 13229 13095 186 132 -7.79 0 0 - - 99 - 0 -2 13513 13486 13310 201 174 -8.66 0 0 - - 99 0 - +2 13490 13553 13675 183 120 -4.02 0 0 0 - 99 0 - +3 13797 13857 13982 183 123 -8.00 0 0 - 0 99 - - +2 13886 13892 14023 135 129 -2.75 0 0 0 - 99 - - +2 14084 14090 14218 132 126 3.77 0 0 0 - 99 - - -2 14317 14305 14162 153 141 -3.42 0 0 - - 99 0 - +2 14219 14246 14371 150 123 -2.25 0 0 0 - 99 - - -3 14501 14459 14325 174 132 -9.13 0 0 - - 99 0 0 -2 14554 14512 14318 234 192 -10.11 0 0 - - 99 0 - 0036 +1 12964 12991 14646 1680 1653 0.46 0 0 - - 99 - - +2 14372 14534 14695 321 159 -3.04 0 - 0 - 99 - - 0037 -1 14868 14859 12805 2061 2052 10.07 99 - - - 99 - - 0038 +2 14696 14819 14944 246 123 2.55 97 - 97 - - 2 - 0039 -2 15034 15031 14705 327 324 -3.16 99 - - - - 99 - 0040 +3 14868 14964 15131 261 165 0.94 99 - - 99 - - - -1 15264 15255 15115 147 138 0.34 1 - 98 - 1 - - 0041 +2 15101 15137 15289 186 150 3.73 99 - 99 - - - - 0042 +1 15187 15316 15495 306 177 -1.28 13 13 - - - 86 - 0043 +3 15357 15393 15518 159 123 -4.63 25 - - 25 - 74 - 0044 -2 15541 15400 15206 333 192 4.65 99 0 - - - 99 - +1 15574 15706 15834 258 126 -3.70 0 0 - 0 0 0 99 -2 15934 15847 15689 243 156 -5.78 0 - - 0 0 0 99 -1 15954 15870 15667 285 201 -7.62 0 - - 0 0 - 99 +3 15519 15645 15992 471 345 0.75 0 - - 0 - - 99 -2 16087 16063 15935 150 126 -5.39 0 - - - - 0 99 0045 -3 16145 16115 15525 618 588 7.29 99 - - - - - 99 +1 16003 16009 16149 144 138 -4.77 0 0 - - 0 - 99 0046 -1 16215 16200 15955 258 243 -5.75 99 - - - 99 - - 0047 -3 16292 16280 16146 144 132 -5.63 30 - - - - 69 30 0048 -2 16297 16267 16136 159 129 -6.91 99 - - - - 99 - 0049 -2 16495 16441 16298 195 141 -2.50 99 - - - - 99 - -2 16654 16624 16496 156 126 -1.58 0 - 0 99 - 0 0 0050 +3 16335 16365 17054 717 687 11.32 99 - - 99 - - 0 0051 -3 17105 16844 16323 780 519 0.04 99 - - - - - 99 +3 17154 17193 17336 180 141 -9.70 0 - 99 0 - 0 - -3 17465 17456 17289 174 165 -9.01 0 - 86 - - 13 0 0052 +2 17027 17117 17497 468 378 5.53 99 - 99 - - 0 - -2 17554 17458 17057 495 399 0.18 0 - 99 - - 0 - 0053 +1 17620 17626 17766 144 138 -0.97 73 73 - - - - 26 +2 17714 17732 17866 150 132 -8.48 0 - 0 - - - 99 0054 -1 18009 17892 17767 240 123 -4.21 94 - - - 94 - 5 -2 18136 18007 17828 306 177 -4.97 0 - - - 1 0 97 0055 -3 18278 18089 17469 807 618 -1.40 99 - - - - - 99 +2 18077 18191 18340 261 147 -8.31 0 - 0 99 - - - 0056 +3 17874 17892 18812 936 918 4.84 99 - - 99 - - - 0057 -3 18860 18815 18279 579 534 -1.14 99 - - - - - 99 -3 19016 18989 18861 153 126 -4.83 0 99 - - 0 - 0 -1 19020 18984 18829 189 153 -6.31 0 99 - - 0 - - -1 19308 19248 19021 285 225 4.29 0 99 - - 0 - - -3 19532 19370 19179 351 189 -0.17 0 99 - - - - 0 0058 +1 18802 18817 19563 759 744 7.17 99 99 - - - - - 0059 -2 19666 19639 19466 198 171 -6.20 99 - - - - 99 - 0060 +2 19493 19610 19762 267 150 -4.73 99 - 99 - - - -