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_FUGG010000231.3023.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_FUGG010000231.3023.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_FUGG010000231.3023.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_FUGG010000231.3023.AOI_01 Sequence length = 14613 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 -2 577 463 314 261 147 -6.59 0 - - - 99 0 - +2 518 647 826 306 177 -6.22 0 99 0 0 - - - 0001 +3 645 762 887 240 123 -4.18 96 3 - 96 - - - -2 940 922 788 150 132 -5.46 3 96 - - - 3 - 0002 -3 1034 1028 888 144 138 -1.13 43 56 - - - - 43 0003 +1 376 895 1185 807 288 -2.91 99 99 - - - - - -1 1386 1293 1147 237 144 -6.12 0 - 99 - 0 - - -1 1575 1566 1387 186 177 -10.41 0 - 1 - 0 98 - +3 1572 1578 1706 132 126 -2.44 0 - 2 0 0 97 0 -1 1776 1698 1576 198 120 -11.34 0 - 2 0 0 97 0 0004 +2 1100 1139 2206 1104 1065 4.46 99 - 99 - - - - +2 2207 2213 2620 411 405 0.72 0 - 0 - - 99 - 0005 +3 2532 2535 2687 153 150 2.21 28 - - 28 - 71 - 0006 -2 2710 2710 1157 1551 1551 5.50 99 - - - - 99 - 0007 +1 2695 2704 2835 138 129 3.62 99 99 - - - - - +1 2836 2839 3000 162 159 1.42 0 0 - - 99 - - +1 3001 3046 3180 177 132 -0.67 0 0 0 - 99 - - +2 3041 3068 3196 153 126 -0.91 6 - 6 - 93 - - 0008 -2 3319 3304 3167 150 135 -0.43 98 - - - 1 98 - 0009 +2 3203 3215 3349 144 132 -1.30 99 - 99 - 0 - - +2 3350 3353 3475 123 120 -9.45 0 - 0 9 0 - 90 0010 -1 3507 3144 2707 798 435 3.99 99 - - - 99 - - +3 3255 3381 3548 291 165 1.87 1 - - 1 - - 98 +1 3406 3541 3705 297 162 -1.36 0 0 0 - - - 99 +2 3536 3575 3745 207 168 -6.14 0 - 0 - - - 99 -2 3805 3805 3680 123 123 -3.68 0 - - 57 - 0 42 0011 +3 3669 3702 3827 156 123 4.16 22 - - 22 - - 77 +1 3931 3958 4119 186 159 -2.52 0 0 - 0 - - 99 +3 3879 3882 4139 258 255 1.95 6 - - 6 - - 93 0012 -3 4340 4310 3267 1071 1041 3.19 99 - - - - - 99 +3 4713 4743 4871 156 126 -2.55 0 - 0 0 - 99 0 0013 -2 5032 5002 4265 765 735 4.60 99 - - - - 99 - 0014 +2 4328 4691 5044 714 351 1.84 99 - 99 - - - - 0015 +3 4872 4926 5069 195 141 -0.56 99 - - 99 - - - 0016 +2 5075 5087 5221 144 132 -2.80 81 13 81 5 - - - +3 5070 5100 5231 159 129 -5.11 3 96 - 3 - - - -1 5364 5355 5218 144 135 -3.56 0 0 99 - 0 - - 0017 +1 5059 5167 5412 351 243 -3.60 99 99 - - - - - +3 5280 5304 5432 150 126 -6.55 0 - 99 0 - - - +3 5433 5520 5678 243 156 -4.65 0 0 99 0 - 0 - +1 5413 5497 5700 285 201 -8.38 0 0 99 - - 0 - -1 5793 5661 5533 258 126 -7.05 0 0 99 0 0 0 - 0018 +2 5222 5252 5842 618 588 4.99 99 - 99 - - - - -2 5848 5722 5375 471 345 0.03 0 - 99 - - 0 - 0019 -2 6010 5974 5849 159 123 -3.39 96 - - 3 - 96 - 0020 +3 5826 5967 6161 333 192 1.39 99 - - 99 0 - - -1 6180 6000 5872 306 126 -5.05 2 - - 83 2 13 - +1 6103 6112 6252 147 138 -2.57 0 0 - - - - 99 0021 -3 6395 6230 6078 315 150 1.60 99 - - - - - 99 0022 +3 6261 6330 6665 402 333 0.05 99 - - 99 - - - 0023 -3 6674 6551 6426 246 123 3.62 81 - - 18 - - 81 -3 6998 6836 6675 321 159 -4.82 0 99 - - - - 0 +2 6869 6911 7045 174 132 -7.68 0 99 0 0 0 - - +3 6816 6858 7052 234 192 -9.64 0 99 - 0 0 - - -3 7151 7124 6999 150 123 -2.89 0 96 - - 3 - 0 +3 