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_JACFSS0100000011.8580.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_JACFSS0100000011.8580.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_JACFSS0100000011.8580.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_JACFSS0100000011.8580.AOI_01 Sequence length = 21128 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 -2 532 304 176 354 126 -8.79 0 99 - - - 0 - -3 692 632 480 210 150 -1.00 0 99 - - - - 0 0001 +1 1 82 696 693 612 11.83 99 99 - - - - - 0002 -1 711 705 487 222 216 2.09 99 - - - 99 - - -2 919 865 743 174 120 -10.36 0 99 - 0 0 0 - 0003 +1 709 721 1236 525 513 13.22 99 99 - - - - - 0004 +1 1237 1294 1803 564 507 13.94 99 99 - - - - - -1 1806 1755 1462 342 291 2.00 0 99 - - 0 - - 0005 -3 2012 1976 1821 189 153 -8.22 99 - - - - - 99 +3 2112 2139 2327 213 186 -7.60 0 99 - 0 - - 0 -3 2504 2306 2121 381 183 -3.06 0 99 - 0 - - 0 +3 2442 2496 2648 204 150 -8.40 0 99 - 0 - - - 0006 +1 1885 1906 2748 861 840 8.77 99 99 - - - - - 0007 -3 2816 2807 2658 156 147 2.73 99 - - - - - 99 +1 2839 2875 3003 162 126 -10.49 0 0 99 - - - - 0008 +2 2804 2825 3061 255 234 8.14 99 - 99 - - - - -3 3167 3131 2997 168 132 -4.13 2 - - - - 97 2 0009 -2 3268 3163 2903 363 258 -0.17 99 - - - - 99 - -2 3649 3517 3269 378 246 0.86 0 - 99 - - 0 - -1 3699 3678 3517 180 159 -0.90 0 - 99 - 0 - - -1 3987 3903 3778 207 123 -2.55 0 - 99 - 0 0 - -1 4137 4122 3988 147 132 -2.53 0 - 99 - 0 0 - 0010 +2 3062 3176 4258 1194 1080 5.55 99 - 99 - - - - 0011 -2 4324 4318 3731 591 585 0.56 99 - - - - 99 - -1 4617 4518 4393 222 123 -3.46 0 - 99 - 0 - 0 -2 4789 4777 4460 327 315 -1.12 0 - 99 - - 0 - -1 4941 4932 4774 165 156 -3.24 0 - 99 - 0 - - -2 5122 4990 4790 330 198 2.05 0 - 99 - - 0 - -2 5275 5260 5123 150 135 -1.65 0 - 99 - - 0 - -1 5475 5472 5209 264 261 0.03 0 - 99 - 0 - - +3 5343 5364 5492 147 126 -9.60 0 0 99 0 - 0 - 0012 +2 4259 4271 5518 1257 1245 4.56 99 - 99 - - - - -2 5533 5431 5276 255 153 0.97 1 - 98 - 0 1 - -3 5867 5825 5664 201 159 -3.70 3 - - 96 - - 3 0013 +3 5592 5724 5924 330 198 1.45 99 - - 99 - - - -1 6189 6177 6016 171 159 0.98 0 - 99 - 0 - - +3 6171 6192 6413 240 219 -6.77 0 - 99 0 - 0 - +3 6414 6471 6620 204 147 -12.53 0 0 99 0 - 0 - -2 6742 6250 6113 627 135 2.78 0 - 99 - - 0 - -1 6825 6702 6538 285 162 -6.28 0 - 99 - 0 0 - +1 6667 6673 6888 219 213 -5.78 0 0 99 - - - - 0014 +2 5909 5945 7024 1113 1077 7.43 99 - 99 - - - - +3 6996 7011 7139 141 126 -3.29 0 99 - 0 - - - -3 7700 7658 7494 204 162 -4.78 0 99 - - 0 - 0 -1 7767 7539 7414 351 123 -1.79 0 99 - - 0 - - 0015 +1 7000 7063 7791 789 726 9.00 99 99 - - - - - +2 7562 7808 7951 387 141 -6.03 0 - 0 99 - 0 - -2 8056 7828 7697 357 129 -4.27 2 - 0 97 - 2 - -2 8431 8428 8282 147 144 -1.42 0 - - 99 - 0 0 -3 8792 8240 8025 765 213 0.87 0 - - 99 - - 0 0016 +3 7689 7770 8801 1110 1029 10.53 99 - - 99 - - - 0017 -2 8875 8875 8651 222 222 -0.72 99 - - - - 99 - 0018 +2 8753 8879 9028 273 147 -2.31 83 - 83 16 - - - 0019 +3 8850 8868 9050 198 