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_Porphyromonadaceae/Porphyromonas_fermentans.result/NZ_JACCCY0100000031.4.AOI_02.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_fermentans.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_fermentans.result/NZ_JACCCY0100000031.4.AOI_02 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_fermentans.result/NZ_JACCCY0100000031.4.AOI_02.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_fermentans.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_JACCCY0100000031.4.AOI_02 Sequence length = 21159 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 +2 2 182 307 303 123 -10.24 0 - 0 99 0 - - -1 342 216 70 270 144 -4.69 0 - 0 99 0 - 0 0001 -2 382 349 218 162 129 1.45 80 - - 19 - 80 - -3 584 542 330 252 210 -2.44 0 - 0 99 - - 0 -1 624 516 343 279 171 -8.60 0 - 0 99 0 - 0 +2 308 479 709 399 228 -4.38 0 - 0 99 - 0 - -3 917 797 615 300 180 -1.08 0 - - 99 - 0 0 -2 940 577 446 492 129 -4.65 0 - 0 99 0 0 0 +1 841 853 1020 177 165 -6.11 0 0 - 99 - - - +2 929 1187 1336 405 147 -3.64 0 - 0 99 - - 0 -3 1355 1154 990 363 162 -3.84 0 - 0 99 - - 0 -2 1363 1342 1220 141 120 -1.76 0 - - 99 - 0 0 +1 1528 1573 1752 222 177 -5.24 0 0 - 99 - - - -1 1869 1782 1633 234 147 -6.56 0 - 0 99 0 - - -2 2059 1888 1736 321 150 -0.21 0 - 0 99 - 0 - -3 2210 2024 1860 348 162 -3.10 0 - 0 99 - 0 0 -1 2427 2358 2188 237 168 -9.34 0 - - 99 0 - - -3 2435 2363 2211 222 150 2.60 5 - - 94 0 - 5 -2 2482 2365 2231 249 132 -2.87 0 - - 95 0 0 4 0002 +3 3 3 2696 2691 2691 4.10 99 - - 99 - - - 0003 +1 2392 2578 2703 309 123 1.02 98 98 1 - - - - 0004 -1 2787 2775 2620 165 153 3.48 99 - - - 99 - - -1 3072 2910 2788 282 120 6.30 0 99 - - 0 - - 0005 +1 2731 2776 3153 420 375 7.05 99 99 - - - - - -3 3188 3128 2865 321 261 2.58 0 99 - - - - 0 0006 -2 3343 3286 3116 225 168 -3.63 99 - - - - 99 - -2 3739 3730 3599 138 129 0.91 0 - 0 99 - 0 - -2 3970 3952 3815 153 135 2.64 0 - 0 99 - 0 - 0007 +3 3189 3231 4268 1077 1035 9.37 99 - - 99 - - - 0008 -2 4681 4609 4160 519 447 1.07 99 - - - - 99 - +3 4446 4527 4685 237 156 -7.81 0 - 99 0 0 0 - +3 4686 4770 4898 210 126 -2.31 0 - 99 0 0 0 0 -1 5022 4671 4525 495 144 -3.18 0 - 99 0 0 0 - -2 5299 5044 4682 615 360 0.67 0 - 99 - - 0 - 0009 +2 4229 4271 5377 1146 1104 11.44 99 - 99 - - - - 0010 -1 5871 5859 5683 186 174 5.96 14 - - - 14 - 85 +3 5928 5970 6248 318 276 1.62 0 - - 0 - - 99 -1 6309 6246 6115 192 129 -10.66 0 - - 36 0 - 63 +1 6196 6301 6438 240 135 -0.35 0 0 - - - - 99 0011 -3 6770 6767 5598 1170 1167 7.58 99 - - - - - 99 -3 7574 7568 7419 153 147 2.36 0 - - 99 - - 0 +1 7579 7591 7716 135 123 0.57 0 0 - 99 - - 0 +1 7729 7762 7902 171 138 -0.85 0 0 - 99 - - - -1 7974 7965 7825 147 138 -4.77 0 - - 99 0 - 0 -3 8063 8021 7767 294 252 0.84 0 - - 99 - - 0 -1 8145 8136 7996 147 138 -5.67 0 - - 99 0 0 - -3 8648 8636 8478 168 156 6.60 0 - - 99 - - 0 +1 8533 8557 8709 174 150 -0.01 0 0 - 99 - - - 0012 +3 7215 7239 8777 1560 1536 8.16 99 - - 99 - - - 0013 -3 8918 8876 8730 186 144 -0.21 99 - - - - - 99 -2 9064 