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_VOHT010000011.8110.AOI_02.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_VOHT010000011.8110.AOI_02 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_VOHT010000011.8110.AOI_02.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_VOHT010000011.8110.AOI_02 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 -1 390 360 31 357 327 2.45 0 99 - - 0 - - 0001 +1 1 28 870 867 840 11.44 99 99 - - - - - +1 871 880 1005 132 123 -0.65 0 0 - 99 0 - - -1 1137 774 445 690 327 2.03 0 99 - - 0 - - +1 1006 1051 1182 174 129 -5.75 0 0 - 99 - - - -3 1304 1217 1059 243 156 -1.88 0 - - 99 - - 0 -1 1338 1326 1174 162 150 -4.50 0 - - 99 0 - - -2 1468 1462 1283 183 177 -0.43 0 - - 99 - 0 - 0002 +3 840 885 1559 717 672 8.44 99 - - 99 - - - -3 1586 1481 1356 228 123 3.26 1 - - 98 - - 1 +3 1629 1710 1850 219 138 -7.37 0 - 99 0 - - - -2 1891 1873 1727 162 144 -3.38 0 - 99 - - 0 - -3 1976 1937 1806 168 129 -4.65 0 - 99 - - - 0 +3 1986 2001 2249 261 246 -1.38 0 - 99 0 - - - +3 2250 2271 2438 186 165 -0.27 0 - 99 0 - - - -1 2733 2727 2599 132 126 0.87 0 - 99 - 0 0 - -2 2746 2572 2312 432 258 -1.04 0 - 99 - - 0 - -3 2870 2822 2679 189 141 -3.68 0 - 99 - - - 0 -3 3281 3239 3117 162 120 -4.78 0 - 99 - - 0 0 -2 3391 2977 2750 639 225 -0.66 0 - 99 - - 0 - -2 3718 3667 3524 192 141 -2.28 0 - 99 - - 0 - -3 3758 3716 3591 165 123 -0.11 0 - 99 - - 0 0 0003 +2 1538 1601 3883 2343 2280 9.02 99 - 99 - - - - +2 3980 4115 4315 333 198 2.51 0 - 0 0 - 99 - +3 4080 4158 4337 255 177 2.26 1 - - 1 - 98 - 0004 -2 4339 4264 3968 369 294 6.00 99 - - - - 99 - +2 4316 4379 4501 183 120 -2.70 0 - 0 - - - 99 0005 -3 4529 4499 4197 330 300 6.23 99 - - - - - 99 0006 +3 4404 4443 4610 204 165 5.83 99 - - 99 - - - -1 5271 5181 4780 489 399 -0.90 0 99 - - 0 - - +3 5106 5121 5300 192 177 -2.26 0 99 - 0 - 0 - -2 5356 5200 5078 276 120 -5.16 0 99 - - 0 0 - -1 5454 5448 5284 168 162 -2.00 0 99 - - 0 - - +2 5327 5330 5458 129 126 -8.00 0 99 0 - 0 - - 0007 +1 4777 4831 5652 873 819 6.22 99 99 - - - - - -1 5901 5877 5665 234 210 -0.55 0 - 99 - 0 - - +3 5832 5898 6047 213 147 -3.15 0 - 99 0 - 0 - -1 6102 6102 5947 153 153 -1.36 0 - 99 - 0 0 - -1 6261 6252 6103 156 147 0.70 0 - 99 - 0 0 - -2 6268 5938 5768 498 168 -3.98 0 - 99 - - 0 - -2 6625 6475 6269 354 204 -3.38 0 - 99 - - 0 - 0008 +2 5567 5696 6781 1212 1083 6.49 99 - 99 - - - - -3 7145 7118 6828 315 288 -1.57 0 99 - - - - 0 -1 7362 7086 6883 477 201 -0.18 0 99 - - 0 - 0 -1 7596 7521 7363 231 156 -6.31 0 99 - - 0 - - +2 7514 7529 7678 162 147 -5.44 0 99 0 - - - - 0009 +1 6766 6808 7836 1068 1026 10.33 99 99 - - - - - 0010 -2 8020 7963 7799 219 162 0.94 30 - - - 69 30 - -3 8057 8054 7896 159 156 -3.00 0 - 99 - 0 - 0 0011 -1 8091 8061 7597 492 462 0.96 99 - - - 99 - - -1 8280 8280 8101 177 177 3.36 0 - 99 - 0 0 - -2 8335 8209 8072 261 135 -8.38 0 - 99 - - 0 - -3 8351 8312 8148 201 162 -3.74 0 0 99 - - 0 0 +3 8298 8322 8447 147 123 -6.33 0 0 99 0 - - - -2 8566 8551 8336 228 213 -1.08 0 - 99 - - 0 - -1 8610 8556 8413 195 141 -1.45 0 - 99 - 0 0 - -3 8642 8582 8436 204 144 -1.59 0 - 99 - 0 - 0 -2 8782 8707 8567 213 138 -4.25 0 - 99 - - 0 - -2 9271 9193 9059 210 132 -7.55 0 0 99 - - 0 - -1 9396 9306 9136 258 168 -1.09 0 - 99 - 0 - - 0012 +2 7844 7862 9400 1554 1536 9.93 99 - 99 - - - - 0013 -3 9422 9422 9288 132 132 -0.90 56 - - - - 43 56 0014 +2 9452 9485 9643 189 156 2.11 99 - 99 - - - - +3 9825 9876 10136 309 258 -2.09 0 - - 0 - 99 - +3 10176 10236 10361 183 123 -1.16 0 - - 0 0 99 - -1 