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_JACFSS0100000041.8595.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_JACFSS0100000041.8595.AOI_02 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_JACFSS0100000041.8595.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_JACFSS0100000041.8595.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 -1 306 237 49 255 186 1.87 0 99 - 0 0 - - 0001 +1 1 40 420 417 378 3.90 99 99 - - - - - -3 425 401 261 162 138 -2.78 0 99 - 0 - - 0 0002 -1 441 429 307 132 120 -1.19 35 - 0 - 35 - 64 +2 311 320 445 132 123 -5.03 0 - 0 - 99 - - 0003 -2 553 550 407 144 141 -1.82 79 - - 20 - 79 - +1 637 661 792 153 129 3.28 0 0 - 0 - - 99 -2 955 811 689 264 120 0.21 0 - - 0 - 0 99 -1 1161 1104 910 249 192 -2.57 0 - - 0 0 - 99 +1 1156 1174 1353 195 177 2.02 0 0 - 0 - - 99 +3 1110 1116 1562 450 444 -0.31 0 - - 0 - - 99 -2 1624 1621 1463 159 156 -4.56 0 - - - - 0 99 +3 1632 1641 1787 153 144 -1.61 0 - - 0 - - 99 +2 1754 1784 1957 201 171 -7.41 0 - 0 - - - 99 +2 1958 1970 2113 153 141 -3.23 0 - 0 - - - 99 0004 -3 2327 2270 426 1899 1842 9.06 99 - - - - - 99 0005 +3 2211 2283 2417 204 132 3.53 99 - - 99 - - - -1 2877 2637 2479 396 156 -2.48 0 99 - - 0 - - -3 2903 2903 2778 123 123 1.12 0 99 - - - - 0 -3 3077 3077 2940 135 135 3.08 0 99 - 0 - - 0 -3 3209 3206 3078 129 126 -1.46 0 99 - - 0 - 0 0006 +1 2323 2359 3294 969 933 11.48 99 99 - - - - - 0007 -2 3346 3298 3167 177 129 -1.58 99 - - - - 99 - 0008 -3 3431 3413 3210 219 201 -0.32 99 - - - - - 99 0009 +3 3225 3363 3518 291 153 -0.34 99 - - 99 - - - 0010 +2 3422 3440 3607 183 165 -2.27 99 - 99 - - - - 0011 -1 3690 3621 3466 222 153 -0.09 99 - - - 99 - - 0012 -2 3763 3751 3602 159 147 2.43 99 - - - - 99 - 0013 -3 3770 3770 3618 150 150 0.10 99 - - - - - 99 0014 +1 3646 3709 3840 192 129 3.10 52 52 - 0 47 - - -1 3852 3831 3691 159 138 1.29 3 96 - 0 3 - - 0015 +3 3663 3687 3884 219 195 -0.84 99 - - 99 - - - 0016 +2 3731 3731 4012 279 279 0.39 99 - 99 - - - - 0017 -3 4118 4037 3903 213 132 -0.66 99 - - - - - 99 0018 +1 3988 4000 4137 147 135 -0.79 99 99 - - - - - 0019 +2 4013 4256 4402 387 144 5.88 99 - 99 - - - - +3 4422 4449 4595 171 144 -11.80 0 99 - 0 - - - -1 4701 4647 4516 183 129 -3.52 0 99 - - 0 - - -3 4853 4808 4671 180 135 -3.07 0 99 - - - - 0 -3 5057 4979 4854 201 123 -1.65 0 99 - 0 0 - 0 -1 5193 5061 4822 369 237 -2.97 0 99 - - 0 - - -2 5317 5266 5069 246 195 -8.40 0 99 - - - 0 - +2 5198 5285 5521 321 234 -6.50 0 99 0 - 0 - - -3 5747 5738 5556 189 180 2.67 0 99 - - 0 - 0 0020 -1 6048 6036 5263 783 771 -3.58 0 99 0 - 0 - - +3 5922 6186 6317 393 129 -9.19 0 99 - 0 0 - - -1 6330 6282 6049 279 231 -6.65 0 99 - 0 0 0 - 0021 +1 4384 4399 6435 2049 2034 9.49 99 99 - - - - - 0022 -1 6669 6516 6352 315 162 -3.92 99 - - - 99 - - -2 6907 6874 6494 411 378 1.07 0 - 99 - - 0 - -3 7160 7028 6888 270 138 -11.14 0 0 99 - 0 - 0 -1 7230 6960 6826 402 132 -4.01 0 0 99 - 0 - - -2 7558 7306 6908 648 396 0.39 0 - 99 - - 0 - +3 7548 7602 7742 192 138 -4.87 0 - 99 0 0 - - -1 7749 7701 7537 210 162 -1.35 0 - 99 - 0 - - -3 7772 7733 7611 159 120 -5.52 0 - 99 0 0 0 0 -1 7932 7929 7783 147 144 -1.72 0 - 99 0 0 0 - -1 8091 8085 7936 153 147 -0.32 0 - 99 0 0 0 0 +3 7743 8016 8138 393 120 -5.82 0 - 99 0 - 0 - 0023 -2 8506 8410 7730 774 678 -1.84 0 - 99 - - 0 - 0024 +2 6428 6482 8524 2094 2040 10.21 99 - 99 - - - - -1 9018 8895 8749 267 144 -0.63 0 99 - - 0 - - -2 9496 9445 9284 210 159 -6.49 0 99 - - - 0 - -3 9548 9518 9375 171 141 -0.42 0 99 - - - - 0 -1 9735 9735 9580 