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_vulgatus.result/NC_0096141.0.AOI_01.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_vulgatus.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_vulgatus.result/NC_0096141.0.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_vulgatus.result/NC_0096141.0.AOI_01.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_vulgatus.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_0096141.0.AOI_01 Sequence length = 21143 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 -1 465 384 226 237 156 -0.47 0 99 - - 0 - - 0001 +1 1 22 1092 1089 1068 10.48 99 99 - - - - - +2 1403 1463 1588 183 123 -5.79 0 99 0 - 0 - - -3 1658 1658 1530 126 126 -1.79 0 99 - - - - 0 -3 2090 2078 1938 150 138 -1.55 0 99 - - - - 0 +3 1995 2004 2129 132 123 -6.92 0 99 - 0 - - - -1 2421 2409 2257 162 150 0.41 0 99 0 - 0 - - +3 2280 2289 2453 171 162 -7.93 0 99 0 0 - - - +2 2243 2243 2566 321 321 -1.96 0 99 0 - - - - +3 2646 2688 2828 180 138 -6.05 0 99 - 0 - - - -3 3068 2990 2844 222 144 -3.90 0 99 - - - - 0 +2 3164 3176 3310 144 132 -7.70 0 99 0 - - - - -3 3323 3323 3180 141 141 0.40 0 99 - - - - 0 -1 3333 3318 3193 138 123 -0.82 0 99 - - 0 - 0 -3 3707 3545 3423 282 120 0.92 0 99 - - - - 0 -3 3899 3893 3708 189 183 -0.19 0 99 - - 0 - 0 -1 3969 3906 3676 291 228 1.78 0 99 - - 0 - - -3 4121 4106 3921 198 183 1.06 0 99 - - - - 0 -1 4266 4194 4021 243 171 -1.22 0 99 - - 0 - - +2 4088 4112 4270 180 156 -6.39 0 99 0 - 0 - - -1 4395 4392 4267 126 123 0.27 0 99 - - 0 - 0 -3 4430 4334 4212 216 120 2.30 0 99 - 0 - - 0 -2 4459 4441 4289 168 150 -8.08 0 99 - - - 0 - -1 4572 4557 4399 171 156 -1.88 0 99 - - 0 - - -3 4976 4973 4851 123 120 7.06 0 99 - - - - 0 -3 5153 5099 4977 174 120 2.53 0 99 - - 0 - 0 0002 +1 1225 1228 5160 3933 3930 10.33 99 99 - - - - - -1 5178 5106 4933 243 171 -1.98 0 99 - - 0 - - 0003 -3 5297 5297 5163 132 132 4.31 99 - - - - - 99 -1 5667 5604 5452 213 150 -3.85 0 - 99 - 0 - - 0004 +2 5408 5417 5671 261 252 4.49 99 - 99 - - - - 0005 -3 5786 5777 5601 183 174 -1.05 99 - - - - - 99 +3 5853 5901 6044 189 141 3.55 0 - 0 0 - 99 - 0006 +2 5675 5747 6136 459 387 -1.75 99 - 99 - - - - +3 6066 6072 6275 207 201 0.71 0 - - 0 - 99 - +3 6276 6291 6428 150 135 -1.14 0 - 0 0 - 99 - +2 6137 6281 6484 345 201 -0.64 0 - 0 - - 99 - -1 6582 6579 6457 123 120 -3.19 0 0 - - 0 99 0 -3 6605 6554 6432 171 120 -6.88 0 0 - - - 99 0 +3 6546 6609 6737 189 126 -3.00 0 - 1 0 - 98 - -1 6912 6813 6658 252 153 -6.42 0 0 - - 0 99 - +2 6845 6866 7057 210 189 -1.50 0 - 0 - - 99 - 0007 -2 7129 7117 5771 1356 1344 8.85 99 - - - - 99 - 0008 +3 6981 7017 7148 165 129 -6.55 17 82 - 17 - - - 0009 -3 7370 7346 7140 228 204 3.56 99 - - - - - 99 -2 7486 7483 7343 141 138 -7.72 0 99 - - - 0 - -3 7781 7739 7581 198 156 0.64 0 99 - - - - 0 0010 +1 7246 7267 7908 660 639 11.02 99 99 - - - - - 0011 -1 8040 7917 7678 360 237 -1.35 99 - - - 99 - - -2 8080 7963 7802 276 159 -12.92 0 - - - 99 0 - -3 8102 8096 7911 189 183 -1.00 0 99 - - - - 0 -1 8406 8310 8041 363 267 -2.97 0 99 - - 0 - - -3 8474 8456 8325 147 129 -8.95 0 99 - - - - 0 -3 8651 8648 8493 156 153 -6.96 0 99 - - 0 0 0 -1 8793 8754 8434 357 318 -1.14 0 99 - - 0 - - -3 8972 8963 8805 165 156 -4.76 0 99 - - - - 0 0012 +1 7915 7921 9000 1083 1077 11.55 99 99 - - - - - -3 9290 9245 9105 183 138 -1.28 0 - - 99 - - 0 -2 9616 9478 9302 312 174 -0.08 0 - - 99 - 0 - -3 9710 9533 9396 312 135 -1.65 0 - - 99 - 0 0 +1 9667 9688 9849 180 159 -11.52 0 0 - 99 - - - -2 9967 9952 9821 144 129 2.72 0 - - 99 - 0 0 0013 +3 8985 8997 9971 984 972 12.99 99 - - 99 - - - -3 9983 9905 9711 270 192 -2.04 0 - - 99 - - 0 -2 10285 10243 10112 171 129 -5.07 0 99 - 0 - 0 - +3 10083 10158 10304 219 144 -5.18 0 99 - 0 - - - -3 10676 10673 10551 123 120 1.04 0 99 - - - - 0 -3 11093 11075 10953 138 120 -5.11 0 99 - - 0 - 0 0014 +1 9997 10000 11157 1158 1155 12.39 99 99 - - - - - -1 11163 11097 10666 495 429 0.97 0 99 - - 0 - - -3 11435 11414 11292 141 120 -8.97 0 - 99 - 0 - 0 -1 11490 11487 11281 207 204 -3.34 0 - 99 - 0 - - -2 11611 11575 11387 222 186 -5.77 0 - 99 - - 0 - +3 11703 11712 11843 138 129 -5.79 0 - 99 0 - 0 - 0015 +2 11141 11180 11866 723 684 11.04 99 - 99 - - - - 0016 -2 11878 11869 11693 183 174 2.42 99 - - - - 99 - -3 12143 12113 11910 231 201 2.21 0 99 - - - - 0 -1 12270 12147 11989 279 156 5.53 1 98 - - 1 - 0 0017 +1 11806 11896 12294 486 396 7.66 99 99 - - - - - 0018 +3 12330 12354 12590 258 234 -2.74 99 - - 99 - - - 0019 +2 12461 12470 12595 132 123 -8.50 99 - 99 - - - - -3 12956 12932 12783 171 147 -3.55 0 - 0 - - 99 0 +2 12713 13208 13372 657 162 -0.72 0 - 0 - - 99 - 0020 -2 13675 13648 12683 990 963 11.27 99 - - - - 99 - 0021 +2 13373 13541 13699 324 156 0.76 99 - 99 - - - - -1 14064 14061 13900 162 159 -3.88 0 - - 0 0 - 99 +1 14077 14113 14244 165 129 -4.66 0 0 - 0 - - 99 -2 14305 14302 14147 156 153 -16.23 0 - - 0 - 0 99 0022 +3 13569 13578 14501 930 921 -2.57 0 - - 0 - - 99 -1 14553 14529 14380 171 147 -6.77 0 - - - 0 - 99 +1 14572 14575 14706 132 129 0.21 3 3 0 0 - - 96 -2 14908 14842 14720 186 120 -14.68 0 1 - 0 - 0 98 0023 -3 14933 14921 13668 1263 1251 5.65 99 - - - - - 99 +3 14502 14703 14993 489 288 -5.29 0 99 - 0 - - - +2 14984 15209 15445 459 234 -2.58 0 0 0 - 99 - - 0024 +1 14707 14707 15546 837 837 -1.01 0 0 - - 99 - - +2 15446 15539 15700 252 159 2.13 0 - 0 - 99 - - +1 15547 15757 15894 345 135 -8.50 0 0 - - 99 - - +2 15779 15848 16033 252 183 1.19 2 - 2 - 97 - - 0025 -1 16110 16107 14959 1149 1146 6.33 99 - - - 99 - - 0026 -2 16399 16354 16142 255 210 1.44 99 - - - - 99 - -2 16894 16603 16478 414 123 -1.58 0 - - 99 - 0 0 -3 16973 16700 16467 504 231 5.55 0 - - 99 - - 0 0027 +3 16182 16200 16982 798 780 12.51 99 - - 99 - - - 0028 -1 17277 17250 17086 189 162 4.18 99 - - - 99 - - +3 17190 17217 17360 168 141 -4.63 0 - 99 0 - 0 - -1 17535 17421 17278 255 141 -1.59 0 - 99 - 0 0 - +1 17461 17470 17670 207 198 -11.89 0 0 99 - - 0 - -3 17834 17684 17505 327 177 -15.90 0 - 99 - - 0 0 +1 17698 17764 17892 192 126 -7.85 0 0 99 - - 0 - -1 18063 17970 17824 237 144 1.77 0 - 99 - 0 0 - 0029 -2 18238 18154 17156 1080 996 -4.05 0 - 99 - - 0 - +3 18558 18606 18770 210 162 -6.92 0 - 99 0 - 0 - -2 18862 18499 18314 546 183 -2.23 0 - 99 - - 0 - -3 18908 18884 18753 153 129 -7.70 0 - 99 - - - 0 -1 18957 18930 18796 159 132 -7.13 0 0 99 - 0 - - +1 18796 18814 18978 180 162 -5.90 0 0 99 - - - - +1 19105 19105 19284 177 177 -2.67 0 0 99 - - - - 0030 +2 17129 17186 19378 2247 2190 11.32 99 - 99 - - - - 0031 -1 19494 19488 19363 129 123 3.33 99 - - - 99 - - +3 19563 19701 19844 279 141 -8.90 0 0 - 0 99 - - +1 19705 19735 19926 219 189 0.60 0 0 - - 99 - - -3 20051 20000 19857 192 141 -1.11 0 - - 0 99 - 0 +3 19845 19923 20138 291 213 -6.15 0 0 - 0 99 - - +1 19927 19942 20184 255 240 -3.66 0 0 - - 99 - - -3 20306 20288 20154 150 132 -9.08 0 - - - 99 - 0 +2 20168 20267 20401 231 132 -2.50 0 0 0 - 99 - - +2 20486 20498 20638 150 138 -5.57 0 0 0 - 99 - - +3 20748 20763 20891 141 126 -9.34 0 0 0 0 99 0 - +2 20696 20741 20905 207 162 1.44 0 0 0 - 99 0 - -2 20941 20926 20714 225 210 -7.18 0 0 - - 99 0 - 0032 -1 21141 21138 19501 1638 1635 10.11 99 - - - 99 - -