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_Bacteroidaceae//Bacteroides_fragilis.result/NZ_QSVT010000011.7305.AOI_01.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_QSVT010000011.7305.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_QSVT010000011.7305.AOI_01.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.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_QSVT010000011.7305.AOI_01 Sequence length = 21005 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 0001 +3 3 3 425 420 420 3.45 99 - - 99 - - - -2 430 406 266 162 138 -2.63 1 - 0 98 - 1 - -3 446 434 312 132 120 -2.10 4 0 - - - 95 4 +1 316 325 450 132 123 -4.31 0 0 - - - - 99 0002 -1 558 555 412 144 141 -1.52 74 - 25 - 74 - - +3 642 666 797 153 129 3.56 0 - 0 0 - 99 - -1 960 816 694 264 120 -0.22 0 - 0 - 0 99 - -3 1166 1109 915 249 192 -3.87 0 - 0 - - 99 0 +3 1161 1179 1358 195 177 1.46 0 - - 0 - 99 - +2 1223 1391 1567 342 174 -1.39 0 - 0 - - 99 - -1 1629 1626 1468 159 156 -4.15 0 - - - 0 99 - +2 1637 1646 1792 153 144 -2.05 0 - 0 - - 99 - +1 1759 1789 1962 201 171 -7.21 0 0 - - - 99 - +1 1963 1975 2118 153 141 -3.81 0 0 - - - 99 - 0003 -2 2332 2275 431 1899 1842 8.79 99 - - - - 99 - 0004 +2 2216 2288 2422 204 132 3.83 99 - 99 - - - - -3 2882 2642 2484 396 156 -1.43 0 - - 99 - - 0 -2 2908 2908 2783 123 123 0.81 0 - - 99 - 0 - -2 3082 3082 2945 135 135 1.55 0 - 0 99 - 0 - -2 3214 3211 3083 129 126 -1.00 0 - - 99 - 0 0 0005 +3 2328 2364 3299 969 933 10.68 99 - - 99 - - - 0006 -1 3351 3303 3172 177 129 -2.43 99 - - - 99 - - 0007 -2 3436 3418 3215 219 201 0.53 99 - - - - 99 - 0008 +2 3230 3368 3523 291 153 0.08 99 - 99 - - - - 0009 +1 3427 3445 3612 183 165 -2.89 99 99 - - - - - 0010 -3 3695 3626 3471 222 153 1.64 99 - - - - - 99 0011 -1 3768 3756 3607 159 147 1.81 99 - - - 99 - - 0012 -2 3775 3775 3623 150 150 0.80 99 - - - - 99 - 0013 +3 3651 3714 3845 192 129 3.79 65 - 0 65 - - 34 -3 3857 3836 3696 159 138 1.59 1 - 0 97 - - 1 0014 +2 3668 3692 3889 219 195 -0.72 99 - 99 - - - - 0015 +1 3736 3736 4017 279 279 0.29 99 99 - - - - - 0016 -2 4123 4042 3908 213 132 -1.40 99 - - - - 99 - 0017 +3 3993 4005 4142 147 135 -0.17 99 - - 99 - - - 0018 +1 4018 4261 4407 387 144 6.23 99 99 - - - - - +2 4427 4454 4600 171 144 -13.45 0 - 0 99 - - - -3 4706 4652 4521 183 129 -3.38 0 - - 99 - - 0 -2 4858 4855 4676 180 177 0.11 0 - - 99 - 0 - -2 5062 4984 4859 201 123 0.57 0 - 0 99 - 0 0 -3 5198 5192 4827 369 363 -1.46 0 - - 99 - - 0 -1 5322 5271 5074 246 195 -7.83 0 - - 99 0 - - +1 5203 5290 5526 321 234 -5.83 0 0 - 99 - - 0 -2 5752 5743 5561 189 180 2.15 0 - - 99 - 0 0 0019 -3 6053 6041 5268 783 771 -2.53 0 0 - 99 - - 0 +2 5927 6191 6322 393 129 -8.34 0 - 0 99 - - 0 0020 +3 4389 4404 6440 2049 2034 8.53 99 - - 99 - - - -3 6674 6287 6054 618 231 -5.47 0 - 0 99 0 - 0 -1 6912 6879 6499 411 378 1.63 0 99 - - 0 - - -2 7165 7033 6893 270 138 -10.91 0 98 - 0 - 0 1 -3 7235 6965 6831 402 132 -2.30 0 99 - 0 - - 0 -1 7563 7311 6913 648 396 0.60 0 99 - - 0 - - +2 7553 7607 7747 192 138 -2.87 0 99 0 - - - 0 -3 7754 7706 7542 210 162 -1.25 0 99 - - - - 0 -2 7777 7738 7616 159 120 -2.20 0 98 0 - 0 0 0 -3 7937 7934 7788 147 144 -0.70 4 91 0 - 3 - 4 -3 8096 8090 7941 153 147 -1.07 0 99 0 - 0 0 0 +2 7748 8021 8143 393 120 -4.81 0 99 0 - 0 - - 0021 -1 8511 8415 7735 774 678 -1.44 0 99 - - 0 - - 0022 +1 6433 6487 8529 2094 2040 4.77 99 99 - - - - - -2 8962 8896 8750 210 144 -0.21 0 - 99 - - 0 - -1 9546 9492 9337 207 153 3.13 1 - 98 - 1 - 0 -2 9733 9733 9578 153 153 -0.92 0 - 99 - - 0 - +3 9615 9636 9761 144 123 4.18 2 - 97 2 - - - 0023 +2 8438 8477 9925 