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_NSLS010000101.1644.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_NSLS010000101.1644.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_NSLS010000101.1644.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_NSLS010000101.1644.AOI_01 Sequence length = 14727 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 0001 -1 405 201 4 399 195 2.51 99 - - - 99 - - 0002 +2 320 359 544 222 183 -8.18 99 - 99 - - - - 0003 -3 719 629 396 321 231 1.97 99 - - - - - 99 +1 466 544 723 255 177 -0.80 6 6 - - - - 93 -2 730 715 572 156 141 -3.25 0 82 - - - 0 16 -1 996 981 841 153 138 -8.86 0 - - 97 0 - 2 -3 1142 1124 780 360 342 1.82 0 - - 99 - - 0 -2 1255 1099 935 318 162 2.16 3 - - 95 - 3 0 0004 +3 681 714 1370 687 654 4.03 99 - - 99 - - - -2 1534 1534 1382 150 150 -4.99 0 99 - 0 - 0 - -3 1649 1574 1398 249 174 -5.72 0 99 - 0 - - 0 -1 1788 1599 1429 357 168 2.11 0 99 - 0 0 - 0 -3 1814 1775 1650 162 123 -5.57 0 99 - - 0 - 0 -3 1982 1976 1848 132 126 -6.65 0 99 - - 0 0 0 -2 2053 2017 1832 219 183 -9.64 0 99 - - 0 0 - +2 1913 1937 2068 153 129 -4.75 0 99 0 - 0 - - +3 1992 2022 2261 267 237 -9.11 0 99 - 0 0 - - -1 2373 2283 1789 582 492 -0.24 0 99 - - 0 - - -3 2495 2444 2310 183 132 -6.01 0 99 - 0 - - 0 0005 +1 1288 1384 2505 1215 1119 4.78 99 99 - - - - - +3 2895 2931 3254 357 321 -7.20 0 99 - 0 0 - - -3 3401 3350 3000 399 348 -3.26 0 99 - - 0 - 0 0006 +1 2560 2569 3564 1002 993 4.18 99 99 - - 0 - - 0007 -1 3573 3129 2374 1197 753 0.72 99 - - - 99 - - -3 3629 3536 3402 225 132 -4.17 0 99 - 0 0 - 0 -3 3779 3755 3630 147 123 2.72 0 99 - 0 0 0 0 -1 3828 3732 3601 225 129 -0.74 0 99 - - 0 - - +2 3833 3833 3958 123 123 -9.98 0 99 0 - 0 - - +3 3933 3987 4208 273 219 -6.59 0 99 - 0 - - 0 -3 4262 4088 3939 321 147 0.44 0 99 - 0 - - 0 -2 4690 4630 4472 216 156 -3.08 0 99 - - 0 0 - 0008 +1 3583 3583 4749 1164 1164 8.70 99 99 - - - - - -1 4830 4632 4420 408 210 1.26 0 99 - - 0 - - -2 5110 5092 4952 156 138 -3.14 0 - - 99 - 0 - +2 4973 5000 5125 150 123 -10.74 0 - 0 99 - - - +1 5029 5071 5223 192 150 -8.98 0 0 - 99 - - 0 -2 5323 5308 5174 147 132 -4.47 0 - - 99 - 0 0 0009 +3 4866 4914 5372 504 456 2.82 99 - - 99 - - - 0010 -2 5536 5500 5324 210 174 -2.98 99 - - - - 99 0 -3 5576 5150 5025 549 123 -2.11 0 0 - 99 - - 0 +2 5504 5504 5641 135 135 -1.95 0 0 0 - 99 - - +1 5338 5506 5688 348 180 2.93 0 0 - - 99 - - -3 5849 5831 5706 141 123 -8.91 0 - - 0 99 - 0 +1 5878 5938 6087 207 147 0.93 0 0 - - 99 - - 0011 -1 6147 6063 5437 708 624 9.33 99 - - - 99 - - 0012 -2 6232 6163 5963 267 198 -7.59 99 - - - - 99 - -2 6412 6361 6233 177 126 -6.09 0 - - - 99 0 - -3 6626 6572 6438 186 132 -6.90 0 26 - - 73 - 0 -2 6856 6829 6653 201 174 -6.83 0 0 - - 99 0 - +2 6833 6896 7018 183 120 -1.40 0 0 0 - 99 0 - +3 7140 7200 7325 183 123 -6.85 0 0 - 0 99 - - +2 7229 7235 7366 135 129 -2.95 0 0 0 - 99 - - +2 7427 7433 7561 132 126 2.69 0 0 0 - 99 - - -2 7660 7648 7505 153 141 -4.74 0 0 - - 99 0 - +2 7562 7574 7714 150 138 -2.20 0 0 0 - 99 - - -3 7844 7802 7668 174 132 -8.13 0 0 - - 99 0 0 -2 7897 7855 7661 234 192 -9.47 0 0 - - 99 0 - 