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_NSLP010000261.1929.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_NSLP010000261.1929.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_NSLP010000261.1929.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_NSLP010000261.1929.AOI_01 Sequence length = 14436 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 0001 +2 197 260 391 192 129 2.42 99 0 99 - - - - 0002 -3 470 443 300 168 141 -0.72 79 1 - - 18 - 79 0003 -1 516 465 289 225 174 -2.34 64 35 - - 64 - - 0004 +1 223 388 558 333 168 -1.18 99 99 - - - - - 0005 +1 577 592 723 144 129 -1.44 90 90 - - 9 - - 0006 +3 810 822 1010 198 186 1.60 99 0 - 99 - - - +1 790 919 1152 360 231 -10.64 0 0 0 - - 99 - 0007 -2 1267 1246 899 366 345 7.97 99 - 0 - - 99 - 0008 +2 893 932 1378 483 444 2.10 99 - 99 - - - - -3 1406 1328 1203 201 123 -3.10 6 0 93 - - - 6 +2 1379 1382 1585 204 201 -0.95 0 0 0 - - 99 - +1 1339 1369 1758 417 387 -6.84 0 0 - - - 99 - -3 1841 1685 1551 288 132 -8.59 0 0 - 0 - 99 0 +2 1718 1727 1852 132 123 -1.11 0 - 0 - - 99 - 0009 -2 1879 1864 1268 609 594 5.11 99 - - - - 99 - 0010 +3 1824 1839 1970 144 129 -5.20 88 11 - 88 - - - +1 2071 2233 2424 351 189 -1.80 0 0 - - - - 99 +3 2295 2355 2582 285 225 2.93 0 - - 0 - - 99 +1 2587 2614 2742 153 126 -4.61 0 0 - 0 - - 99 +3 2583 2619 2774 189 153 -5.95 0 - - 0 - - 99 0011 -3 2801 2786 2040 759 744 6.70 99 - - - - - 99 0012 +1 2743 2788 3324 579 534 -1.32 99 99 - - - - - -2 3526 3412 3263 261 147 -7.47 0 - - - 99 0 - 0013 -1 3729 3711 2791 936 918 4.35 99 - - - 99 - - +2 3467 3596 3775 306 177 -4.76 0 97 0 2 - - - 0014 +3 3594 3711 3836 240 123 -4.56 93 6 - 93 - - - -2 3889 3871 3737 150 132 -8.08 0 99 - - - 0 - 0015 -3 3983 3977 3837 144 138 0.19 82 17 - - - - 82 0016 +1 3379 3847 4134 753 285 -2.49 99 99 - - - - - +1 4138 4147 4314 174 165 -8.56 0 0 0 - - 99 - 0017 -2 4342 4312 4106 234 204 6.14 99 - 0 - - 99 - 0018 +2 4049 4145 4348 297 201 0.19 99 - 99 - - - - +2 4715 4745 4873 156 126 -3.44 0 0 0 - 99 0 - 0019 -1 5034 5004 4267 765 735 9.66 99 - - - 99 - - 0020 +1 4330 4525 5046 714 519 0.16 99 99 - - - - - 0021 +2 4874 4928 5071 195 141 -2.62 99 - 99 - - - - +1 5077 5089 5223 144 132 -5.26 1 1 8 90 - - - +2 5072 5102 5233 159 129 -5.46 0 - 0 99 - - - -3 5366 5360 5220 144 138 -3.80 0 99 - 0 - - 0 0022 +3 5061 5169 5414 351 243 -5.71 99 - - 99 - - - +2 5282 5306 5434 150 126 -6.51 0 99 0 - - - - +2 5435 5522 5680 243 156 -6.33 0 99 0 0 0 - - +3 5415 5499 5702 285 201 -7.18 0 99 - 0 0 - - -3 5795 5663 5535 258 126 -3.81 0 99 0 0 0 - 0 0023 +1 5224 5254 5844 618 588 6.08 99 99 - - - - - -1 5880 5724 5377 501 345 0.51 0 99 - - 0 - - 0024 +3 5763 5841 5966 201 123 -2.68 69 4 - 69 - 25 - -2 6010 5902 5759 249 141 -6.97 2 - - 97 - 2 - 0025 +1 5845 5908 6048 201 138 2.22 26 26 - - 72 - 1 0026 -3 6077 5975 5850 225 123 -5.37 29 44 - - - 25 29 0027 +2 5918 5939 6157 237 216 -0.84 58 - 58 - 41 - - 0028 -1 6180 6051 5899 279 150 2.24 96 - - - 96 - 3 +1 6103 6112 6252 147 138 1.78 9 9 - - - - 90 0029 -3 6395 6230 6078 315 150 3.50 99 - - - - - 99 0030 +1 6334 6337 6483 147 144 -3.26 14 14 - 85 - - - 