1485 1446 4.12 99 - 99 - - - - 0024 +1 9892 9895 10044 150 147 0.76 99 99 - - - - - -1 10422 10350 10228 192 120 -2.14 0 - 99 - 0 - - +3 10626 10626 10790 162 162 2.07 0 - 99 0 - - - -1 10830 10770 10645 183 123 -3.04 0 - 99 0 0 - - -1 11181 11067 10870 309 195 -2.36 0 - 99 - 0 - - 0025 +2 9980 9992 11452 1470 1458 5.49 99 - 99 - - - - 0026 -2 11554 11521 11363 189 156 3.28 99 - - - - 99 - +3 11610 11700 11870 258 168 -1.42 0 - - 0 - 99 - +2 11714 11813 11947 231 132 -5.27 0 - 0 - - 99 0 +2 12224 12299 12439 213 138 -4.43 0 - 0 - - 99 - +1 12364 12424 12570 204 144 -1.09 0 0 - 0 - 99 - +3 12396 12450 12593 195 141 -1.20 0 - 0 0 - 99 - +2 12440 12455 12670 228 213 -1.04 0 - 0 - - 99 - -1 12708 12684 12559 147 123 -5.31 0 - - - 0 99 0 +1 12655 12694 12858 201 162 -2.60 0 0 0 - - 99 0 +3 12726 12726 12905 177 177 1.47 0 - 0 0 - 99 - +2 12671 12797 12934 261 135 -7.64 0 - 0 - - 99 - +1 12949 12952 13110 159 156 -2.46 0 0 - 0 - 99 - 0027 -2 13162 13144 11606 1554 1536 10.28 99 - - - - 99 - 0028 +2 12986 13043 13207 219 162 -0.10 30 - 30 69 - - - 0029 +3 12915 12945 13409 492 462 0.54 99 - - 99 - - - -2 13492 13477 13328 162 147 -5.23 0 - - - - 0 99 +3 13410 13485 13643 231 156 -6.63 0 - - 0 - - 99 +3 13644 13920 14123 477 201 -0.90 0 0 - 0 - - 99 +1 13861 13888 14178 315 288 -1.47 0 0 - - - - 99 0030 -3 14240 14198 13170 1068 1026 10.16 99 - - - - - 99 +2 14381 14531 14737 354 204 -3.13 0 - 0 - - 99 - +3 14745 14754 14903 156 147 -0.40 0 - 0 0 - 99 - +3 14904 14904 15059 153 153 -0.90 0 - 1 0 - 98 - -1 15174 15108 14959 213 147 -2.28 0 - 0 - 0 99 - +2 14738 15065 15238 498 171 -4.34 0 - 0 - - 99 - +3 15105 15129 15341 234 210 -1.41 0 - - 0 - 99 - 0031 -2 15439 15310 14225 1212 1083 6.14 99 - - - - 99 - -2 15679 15676 15548 129 126 -6.41 0 - - 0 - 0 99 +3 15552 15558 15722 168 162 -1.71 0 - - 0 - - 99 -1 15900 15885 15706 192 177 -1.93 0 - 0 - 0 - 99 +2 15650 15806 15928 276 120 -3.81 0 - 0 0 - - 99 +3 15735 15825 16226 489 399 -1.39 0 - - 0 - - 99 0032 -3 16229 16175 15354 873 819 5.62 99 - - - - - 99 0033 -1 16602 16563 16396 204 165 6.14 99 - - - 99 - - -2 16690 16627 16505 183 120 -2.37 0 99 - - - 0 - 0034 +1 16477 16507 16809 330 300 6.43 99 99 - - - - - 0035 -1 16926 16848 16669 255 177 2.99 24 - 75 - 24 - - -2 17026 16891 16691 333 198 2.03 3 - 95 - 0 3 - 0036 +2 16667 16676 17038 369 360 4.31 99 - 99 - - - - +1 17248 17290 17415 165 123 -1.65 0 0 0 - - 99 - +2 17288 17339 17491 201 150 -4.79 0 - 0 - - 99 - 0037 -2 17494 17455 17123 369 330 5.01 99 - - - - 99 - +3 17724 17766 17888 162 120 -5.45 0 0 - 0 99 - - +1 17614 18028 18255 639 225 -1.43 0 0 - - 99 - - +3 18135 18183 18326 189 141 -4.28 0 - - 0 99 - - +2 18272 18278 18406 132 126 -0.69 0 0 0 - 99 - - +1 18256 18433 18693 435 258 -0.26 0 0 - - 99 - - -3 18755 18734 18567 186 165 0.19 0 - - - 99 - 0 -3 19019 18971 18756 261 213 -0.47 0 - - - 99 - 0 +3 19029 19068 19199 168 129 -4.35 0 - - 0 99 - - +1 19114 19132 19278 162 144 -4.06 0 0 - - 99 - - -3 19376 19295 19155 219 138 -6.41 0 - - - 99 - 0 0038 -1 19467 19404 17389 2076 2013 9.11 99 - - - 99 - - +3 19419 19524 19649 228 123 3.12 0 - - 0 - - 99 +1 19537 19543 19722 183 177 -1.87 0 0 - - - - 99 +2 19667 19679 19831 162 150 -3.64 0 - 0 - - - 99 +3 19701 19788 19946 243 156 -2.18 0 - - 0 - - 99 -2 19999 19954 19823 174 129 -5.13 0 - - - - 0 99 -2 20134 20125 20000 132 123 0.27 0 - 0 - - 0 99 0039 -3 20165 20120 19446 717 672 9.28 99 - - - - - 99 +2 19868 20231 20560 690 327 1.14 0 - 0 - - 99 - +2 20615 20645 20974 357 327 2.19 0 - 0 - - 99 - 0040 -2 21004 20977 20135 867 840 11.40 99 - - - - 99 -