0013 +1 6307 6334 7989 1680 1653 0.80 0 0 - - 99 - - +2 7715 7862 8038 321 174 -2.17 0 - 0 - 99 - - 0014 -1 8211 8202 6148 2061 2052 9.73 99 - - - 99 - - 0015 +2 8039 8093 8287 246 192 1.92 99 - 99 - - 0 - 0016 -2 8377 8374 8048 327 324 -2.45 99 - - - - 99 - 0017 -3 8450 8414 8274 174 138 0.70 31 - - 68 - - 31 0018 +3 8211 8307 8474 261 165 0.20 99 - - 99 - - - 0019 -2 8608 8599 8411 195 186 0.33 99 - - - - 99 - 0020 +3 8475 8481 8633 156 150 2.87 99 - - 99 - - - 0021 -3 8825 8771 8550 273 219 2.68 99 - 0 - - - 99 0022 +2 8531 8660 8860 327 198 -2.34 80 - 80 - 19 - - -1 8883 8742 8554 327 186 -1.10 0 - 0 - 0 - 99 +3 8916 9048 9176 258 126 -4.51 0 - 0 0 0 99 0 -1 9276 9189 9031 243 156 -5.37 0 - 0 - 0 99 0 -3 9296 9212 9009 285 201 -8.10 0 - 0 - - 99 0 +2 8861 8987 9334 471 345 0.29 0 - 0 - - 99 - -1 9429 9405 9277 150 126 -6.48 0 - - - 0 99 - 0023 -2 9487 9457 8867 618 588 6.65 99 - - - - 99 - +3 9345 9354 9491 144 135 -4.66 1 - - 1 - 98 0 0024 -3 9557 9542 9297 258 243 -4.09 99 - - - - - 99 0025 -2 9634 9622 9488 144 132 -5.29 18 - - - 81 18 - 0026 -1 9639 9609 9478 159 129 -5.42 99 - - - 99 - - 0027 -1 9837 9822 9640 195 180 -0.91 99 - - - 99 - - -1 9996 9966 9838 156 126 -1.87 0 0 99 - 0 0 - 0028 -2 10381 10186 9665 714 519 0.35 99 - - - - 99 - 0029 +2 9677 9707 10444 765 735 9.47 99 - 99 - - - - -2 10573 10564 10397 174 165 -8.39 0 99 - - 0 0 - 0030 +1 10369 10399 10605 234 204 6.05 99 99 - - 0 - - 0031 -1 10662 10566 10363 297 201 0.20 99 - - - 99 - - 0032 +3 10728 10734 10874 144 138 0.85 92 - - 92 - 7 - +1 10822 10840 10974 150 132 -7.16 0 0 - - - 99 - 0033 -3 11117 11000 10875 240 123 -4.23 94 - - - - 5 94 -1 11244 11115 10936 306 177 -4.44 0 - - - 0 97 1 0034 -2 11332 10867 10577 753 288 -1.81 99 - - - - 99 - +1 11185 11299 11448 261 147 -6.45 0 0 99 - - - - 0035 +2 10982 11000 11920 936 918 4.15 99 - 99 - - - - 0036 -2 11968 11923 11387 579 534 -0.79 99 - - - - 99 - -2 12124 12097 11969 153 126 -2.74 0 - - 99 - 0 0 -3 12128 12092 11937 189 153 -3.64 0 - - 99 - - 0 -3 12416 12356 12129 285 225 3.48 0 - - 99 - - 0 -2 12640 12478 12287 351 189 -1.30 0 - - 99 - 0 - 0037 +3 11910 11925 12671 759 744 7.11 99 - - 99 - - - 0038 -3 12887 12872 12741 144 129 -3.87 98 - - - - 1 98 -1 12993 12984 12859 132 123 -0.22 0 99 - - 0 - - +3 12870 13026 13160 288 132 -8.19 0 99 - 0 - 0 - -1 13332 13329 13126 204 201 -1.90 0 99 - - 0 0 - -2 13372 13168 12953 417 213 -6.76 0 99 - - - 0 - 0039 +1 12832 12847 13443 609 594 4.63 99 99 - - - - - +3 13302 13383 13508 204 123 -2.14 6 - - 6 93 0 - 0040 +1 13444 13465 13812 366 345 7.81 99 99 - - 0 - - 0041 -1 13818 13779 13333 483 444 1.65 99 - - - 99 - - 0042 -3 13901 13889 13701 198 186 1.67 99 - - - - 0 99 -2 13945 13804 13559 384 243 -8.65 0 99 - - 0 0 - 0043 +3 13809 13809 13991 180 180 -2.67 99 - - 99 - - - +1 14017 14023 14196 177 171 -6.52 0 0 - - - - 99 +3 14061 14115 14276 213 159 -1.15 0 - - 0 - - 99 +1 14197 14245 14466 267 219 -0.08 0 0 - - - - 99 -2 14527 14479 14336 189 141 -1.61 0 - - 0 - 0 99 +3 14277 14283 14570 291 285 -3.28 0 - - 0 - - 99 0044 -3 14726 14669 13938 786 729 5.50 99 - - - - - 99