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_VOHY010000171.8078.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_VOHY010000171.8078.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_VOHY010000171.8078.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_VOHY010000171.8078.AOI_01 Sequence length = 21515 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 0001 +3 99 141 500 399 357 2.62 99 - - 99 - - - 0002 -3 539 512 186 351 324 11.33 99 - - - - - 99 0003 +1 397 436 726 327 288 -8.99 99 99 - - - - - +3 669 867 1001 330 132 1.21 0 - - 0 - 99 - 0004 -2 1123 1111 509 612 600 10.28 99 - - - - 99 - 0005 -2 1252 1246 1124 126 120 -9.33 99 - - - - 99 - +2 1160 1160 1372 210 210 -0.36 0 0 0 - 99 - - -2 1660 1522 1322 336 198 -6.71 0 - - - 99 0 - +1 1492 1579 1809 315 228 -1.51 0 0 - - 99 - - 0006 -1 1860 1839 1156 702 681 11.44 99 - - - 99 - - -2 1897 1879 1661 234 216 -7.55 0 - 99 - - 0 - 0007 +2 1601 1742 2032 429 288 -3.80 99 - 99 - - - - +3 1857 1947 2072 213 123 -4.25 0 0 - 0 - - 99 -2 2143 2116 1985 156 129 -8.10 0 0 - - - 0 99 +2 2033 2051 2230 195 177 -13.27 0 0 0 - - - 99 +1 1819 2104 2322 501 216 -1.91 0 0 - 0 - - 99 +2 2231 2264 2389 156 123 -13.43 0 - 0 0 0 - 99 +1 2323 2326 2448 123 120 2.83 0 0 - 0 0 - 99 +3 2073 2643 2774 699 129 0.10 0 - - 0 - - 99 +2 2753 2858 2995 240 135 -14.53 0 0 0 0 - - 99 +1 2815 3058 3210 393 150 -3.09 0 0 - - - - 99 +3 3075 3156 3305 228 147 -3.53 0 - - 0 - 0 99 -2 3454 3259 3134 318 123 -8.77 0 - - 0 - 0 99 +1 3253 3268 3471 216 201 0.69 0 0 - - - - 99 +3 3390 3465 3629 237 162 0.96 0 - - 0 - - 99 +3 3711 3717 3854 141 135 -3.77 0 0 0 0 - - 99 +2 3599 3719 3895 294 174 -12.51 0 0 0 - - - 99 +1 3553 3568 3984 429 414 2.68 0 0 - - - - 99 +1 4141 4162 4326 183 162 -2.18 0 0 - 0 - - 99 +2 4592 4637 4759 165 120 -15.41 0 - 0 0 - - 99 0008 +3 4053 4251 4823 768 570 -3.40 0 0 - 0 - - 99 +1 4666 4786 4992 324 204 -1.29 0 0 - - - - 99 +3 4824 4848 5030 204 180 -0.59 0 - - 0 - - 99 +2 4889 4934 5059 168 123 -9.58 0 - 0 - 0 - 99 +2 5156 5159 5338 180 177 -9.08 0 0 0 0 - - 99 +3 5031 5190 5522 489 330 -3.46 0 0 - 0 - - 99 +1 5140 5419 5577 435 156 -0.19 0 0 - - - - 99 +1 5806 5827 5961 153 132 -2.05 0 0 - 0 - 0 99 -2 5965 5959 5807 156 150 -8.69 0 0 - 0 0 0 99 +3 5523 5574 6002 477 426 0.25 0 - - 0 - - 99 -2 6163 6136 5999 162 135 -11.97 0 - - - 0 0 99 -1 6198 6141 5956 240 183 -10.72 0 - - - 0 - 99 +3 6015 6096 6242 225 144 -2.53 0 0 - 0 - - 99 0009 -3 6251 6167 1848 4401 4317 11.62 99 - - - - - 99 0010 +1 6094 6142 6318 222 174 1.60 99 99 - - - - - -2 6658 6619 6494 162 123 -15.81 0 - - - - 0 99 +1 6544 6676 6801 255 123 -0.62 0 0 - 0 - - 99 +3 6525 6861 7025 498 162 -8.37 0 - 0 0 - - 99 +2 6818 6911 7084 264 171 -15.51 0 - 0 - 0 - 99 +3 7026 7029 7187 159 156 -2.00 0 - - 0 0 - 99 -2 7378 7309 7172 204 135 -5.07 0 - - - - 0 99 +3 7188 7581 7739 549 156 0.18 0 - - 0 - - 99 +1 7645 7669 7812 165 141 -5.31 0 0 - - 0 - 99 0011 -3 8414 8396 6252 2160 2142 11.19 99 - - - - - 99 0012 -1 8457 8454 8320 135 132 3.15 95 0 4 - 95 - - 0013 +1 8215 8230 8535 318 303 -5.09 99 99 - - - - - 0014 +2 8267 8372 8605 336 231 -3.93 99 - 99 - - - - +1 8620 8665 8793 171 126 -12.92 0 0 0 - - 99 - -1 8958 8925 8797 159 126 -8.73 0 - 0 - 0 99 - +2 8669 8759 9007 336 246 0.71 0 - 0 - - 99 - 0015 -2 9103 9082 8426 675 654 9.12 99 - - - - 99 - 0016 +3 8958 9066 9341 381 273 1.30 99 - - 99 - - - -1 9546 9531 9403 141 126 -5.75 0 - - - 0 99 - +3 9498 9603 9731 231 126 -0.99 0 - 0 0 - 99 - +2 9578 9581 9778 198 195 1.35 0 - 0 - - 99 - 0017 -2 9976 9955 9104 870 849 8.09 99 - - - - 99 - 0018 +1 9970 9970 10092 120 120 -6.82 99 99 - - - - - +1 10300 10402 10560 258 156 -0.06 0 0 - - - - 99 +1 10831 10837 10965 132 126 -6.35 0 0 - - - - 99 +1 10966 11134 11286 318 150 -1.73 0 0 - - - - 99 +1 11332 11356 11487 153 129 -5.54 0 0 - - - - 99 0019 -3 11570 11516 9996 1572 1518 7.74 99 - - - - - 99 0020 +1 11626 11626 11766 138 138 0.38 99 99 - - - - - 0021 +2 11792 11795 11947 153 150 -4.89 99 - 99 - - - - 0022 -2 12028 11965 11807 219 156 -0.54 99 - - - - 99 - 0023 +2 12131 12140 12274 141 132 -0.31 59 40 59 - - - - -1 12426 12420 12214 210 204 -1.25 0 99 - - 0 - - 0024 +1 12022 12154 12438 414 282 4.48 99 99 - - - - - -1 12765 12702 12562 201 138 -11.38 0 - - 99 0 - 0 +1 12571 12685 12819 246 132 -5.57 0 0 - 99 - - 0 -2 12952 12892 12734 216 156 1.73 0 - - 99 - 0 0 0025 -3 13082 12647 12435 645 210 1.25 99 - - - - - 99 +2 12926 13028 13150 222 120 -15.03 0 - 0 99 - 0 - -2 13195 13081 12953 240 126 3.39 0 - 0 99 - 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99 - - 0 0 0034 +2 15833 15839 16519 684 678 9.42 99 - 99 - - - - -3 16733 16679 16533 198 144 0.35 0 99 - - 0 - 0 +3 16539 16539 16739 198 198 -8.23 0 99 - 0 0 - - -1 16758 16512 16390 366 120 -1.64 0 - 99 - 0 - - -3 16991 16937 16734 255 201 2.13 0 99 - - - - 0 -1 17124 17079 16798 324 279 -5.27 0 99 - 0 0 - - -3 17255 17189 17016 237 171 4.30 0 99 - 0 - - 0 0035 +3 16740 16788 17681 939 891 -8.91 0 99 - 0 - - - -3 17759 17753 17610 147 141 0.60 0 99 - - 0 - 0 0036 +1 16498 16516 18045 1545 1527 10.92 99 99 - - - - - -3 18107 17996 17847 258 147 -0.61 0 99 - - 0 - 0 -1 18141 17790 17392 747 396 -1.06 0 99 - - 0 - - -1 18597 18543 18409 186 132 -3.16 0 - 0 98 0 - 1 +2 18296 18341 18610 312 267 -8.72 0 - 0 99 - - - -2 18673 18643 18485 186 156 -2.40 0 - - 99 - 0 - -2 18979 18925 18731 246 192 -1.92 0 - 0 99 - 0 0 -3 19106 18707 18570 534 135 3.04 0 - - 99 - - 0 +2 18620 18935 19162 540 225 -5.24 0 - 0 99 - - - 0037 +3 18174 18198 19385 1209 1185 10.32 99 - - 99 - - - 0038 -1 19416 19407 19258 156 147 -4.15 37 - - - 37 9 53 0039 -2 19441 19438 19250 189 186 -2.65 99 - - - - 99 0 0040 +2 19361 19394 19564 201 168 0.65 99 - 99 - - - 0 -3 19589 19328 19107 480 219 -0.28 0 - - 99 - - 0 +3 19611 19626 19748 135 120 -5.64 0 99 - 0 - - - 0041 +1 19561 19798 19959 396 159 0.63 99 99 - - 0 - - 0042 -1 19983 19809 19660 321 147 -1.04 40 59 - - 40 - - 0043 +2 19817 19856 20005 186 147 -6.70 99 - 99 - - - - -1 20175 20136 20014 159 120 -1.46 0 - 99 - 0 0 - -1 20538 20445 20236 300 207 3.88 0 - 99 - 0 0 - +3 20460 20517 20672 210 153 -9.36 0 0 99 0 - 0 - +1 20506 20545 20745 237 198 -13.83 0 0 99 - - 0 - -1 20865 20772 20641 222 129 -1.34 0 - 99 - 0 0 - +3 20859 20862 21014 153 150 -2.95 0 - 99 0 - 0 - 0044 -2 21031 20170 19988 1041 180 0.32 99 - - - - 99 - -3 21263 21251 21114 147 135 -7.35 0 - 99 - - 0 0 -2 21514 21163 21032 480 129 1.57 0 - 99 - - 0 -