153 153 -0.09 0 99 - - 0 - - +2 9617 9638 9763 144 123 3.17 0 99 0 - - - - 0025 +1 8476 8560 9927 1449 1365 9.30 99 99 - - - - - -3 10424 10352 10230 192 120 -2.26 0 99 - - - - 0 +2 10628 10628 10792 162 162 1.67 0 99 0 - - - - -3 10832 10772 10647 183 123 -1.64 0 99 0 - - - 0 -3 11183 11132 10872 309 258 -1.94 0 99 - - - - 0 0026 +1 9982 9994 11454 1470 1458 6.71 99 99 - - - - - 0027 -1 11556 11523 11365 189 156 2.64 99 - - - 99 - - +2 11612 11702 11872 258 168 -1.11 0 - 0 - 99 - - +1 11716 11815 11949 231 132 -7.45 0 0 - - 99 0 - +1 12034 12037 12186 150 147 -1.26 0 0 - - 99 - - +1 12226 12301 12441 213 138 -3.39 0 0 - - 99 - - +3 12366 12426 12572 204 144 -1.46 0 - 0 0 99 - - +2 12398 12452 12595 195 141 -0.82 0 0 0 - 99 - - +1 12442 12457 12672 228 213 -0.91 0 0 - - 99 - - -3 12695 12686 12561 132 123 -6.08 0 - - - 99 0 0 +2 12728 12728 12907 177 177 2.96 0 0 0 - 99 - - +1 12673 12799 12936 261 135 -8.68 0 0 - - 99 - - +3 12951 12954 13112 159 156 -2.88 0 - 0 0 99 - - 0028 -1 13164 13146 11608 1554 1536 10.02 99 - - - 99 - - +1 12988 13045 13209 219 162 0.03 9 9 90 - - - - 0029 +2 12917 12947 13411 492 462 0.64 99 - 99 - - - - -1 13494 13479 13330 162 147 -5.93 0 - - - 0 99 - +2 13412 13487 13645 231 156 -7.51 0 - 0 - - 99 - +3 13863 13890 14084 219 192 -0.85 0 - 0 0 - 99 - +2 13646 13922 14125 477 201 0.42 0 - 0 - - 99 - 0030 -2 14242 14200 13172 1068 1026 10.06 99 - - - - 99 - +1 14383 14533 14739 354 204 -4.15 0 0 - - 99 - - +2 14747 14756 14905 156 147 0.06 0 0 0 - 99 - - +2 14906 14906 15061 153 153 -1.53 0 0 0 - 99 - - -3 15176 15110 14961 213 147 -3.26 0 0 - - 99 - 0 +1 14740 15070 15240 498 168 -4.23 0 0 - - 99 - - +2 15107 15131 15343 234 210 -0.08 0 - 0 - 99 - - 0031 -1 15441 15396 14227 1212 1167 5.94 99 - - - 99 - - -1 15681 15678 15550 129 126 -7.79 0 - 0 - 0 99 - +2 15554 15560 15724 168 162 -1.88 0 - 0 - - 99 - -3 15902 15887 15708 192 177 -1.54 0 0 - - - 99 0 +1 15652 15808 15930 276 120 -5.55 0 0 0 - - 99 - +2 15737 15827 16228 489 399 -0.68 0 - 0 - - 99 - 0032 -2 16231 16177 15356 873 819 6.47 99 - - - - 99 - 0033 -3 16604 16565 16398 204 165 6.50 99 - - - - - 99 -1 16692 16629 16507 183 120 -2.13 0 - - 99 0 - - 0034 +3 16479 16509 16811 330 300 5.73 99 - - 99 - - - -3 16928 16850 16671 255 177 2.53 2 97 - - - - 2 -1 17028 16893 16693 333 198 2.32 0 99 - - 0 - 0 0035 +1 16669 16744 17040 369 294 6.02 99 99 - - - - - +3 17250 17292 17417 165 123 -0.16 0 0 - 0 99 - - +1 17290 17443 17616 324 171 -2.79 0 0 - - 99 - - +1 17617 18031 18258 639 225 -0.06 0 0 - - 99 - - +3 18138 18186 18329 189 141 -3.91 0 - - 0 99 - - +2 18275 18281 18409 132 126 1.75 0 0 0 - 99 - - +1 18262 18436 18696 432 258 -0.92 0 0 - - 99 - - -3 18758 18737 18570 186 165 -0.44 0 - - - 99 - 0 -3 19010 18974 18759 249 213 -0.93 0 - - - 99 - 0 +3 19032 19071 19202 168 129 -5.16 0 - - 0 99 - - +1 19117 19135 19281 162 144 -2.43 0 0 - - 99 - - -3 19379 19298 19158 219 138 -6.07 0 - - - 99 - 0 0036 -1 19470 19407 17125 2343 2280 9.22 99 - - - 99 - - +3 19422 19527 19652 228 123 3.13 1 - - 1 - - 98 +1 19540 19546 19725 183 177 -0.32 0 0 - - - - 99 +2 19670 19682 19834 162 150 -4.45 0 - 0 - - - 99 +3 19704 19788 19949 243 159 -1.78 0 - - 0 - - 99 -2 20002 19957 19826 174 129 -6.11 0 - - - - 0 99 -2 20137 20128 20003 132 123 -0.79 0 - 0 - - 0 99 0037 -3 20168 20123 19449 717 672 8.49 99 - - - - - 99 +2 19871 20234 20563 690 327 1.59 0 - 0 - - 99 - +2 20618 20648 20977 357 327 2.39 0 - 0 - - 99 - 0038 -2 21004 20980 20138 864 840 11.24 99 - - - - 99 -