10380 10380 10216 162 162 2.12 0 - - - 0 99 - +3 10584 10656 10778 192 120 -2.05 0 - - 0 - 99 - 0015 -2 11026 11014 9554 1470 1458 6.61 99 - - - - 99 - -1 11391 11370 11245 144 123 3.04 0 - - - 0 99 - +2 11273 11273 11428 153 153 -0.82 0 - 0 - - 99 - +3 11460 11490 11633 171 141 -0.56 0 - - 0 - 99 - +1 11512 11563 11724 210 159 -6.45 0 0 - - - 99 - +2 11990 12113 12259 267 144 -0.70 0 - 0 - - 99 - 0016 -2 12532 12448 11081 1449 1365 9.34 99 - - - - 99 - +2 12917 12923 13072 153 147 -0.05 0 0 0 0 99 - 0 +2 13076 13079 13225 147 144 -1.81 0 0 0 - 99 - 0 -3 13265 12992 12870 393 120 -5.87 0 0 - - 99 - 0 0017 +1 12502 12598 13278 774 678 -2.12 0 0 - - 99 - - -3 13460 13406 13266 192 138 -3.39 0 - 0 - 99 - 0 +1 13450 13702 14100 648 396 0.78 0 0 - - 99 - - +2 13778 14048 14182 402 132 -2.20 0 - 0 - 99 0 - +1 14101 14134 14514 411 378 0.54 0 0 - - 99 - - 0018 -1 14580 14526 12484 2094 2040 10.10 99 - - - 99 - - 0019 +2 14339 14492 14656 315 162 -4.31 99 - 99 - - - - +2 14657 14726 14959 300 231 -6.64 0 0 0 - - 99 0 -3 15086 14822 14691 393 129 -9.61 0 - 0 - - 99 0 +3 15261 15270 15452 189 180 1.67 0 - 0 0 - 99 - 0020 +2 14960 14972 15745 783 771 -2.97 0 - 0 - 0 99 - -1 15810 15723 15487 321 234 -6.66 0 - 0 - 0 99 - +1 15691 15742 15939 246 195 -8.69 0 0 - - - 99 - +3 15951 16029 16154 201 123 -1.21 0 - 0 0 - 99 0 +2 15815 15947 16186 369 237 -2.64 0 - 0 - - 99 - +3 16155 16200 16337 180 135 -1.49 0 - - 0 - 99 - +2 16307 16361 16492 183 129 -3.59 0 - 0 - - 99 - -3 16586 16559 16413 171 144 -13.33 0 - - - - 99 0 0021 -2 16624 16609 14573 2049 2034 9.68 99 - - - - 99 - 0022 -1 16995 16752 16606 387 144 5.61 99 - - - 99 - - 0023 -2 17020 17008 16871 147 135 -1.03 99 - - - - 99 - 0024 +3 16890 16971 17105 213 132 0.61 99 - - 99 - - - 0025 -1 17277 17160 16996 279 162 -1.34 99 - - - 99 - - +2 17156 17177 17317 159 138 0.75 1 - 1 - - 98 0 0026 -3 17345 17321 17124 219 195 -0.69 99 - - - - - 99 0027 -2 17362 17299 17168 192 129 3.36 73 - 26 - - 73 0 0028 +3 17238 17238 17390 150 150 0.66 99 - - 99 - - - 0029 +1 17245 17257 17406 159 147 2.67 99 99 - - - - - 0030 +2 17318 17387 17542 222 153 1.16 99 - 99 - - - - 0031 -1 17586 17568 17401 183 165 -1.21 99 - - - 99 - - 0032 -3 17783 17699 17490 291 207 0.79 99 - - - - - 99 0033 +3 17577 17595 17798 219 201 -1.90 99 - - 99 - - - 0034 +1 17662 17710 17841 177 129 -1.92 99 99 - - - - - +3 17799 17802 17930 129 126 -1.85 0 - 0 0 - 99 - +3 17931 17931 18068 135 135 2.96 0 - - 0 - 99 0 +3 18105 18105 18230 123 123 0.18 0 - - 0 - 99 - +2 18131 18371 18529 396 156 -2.93 0 - 0 - - 99 - 0035 -2 18685 18649 17714 969 933 11.28 99 - - - - 99 - 0036 -3 18797 18725 18591 204 132 3.87 99 - - - - - 99 -1 19050 19038 18895 153 141 -3.12 0 - - 99 0 - - -1 19254 19224 19051 201 171 -7.53 0 - - 99 0 - - -3 19376 19367 19221 153 144 -1.46 0 - - 99 - - 0 +1 19384 19387 19545 159 156 -5.47 0 0 - 99 - - - -2 19852 19834 19655 195 177 2.04 0 - - 99 - 0 0 +2 19847 19904 20098 249 192 -3.43 0 - 0 99 - - 0 +1 20053 20197 20319 264 120 -0.43 0 0 - 99 - - 0 -2 20371 20347 20216 153 129 3.02 0 - - 99 - 0 0 0037 -3 20450 19904 19446 1002 456 -0.49 0 - - 99 - - 0 0038 +3 18681 18738 20582 1899 1842 8.98 99 - - 99 - - - 0039 +1 20455 20458 20601 144 141 -2.02 73 73 - - - - 26 -1 20697 20688 20563 132 123 -5.43 0 - 99 - 0 - - 0040 +2 20567 20579 20701 132 120 -1.73 35 - 35 64 0 - - +3 20583 20607 20747 162 138 -3.24 0 - - 0 - 99 0 +2 20702 20771 20959 255 186 1.70 0 - 0 - - 99 0 0041 -2 21004 20968 20588 414 378 4.01 99 - - - - 99 -