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/NC_0063471.0.AOI_03.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/NC_0063471.0.AOI_03 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NC_0063471.0.AOI_03.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% >NC_0063471.0.AOI_03 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 -2 256 163 29 225 132 -8.15 0 - - 99 - 0 - +1 148 235 369 219 132 -2.72 0 0 - 99 - - 0 -3 602 302 144 456 156 0.09 0 0 - 99 - - 0 -2 679 523 326 351 195 -2.57 0 - - 99 - 0 0 0001 +3 3 36 959 954 921 11.95 99 - - 99 - - - -2 1459 1447 1286 171 159 -0.93 0 - - 99 - 0 0 -1 1548 1524 1402 144 120 -2.99 0 - - 99 0 - 0 +1 1414 1510 1632 216 120 -4.50 0 0 - 99 - - 0 -2 2233 2221 2060 171 159 -1.33 0 - - 99 - 0 0 0002 -3 2345 1289 1002 1341 285 2.69 99 - - - - - 99 0003 +3 1170 1182 2582 1410 1398 8.18 99 - - 99 - - - -3 2591 2468 2346 243 120 -3.25 0 - - 99 - 0 0 -2 2614 2392 2234 378 156 -2.21 0 - - 99 - 0 - 0004 +1 2449 2500 2631 180 129 -1.71 99 99 - - - - - 0005 +1 2632 2641 2976 342 333 9.81 99 99 - - 0 - - -3 3203 3200 3015 186 183 -2.73 0 99 - - - - 0 +2 3074 3077 3220 144 141 -8.55 0 99 0 - 0 - - -1 3420 3381 3217 201 162 -1.49 0 99 - - 0 - - +2 3323 3356 3502 177 144 -3.00 0 99 0 - - - - 0006 +1 3004 3022 3786 780 762 7.97 99 99 - - - - - +2 3671 3671 3823 150 150 -5.43 0 - 0 - 99 - - -1 3831 3780 3448 381 330 1.47 0 99 - - 0 - - +3 3756 3870 4019 261 147 -5.59 0 - - 0 - - 99 +2 4280 4280 4486 204 204 -11.33 0 0 0 - - - 99 0007 -3 4511 4508 3816 693 690 9.75 99 - - - - - 99 +1 4165 4258 4515 348 255 0.74 0 0 - - - - 99 0008 -1 4554 4548 4411 141 135 -3.72 99 - - - 99 - - 0009 -2 4798 4735 4505 291 228 -2.84 99 - - - - 99 - -1 4908 4767 4579 327 186 -6.18 0 - - - 0 0 99 +3 4803 4824 5036 231 210 3.95 0 - - 0 - - 99 +1 4861 4897 5043 180 144 0.31 0 0 - - - - 99 +1 5152 5173 5325 171 150 -1.34 0 0 - 0 - - 99 +3 5037 5163 5423 384 258 0.54 0 - - 0 - - 99 0010 -3 5609 5564 4551 1056 1011 9.91 99 - - - - - 99 0011 +2 5558 5573 5785 225 210 -3.38 99 - 99 - - - - 0012 +1 5731 5779 5925 192 144 -3.14 65 65 - - 34 - - 0013 -1 6030 5838 5659 369 177 -3.65 99 - - - 99 - - 0014 +2 5891 5909 6067 174 156 -3.20 99 - 99 - - - - +3 6099 6294 6572 471 276 4.89 0 - - 0 - - 99 0015 -3 6578 6566 6000 576 564 13.14 99 - - - - - 99 0016 +1 6745 6760 6921 174 159 2.82 99 99 - - 0 - - 0017 -3 7058 7034 6774 282 258 0.15 99 - - - - - 99 -1 7329 7254 7117 210 135 3.33 0 - 99 - 0 0 - 0018 +2 7121 7133 7774 651 639 8.59 99 - 99 - - 0 - 0019 +3 7674 7674 7823 147 147 -0.73 97 - - 97 - 2 - 0020 -2 7924 7333 7004 918 327 -0.45 99 - - - - 99 - -3 8036 8015 7881 153 132 -0.33 0 99 - - 0 - 0 0021 -1 8316 8196 7771 543 423 -0.16 99 - - - 99 - - -3 8423 8417 8256 165 159 -10.76 0 99 0 - - - 0 +2 8162 8276 8446 282 168 -10.85 0 99 0 - - - - +2 8447 8453 8617 168 162 -7.10 0 99 0 - 0 - - -3 8849 8822 8682 165 138 -3.90 0 77 - - 22 - 0 +3 8694 8727 8858 162 129 -4.53 0 99 - 0 0 - - -1 8868 8748 8317 549 429 2.43 0 99 - - 0 - - 0022 +1 7795 7804 8877 1080 1071 6.13 99 99 - - - - - 0023 -3 9182 9023 8850 330 171 0.39 99 - - - - - 99 +1 9169 9256 9381 210 123 -5.00 0 0 - 99 - - - -3 9644 9410 9282 360 126 -1.54 0 - - 99 - - 0 0024 +3 8862 8874 9848 984 972 10.71 99 - - 99 - - - 0025 -3 9869 9866 9645 222 219 -0.27 99 - - - - - 99 -2 10189 10132 9959 228 171 1.96 0 - 99 - - 0 - -3 10241 10130 9987 252 141 -8.29 0 - 99 - - 0 0 +3 10101 10200 10328 225 126 -2.97 0 - 99 0 - - - +3 10449 10458 10631 180 171 -11.05 0 - 99 0 - 0 - -2 10852 10801 10418 432 381 -2.83 0 - 99 - - 0 - 0026 +2 9938 9989 11137 1197 1146 10.53 99 - 99 - - - - -2 11284 10984 10853 429 129 3.10 0 - 99 - - 0 - -1 11340 11277 11149 189 126 2.21 0 99 - - 0 0 - -3 11372 11348 11217 153 129 -4.93 0 99 - - - - 0 -1 11634 11634 11425 207 207 1.93 0 99 - - 0 - - 0027 +1 11080 11170 11829 747 657 6.65 99 99 - - - - - -1 12078 11991 11830 246 159 3.45 0 - 99 - 0 - - -2 12100 11971 11849 249 120 -3.39 0 - 99 - 0 0 - +3 11952 12054 12221 267 165 -5.31 0 - 99 0 - - - 0028 +2 11816 11834 12229 411 393 9.49 99 - 99 - - - - 0029 -1 12279 12261 12079 198 180 -2.79 99 - - - 99 - - 0030 -2 12376 12250 12101 273 147 -2.52 84 - - - 15 84 - 0031 +2 12254 12254 12478 222 222 -0.82 99 - 99 - - - - +2 12698 12701 12847 147 144 -1.31 0 0 0 - 99 - - 0032 +1 12337 12409 13170 831 759 -0.48 0 0 - - 99 - - +2 13073 13301 13432 357 129 -4.31 1 - 1 - 98 0 - 0033 -1 13440 13359 12328 1110 1029 10.75 99 - - - 99 - - -2 13567 13321 13178 387 141 -6.13 0 - 0 - 99 0 - +1 13429 13471 13635 204 162 -4.70 0 0 - 0 - - 99 +3 13362 13590 13715 351 123 -2.24 0 - - 0 - - 99 0034 -3 14129 14066 13338 789 726 9.01 99 - - - - - 99 -1 14133 14118 13990 141 126 -3.65 0 - - - 0 - 99 -3 14462 14456 14241 219 213 -5.86 0 - - - - 99 0 +3 14304 14427 14591 285 162 -6.42 0 - 0 0 - 99 - -1 14715 14658 14509 204 147 -12.13 0 - 0 - 0 99 0 -1 14958 14937 14716 240 219 -7.73 0 - 0 - 0 99 - +2 14387 14879 15016 627 135 2.69 0 - 0 - - 99 - +3 14940 14952 15113 171 159 0.92 0 - - 0 - 99 - 0035 -2 15220 15184 14105 1113 1077 7.34 99 - - - - 99 - +1 15262 15304 15465 201 159 -3.60 3 3 - - 96 - - 0036 -1 15537 15405 15205 330 198 1.43 99 - - - 99 - - -1 15786 15765 15637 147 126 -9.27 0 - 0 - 0 99 0 +2 15596 15698 15853 255 153 1.03 1 - 1 0 - 98 - +3 15654 15657 15920 264 261 -0.49 0 - - 0 - 99 - +2 15854 15869 16006 150 135 -1.98 0 - 0 - - 99 - +2 16007 16139 16339 330 198 1.88 0 - 0 - - 99 - +3 16188 16197 16355 165 156 -3.36 0 - - 0 - 99 - +2 16340 16352 16669 327 315 -1.08 0 - 0 - - 99 - +3 16512 16611 16736 222 123 -3.44 0 0 - 0 - 99 - 0037 -2 16870 16858 15611 1257 1245 4.57 99 - - - - 99 - +3 16992 17007 17141 147 132 -2.63 0 - 0 0 - 99 - +3 17142 17226 17351 207 123 -2.85 0 - 0 0 - 99 - 0038 +2 16805 16811 17398 591 585 0.74 99 - 99 - - - - +3 17430 17451 17612 180 159 -0.71 0 - - 0 - 99 - +2 17480 17612 17860 378 246 0.38 0 - 0 - - 99 - 0039 -2 18112 17953 16871 1239 1080 5.63 99 - - - - 99 - 0040 +2 17861 17966 18118 255 150 -0.08 99 0 99 - - - - -2 18289 18253 18125 162 126 -11.25 0 0 - - 99 0 - 0041 -1 18324 18303 18067 255 234 8.57 99 0 - - 99 - - 0042 +1 17962 17998 18357 393 357 -2.41 99 99 - - - - - 0043 +3 18312 18321 18470 156 147 2.32 99 - - 99 - - - -3 18686 18632 18480 204 150 -8.53 0 - - - - 99 0 +3 18624 18822 19007 381 183 -2.61 0 - - 0 - 99 0 -3 19016 18989 18801 213 186 -7.88 0 - - 0 - 99 0 0044 -2 19243 19222 18380 861 840 8.70 99 - - - - 99 - 0045 +3 19116 19152 19307 189 153 -8.23 99 - - 99 - - - +2 19322 19373 19666 342 291 2.21 0 - 0 - - 99 - 0046 -2 19891 19834 19325 564 507 13.88 99 - - - - 99 - +1 20209 20263 20385 174 120 -10.81 0 0 0 - - 99 0 0047 -2 20419 20407 19892 525 513 13.35 99 - - - - 99 - 0048 +2 20417 20423 20641 222 216 1.82 99 - 99 - - - - +3 20436 20496 20648 210 150 -1.09 0 - - 0 - 99 - +1 20596 20824 20952 354 126 -8.63 0 0 - - - 99 - 0049 -2 21127 21046 20432 693 612 11.84 99 - - - - 99 -