0031 +3 6261 6330 6665 402 333 -1.51 99 - - 99 - - - 0032 -3 6674 6551 6426 246 123 2.68 95 - - 4 - - 95 -3 6998 6836 6675 321 159 -3.13 0 99 - - - - 0 +2 6869 6911 7045 174 132 -8.57 0 99 0 0 0 - - +3 6816 6858 7052 234 192 -9.29 0 99 - 0 0 - - -3 7151 7121 6999 150 120 -2.14 0 99 - - 0 - 0 +3 7053 7065 7208 153 141 -4.20 0 99 - 0 0 - - -3 7286 7280 7152 132 126 3.53 0 99 - - 0 - 0 -3 7484 7478 7347 135 129 -3.31 0 99 - - 0 - 0 -3 7880 7817 7695 183 120 -3.55 0 99 - 0 0 - 0 +3 7857 7884 8060 201 174 -7.62 0 99 - 0 0 - - +2 8087 8129 8305 216 174 -5.55 0 99 0 - 0 - - 0033 -1 8406 8379 6724 1680 1653 0.55 0 99 - - 0 - - +3 8301 8352 8480 177 126 -4.94 0 99 - 0 - - - 0034 +1 6502 6511 8565 2061 2052 9.84 99 99 - - - - - 0035 +3 8481 8550 8750 267 198 -8.05 99 - - 99 - - - -1 8835 8775 8626 207 147 0.54 0 99 - - 0 - - +2 8864 8882 9007 141 123 -9.68 0 99 0 - - 0 - 0036 +1 8566 8650 9276 708 624 9.41 99 99 - - - - - -1 9375 9207 9025 348 180 3.67 0 99 - - 0 - - 0037 +3 9177 9213 9389 210 174 -4.23 96 - 3 96 - - - +3 9390 9405 9539 147 132 -4.15 0 - 0 0 - 99 - -1 9684 9642 9490 192 150 -9.68 0 - 0 - 0 99 - +2 9137 9563 9688 549 123 -1.61 0 - 0 - 0 99 - -3 9740 9713 9588 150 123 -9.78 0 - - - - 99 0 +3 9603 9663 9797 192 132 -0.48 10 - - 10 - 89 - 0038 -2 9979 9934 9341 636 591 6.97 99 - - - - 99 - +1 10039 10099 10257 216 156 -3.40 0 0 0 - - 99 - 0039 +2 9845 9971 10309 462 336 1.11 99 - 99 - - - - +1 10258 10312 10491 231 177 -9.24 0 0 - - - 99 - +3 10467 10641 10790 321 147 -0.10 0 - - 0 - 99 0 -3 10796 10742 10521 273 219 -6.58 0 - - 0 - 99 0 -1 10896 10896 10771 123 123 -10.08 0 - 0 - 0 99 - +3 10950 10974 11099 147 123 3.26 0 0 0 0 - 99 0 +2 10901 10997 11128 225 129 0.37 0 - 0 - - 99 - 0040 -2 11146 11146 9980 1164 1164 8.32 99 - - - - 99 - +3 11100 11193 11327 225 132 -4.19 0 - 0 0 - 99 0 -1 11559 11556 11434 123 120 -6.30 0 - 1 0 0 98 - +3 11328 11445 11729 399 282 -4.32 0 - 0 0 - 99 - -3 11834 11798 11475 357 321 -7.77 0 - 0 - - 99 0 0041 -2 12169 12160 11165 1002 993 4.19 99 - 0 - - 99 - 0042 +2 11156 12203 12355 1197 150 2.91 99 - 99 - 0 - - +3 12234 12249 12419 183 168 -5.57 0 - - 0 - 99 - +1 12337 12379 12510 171 129 -6.00 0 0 0 - - 99 - -3 12737 12707 12468 267 237 -9.93 0 - 0 - - 99 0 -1 12816 12792 12661 153 129 -5.73 0 - 0 - 0 99 - +3 12747 12753 12881 132 126 -6.74 0 0 0 0 - 99 - +1 12676 12712 12897 219 183 -9.48 0 0 0 - - 99 - +2 12356 12446 12940 582 492 0.08 0 - 0 - - 99 - +3 12915 12954 13079 162 123 -6.29 0 - 0 0 - 99 - +2 12941 13130 13300 357 168 1.90 0 - 0 0 - 99 0 +3 13080 13155 13331 249 174 -6.30 0 - - 0 - 99 0 +1 13195 13195 13347 150 150 -6.14 0 0 - - - 99 0 0043 -2 13441 13345 12224 1215 1119 5.25 99 - - - - 99 - +1 13474 13630 13794 318 162 1.54 1 1 - 0 - - 98 +2 13733 13748 13888 153 138 -10.11 0 - 0 0 - - 99 +3 13587 13605 13949 360 342 1.12 0 - - 0 - - 99 0044 -3 14048 14015 13359 687 654 3.77 99 - - - - - 99 +1 13999 14014 14157 156 141 -2.37 1 1 - 6 - 92 - 0045 -2 14263 14185 14006 255 177 -0.20 15 - - 84 - 15 - 0046 +3 14010 14010 14333 321 321 1.75 99 - - 99 - - - 0047 -1 14409 14370 14185 222 183 -6.94 99 - - - 99 - -