7053 7065 7208 153 141 -3.91 0 99 - 0 0 - - 0024 -3 7286 7280 7152 132 126 -0.49 56 42 - - 0 - 56 -3 7484 7478 7347 135 129 -5.18 0 58 - - 41 - 0 0025 -1 7563 7506 6724 837 780 1.05 0 99 - - 0 - - -2 7573 7513 7388 183 123 -6.79 0 81 - - 18 0 - -3 7880 7817 7695 183 120 -4.04 0 99 - 0 0 - 0 +3 7857 7884 8060 201 174 -7.30 0 1 - 0 98 - - +2 8087 8141 8275 186 132 -7.80 0 2 0 - 97 - - 0026 -1 8406 8379 7564 840 813 1.28 0 99 - - 0 - - +3 8301 8352 8480 177 126 -7.10 0 99 - 0 - - - 0027 +1 6502 6511 8565 2061 2052 3.00 99 99 - - - - - 0028 +3 8481 8550 8699 216 147 -5.73 99 - - 99 - - - -1 8835 8775 8626 207 147 0.94 0 99 - - 0 - - +2 8864 8882 9007 141 123 -4.17 0 99 0 - - 0 - -3 9209 9209 9072 135 135 -4.84 0 99 - - 0 - 0 0029 +1 8566 8650 9276 708 624 7.93 99 99 - - - - - -1 9342 9207 9025 315 180 1.71 0 99 - - 0 - - +3 9177 9213 9353 174 138 -3.67 10 - 87 10 - - 1 0030 +2 9137 9224 9391 252 165 -2.16 99 - 99 - - - - +2 9392 9407 9541 147 132 -4.66 0 0 0 - 99 - - -3 9686 9644 9492 192 150 -7.93 0 0 - - 99 - 0 +1 9277 9565 9690 411 123 -1.56 0 0 - - 99 - 0 -2 9742 9715 9590 150 123 -8.37 0 - - - 99 0 - 0031 -1 9765 9762 9343 420 417 5.34 99 - - - 99 - - +2 9605 9623 9769 162 144 -2.78 0 - 0 - 99 - - 0032 -3 9980 9935 9729 249 204 0.80 99 - - - - - 99 +2 10040 10100 10258 216 156 -3.33 0 - 0 67 - - 32 0033 +3 9846 9972 10403 555 429 0.90 99 - - 99 - - - +2 10259 10274 10423 162 147 -6.91 0 - 0 - - - 99 +1 10468 10642 10791 321 147 -3.76 0 0 - - 0 - 99 -1 10797 10743 10522 273 219 -6.18 0 0 - - 0 - 99 -2 10897 10897 10772 123 123 -8.39 0 - - 0 - 0 99 +1 10951 10975 11100 147 123 -0.69 2 2 0 0 0 - 96 +3 10902 10998 11129 225 129 -0.40 1 - - 1 - - 98 0034 -3 11147 11147 9981 1164 1164 3.09 99 - - - - - 99 +1 11101 11194 11328 225 132 -1.65 0 0 - 0 0 - 99 -2 11560 11557 11435 123 120 -7.92 0 0 - 39 - 0 60 +1 11329 11452 11730 399 276 -4.13 0 0 - 0 - - 99 -1 11835 11799 11476 357 321 -7.54 0 - - 0 0 - 99 0035 -3 12170 12161 11166 1002 993 3.31 99 - - 0 - - 99 0036 +3 11157 12204 12356 1197 150 -0.41 99 - - 99 - 0 - +1 12235 12286 12420 183 132 -6.68 0 0 - - 0 - 99 +3 12357 12447 12713 354 264 -0.52 1 - - 1 - - 98 -1 12738 12708 12469 267 237 -7.88 0 - - 0 0 - 99 +1 12748 12754 12882 132 126 -7.45 0 0 0 0 - - 99 +2 12677 12713 12898 219 183 -7.96 0 - 0 3 - - 96 +3 12714 12729 12941 225 210 -0.41 0 - - 0 - - 99 +1 12916 12955 13080 162 123 -5.72 0 0 - 0 - - 99 +3 12942 13134 13301 357 165 2.87 0 0 - 0 0 - 99 +1 13081 13180 13332 249 150 -8.88 0 0 - - 0 - 99 +2 13196 13196 13348 150 150 -6.45 0 - 0 - 0 - 99 0037 -3 13442 13346 12225 1215 1119 2.78 99 - - - - - 99 +2 13475 13631 13795 318 162 -1.13 0 0 0 - 99 - - +3 13734 13749 13889 153 138 -5.41 0 8 - 0 91 - - +1 13588 13606 13950 360 342 0.46 0 0 - - 99 - - 0038 +3 13944 14034 14159 213 123 -2.39 39 - 0 39 60 - - 0039 -1 14265 14016 13360 903 654 2.03 99 - - - 99 - - 0040 +2 14000 14192 14329 327 135 2.02 99 - 99 - - - 0 0041 -3 14405 14384 14187 216 195 -6.01 99 - - - - - 99 0042 -1 14469 14427 14266 201 159 -1.00 93 3 - - 93 3 - 0043 -2 14548 14518 14252 294 264 -2.34 99 - - - - 99 -