8947 8801 261 144 -0.20 0 - 99 - - 0 - -2 9358 9352 9065 291 285 5.78 0 - 99 - - 0 - 0014 +2 8768 8780 9553 783 771 10.46 99 - 99 - - - - 0015 -1 9765 9747 9550 213 195 6.49 99 - - - 99 - - 0016 -2 9997 9988 9632 363 354 9.38 99 - - - - 99 - -2 11248 11227 11105 141 120 5.53 3 - - - - 3 96 0017 -3 11279 11270 9993 1284 1275 11.13 99 - - - - - 99 +1 11296 11314 11670 372 354 1.43 0 0 - - 99 - - +2 11897 11939 12190 291 249 1.04 0 - 0 - 99 - - 0018 -1 13155 13125 11245 1908 1878 11.90 99 - - - 99 - - 0019 +3 13146 13188 13331 183 141 0.38 99 - - 99 - - - 0020 -3 13415 13403 13197 216 204 6.68 99 - - - - - 99 0021 -2 13708 13684 13547 159 135 8.41 99 - - 0 - 99 - 0022 -1 13776 13764 13639 135 123 10.12 99 - - - 99 - - +2 14351 14366 14524 171 156 10.92 4 - 4 - - 95 - 0023 -2 14524 14494 13886 636 606 12.35 99 - - - - 99 - 0024 +2 14612 14612 14839 225 225 -0.66 99 - 99 - - - - -3 15470 15434 15249 219 183 -3.09 0 - - 99 - 0 0 0025 -2 15490 15259 15134 354 123 4.27 88 - - 11 - 88 - 0026 +3 14853 14895 15494 639 597 7.37 99 - - 99 - - - +3 15564 15576 15725 159 147 -15.36 0 99 - 0 - 0 - +2 15602 15662 15814 210 150 -3.10 0 1 0 - 98 - - +3 15726 15726 15872 144 144 -8.64 0 11 - 0 88 - - 0027 +1 15490 15580 16041 549 459 4.50 99 99 - - - - - 0028 -1 16059 16047 15598 459 447 7.01 99 - - - 99 - - +2 16082 16103 16228 144 123 -1.76 0 0 0 - 99 - - -3 16949 16907 16785 162 120 -7.32 0 0 0 - 99 - 0 -3 17189 17147 16962 225 183 -3.34 0 0 0 - 99 - 0 0029 +2 16460 16493 17287 825 792 -1.51 0 0 0 - 99 - - 0030 +1 16042 16582 17304 1260 720 -0.11 0 0 - - 99 - - 0031 -1 17472 17439 16078 1392 1359 6.61 99 - - - 99 - - 0032 +2 17414 17414 17581 165 165 -0.05 99 - 99 - - - - 0033 +1 17425 17440 17652 225 210 0.95 99 99 - - - - - +1 17779 17800 17994 213 192 -1.77 0 0 - - - - 99 +3 17961 18081 18260 297 177 -0.57 0 - - 0 - - 99 +1 18163 18277 18417 252 138 -0.13 0 0 - 0 - - 99 -2 18505 18445 18323 180 120 -9.55 0 - - 0 - 0 99 +3 18261 18315 18554 291 237 -2.44 0 - - 0 - - 99 +1 18418 18466 18609 189 141 -4.61 0 0 - - 0 - 99 +3 18564 18606 18785 219 177 2.30 0 - - 0 - - 99 0034 -3 18851 18839 17466 1383 1371 8.97 99 - - - - - 99 0035 +1 18718 18724 18867 147 141 3.01 99 99 - - - - - +2 19088 19136 19399 309 261 -2.60 0 - 0 - - 99 - +3 19275 19323 19454 177 129 -3.03 0 - - 0 - 99 - -1 19527 19527 19405 120 120 -9.15 0 - 0 - 0 99 0 +2 19400 19412 19540 138 126 0.86 0 - 0 - - 99 0 -3 19571 19457 19332 237 123 -9.58 0 - - - - 99 0 0036 -2 19579 19552 18824 753 726 9.51 99 - - - - 99 - +3 19509 19521 19646 135 123 -5.89 1 98 - 1 - - - +1 19483 19567 19905 420 336 -2.29 0 0 - - 99 - - -2 20080 19945 19625 453 318 -7.54 0 - - - 99 0 - +2 19991 20045 20206 213 159 0.58 0 0 0 - 99 - - -2 20323 20215 20081 240 132 -8.76 0 0 - - 99 0 - +2 20474 20501 20653 177 150 -4.17 0 - 0 - 99 - - +1 20665 20671 20799 132 126 -4.76 0 0 - - 99 - - 0037 -1 20982 20976 19549 1431 1425 8.46 99 - - - 99 - - -1 21126 21120 20983 141 135 -10.33 0 - 0 0 0 99 - 0038 -2 21157 21154 20966 189 186 7.72 99 - 0 0 - 99 -