180 -2.57 99 - - 99 - - - -1 9177 9075 8908 267 165 -5.27 0 - - - 0 99 - +2 9029 9158 9280 249 120 -3.49 0 - 0 0 - 99 - +3 9051 9114 9299 246 183 3.04 0 - - 0 - 99 - 0020 -2 9313 9295 8900 411 393 9.53 99 - - - - 99 - +3 9495 9495 9704 207 207 2.16 0 - - 0 - - 99 +1 9757 9781 9912 153 129 -4.80 0 0 - - - - 99 +3 9789 9852 9980 189 126 2.24 0 - 0 0 - - 99 0021 -3 10049 9959 9300 747 657 6.51 99 - - - - - 99 +2 9845 10145 10276 429 129 3.23 0 - 0 - - 99 - -1 10680 10671 10498 180 171 -10.51 0 - 0 - 0 99 - +2 10277 10328 10711 432 381 -3.01 0 - 0 - - 99 - -1 11028 10929 10801 225 126 -2.73 0 - - - 0 99 - +1 10888 10999 11142 252 141 -7.95 0 0 0 - - 99 - +2 10940 10997 11170 228 171 1.90 0 - 0 - - 99 - 0022 -2 11191 11140 9992 1197 1146 10.56 99 - - - - 99 - 0023 +1 11260 11263 11484 222 219 -0.19 99 99 - - - - - +1 11485 11719 11847 360 126 -1.34 0 0 - - 99 - - -3 11960 11873 11748 210 123 -4.63 0 - - - 99 - 0 0024 -1 12267 12255 11281 984 972 10.69 99 - - - 99 - - 0025 +1 11947 12106 12279 330 171 0.63 99 99 - - - - - -1 12435 12402 12271 162 129 -4.64 0 - - 0 0 - 99 +1 12280 12307 12447 165 138 -4.05 0 0 - 23 - - 76 -2 12682 12676 12512 168 162 -6.88 0 - - 0 - 0 99 +3 12261 12381 12812 549 429 2.52 0 - - 0 - - 99 +1 12706 12712 12873 165 159 -10.82 0 0 - - - 0 99 -2 12967 12853 12683 282 168 -10.77 0 - - - - 0 99 +1 13093 13114 13248 153 132 -0.02 0 0 - 0 - - 99 0026 -3 13334 13325 12252 1080 1071 6.20 99 - - - - - 99 0027 +3 12813 12933 13358 543 423 -0.51 99 - - 99 - - - 0028 -1 13455 13455 13306 147 147 -0.37 98 - 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- 99 - - - -2 16849 16849 16643 204 204 -10.94 0 99 - - - 0 0 -3 16964 16871 16614 348 255 0.68 0 99 - - - - 0 0041 +1 16618 16621 17313 693 690 9.76 99 99 - - - - - -1 17373 17259 17110 261 147 -5.20 0 99 - - 0 - - -2 17458 17458 17306 150 150 -5.64 0 - - 99 - 0 - +3 17298 17349 17681 381 330 1.47 0 - - 0 - - 99 -2 17806 17773 17627 177 144 -2.57 0 - - - - 0 99 +3 17709 17748 17912 201 162 -1.43 0 - - 0 - - 99 -2 18055 18052 17909 144 141 -8.29 0 - - 0 - 0 99 +1 17926 17929 18114 186 183 -2.98 0 0 - - - - 99 0042 -3 18125 18107 17343 780 762 7.74 99 - - - - - 99 0043 -3 18497 18488 18153 342 333 9.94 99 - - 0 - - 99 0044 -3 18680 18629 18498 180 129 -1.84 99 - - - - - 99 +2 18515 18572 18697 180 123 -0.03 0 0 0 - 99 - - +1 18538 18661 18783 243 120 -2.26 0 0 - - 99 - - +2 18698 18737 18895 195 156 -2.28 0 - 0 - 99 - - +2 18896 18908 19069 171 159 -1.25 0 0 0 - 99 - - -3 19715 19619 19497 216 120 -4.19 0 0 - - 99 - 0 +3 19581 19605 19727 144 120 -2.76 0 0 - 0 99 - - +2 19670 19682 19843 171 159 -0.90 0 0 0 - 99 - - 0045 -1 19959 19947 18547 1410 1398 8.31 99 - - - 99 - - 0046 +1 18784 19840 20127 1341 285 2.43 99 99 - - - - - +2 20450 20606 20803 351 195 -2.42 0 0 0 - 99 - - -3 20981 20894 20760 219 132 -2.73 0 0 - - 99 - 0 +1 20527 20911 21063 534 150 0.52 0 0 0 - 99 - - +2 20873 20966 21100 225 132 -7.09 0 - 0 - 99 - - 0047 -1 21126 21093 20170 954 921 12.23 99 - - - 99 - -