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_bennonis.result/NZ_AQWR010000261.30.AOI_01.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_bennonis.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_bennonis.result/NZ_AQWR010000261.30.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_bennonis.result/NZ_AQWR010000261.30.AOI_01.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_bennonis.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_AQWR010000261.30.AOI_01 Sequence length = 17802 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 0001 +1 1 40 480 477 438 7.65 99 99 - - - - - -3 596 398 240 354 156 -5.34 0 99 - - 0 - 0 -3 785 779 657 126 120 -10.92 0 0 0 - 99 0 0 +2 593 707 850 255 141 3.49 0 0 0 - 99 - - +1 634 685 987 351 300 5.01 0 0 - - 99 - - +1 988 1015 1221 231 204 1.47 0 0 - - 99 - - -3 1223 1214 1074 147 138 -7.10 0 0 - 0 99 0 0 0002 -1 1371 1227 643 726 582 12.65 99 - - - 99 - - -2 1405 1342 1211 192 129 -13.43 0 - 0 99 0 0 - +3 1053 1245 1409 354 162 9.63 3 - - 3 - 0 96 -2 1606 1585 1460 144 123 -19.21 0 0 - 0 - 0 99 +1 1285 1519 1644 357 123 -6.23 0 0 - 0 - - 99 0003 -3 1871 1868 1227 642 639 11.95 99 - - - - - 99 +1 1729 1756 1899 168 141 -5.54 0 0 - 99 - - - +1 1900 2032 2220 318 186 -2.25 0 0 - 0 - - 99 -2 2383 2284 2111 270 171 -19.01 0 - - 0 - 0 99 +2 2537 2579 2701 162 120 -18.74 0 - 0 0 - 0 99 -2 2770 2635 2501 267 132 -6.63 0 - - 53 - 0 46 0004 +3 1410 1479 2774 1362 1293 1.11 99 - - 99 - - - -2 2971 2962 2831 138 129 -17.83 0 - - 0 0 0 99 +3 2775 2826 2993 216 165 -2.61 0 - - 0 0 - 99 +3 2994 3024 3251 255 225 0.44 0 - - 0 - - 99 +3 3252 3273 3518 264 243 -2.28 0 - - 0 - 0 99 -2 3589 3451 3248 339 201 -20.96 0 - - 0 - 0 99 +2 3470 3515 3721 249 204 -21.95 0 - 0 0 0 - 99 +1 3631 3655 3783 150 126 -1.37 0 0 - 0 0 - 99 +1 3784 3889 4014 228 123 5.33 0 0 - 0 - 0 99 -2 4033 3997 3842 189 153 -24.14 0 0 - 0 - 0 99 +3 3519 3528 4196 675 666 1.80 0 - - 0 - - 99 -1 4419 4413 4234 183 177 -10.31 0 - - - 0 - 99 0005 -3 4664 4190 1872 2790 2316 11.43 99 - - - - - 99 -1 4752 4737 4420 330 315 4.64 0 99 - 0 0 - - +3 4347 4386 4985 636 597 -11.79 0 99 - 0 - - - -2 5071 5050 4922 147 126 -23.13 0 99 - - 0 0 0 0006 -1 5526 5064 4753 771 309 3.05 0 99 - - 0 - - +3 5379 5427 5564 183 135 -11.58 0 99 - 0 - - 0 -3 5567 5513 4830 735 681 1.22 0 99 - - 0 - 0 0007 +1 4387 4417 5736 1347 1317 9.83 99 99 - - - - - -2 5959 5938 5762 195 174 -21.10 0 99 - 0 - 0 - -1 6006 5922 5773 231 147 1.53 0 99 - 0 0 0 - -3 6098 6056 5919 177 135 -13.22 0 99 - - - - 0 -3 6227 6224 6099 126 123 -2.85 0 99 - - 0 - 0 -3 6719 6674 6543 174 129 -10.38 0 99 - - 0 0 0 0008 +1 5740 5803 6822 1080 1017 17.27 99 99 - - - - - 0009 -1 6855 6588 6034 819 552 1.45 0 99 - - 0 - - 0010 -3 6917 6896 6720 195 174 -2.47 99 - - - - - 99 -3 7052 7040 6918 132 120 -7.64 0 99 - - - - 0 +2 7076 7157 7306 228 147 -23.68 0 99 0 - 0 - - 0011 +1 6823 6835 7974 1149 1137 16.14 99 99 - - - - - -1 7992 7713 7522 468 189 -3.65 0 99 - - 0 - - +2 7700 7853 7996 294 141 -19.16 0 - 0 - 99 - - +2 8000 8090 8224 222 132 -4.43 0 0 0 - 99 - - +3 8571 8571 8696 123 123 -14.28 0 0 0 0 99 - 0 -3 8747 8540 8346 399 192 -20.08 0 0 0 - 99 - 0 0012 -1 8763 8751 8056 705 693 17.66 99 0 - - 99 - - +2 8312 8606 8770 456 162 -2.71 1 98 1 - - - - 0013 +1 7975 8287 8781 804 492 3.89 99 99 - - - - - -2 8998 8902 8759 237 141 -22.61 0 - - 99 - 0 - +3 8754 8877 9215 459 336 5.73 0 - - 0 - - 99 0014 -3 9518 9497 8799 717 696 13.55 99 - - - - - 99 -1 9603 9570 9262 339 306 -16.12 0 - 0 99 0 - - 0015 +3 9216 9288 9665 447 375 0.88 99 - 0 99 - - - -1 9822 9804 9682 138 120 -21.41 0 - 0 - 0 99 - 0016 +2 9260 9455 9955 693 498 -2.16 99 - 99 - - - - 0017 -2 9973 9946 9500 471 444 13.79 99 - 0 - - 99 - -1 10209 10161 10039 168 120 -13.70 0 0 0 - 0 99 - +1 10012 10045 10320 306 273 -21.47 0 0 0 - - 99 - -1 10344 10344 10210 132 132 -14.43 0 - 0 - 0 99 - +2 9971 10043 10480 507 435 0.30 0 - 0 - - 99 - -1 10986 10953 10771 213 180 -19.96 0 - 0 0 0 99 0 +3 10461 10890 11159 696 267 -3.97 0 - 0 0 - 99 - +2 10481 10844 11176 693 330 2.94 0 - 0 - - 99 - 0018 -2 11215 11170 9974 1239 1194 11.72 99 - - - - 99 - +3 11190 11322 11510 318 186 -8.42 0 - - 0 - 99 - -3 11591 11591 11457 132 132 -16.99 0 0 - - 0 99 0 -1 11598 11514 11380 216 132 -6.01 1 - - - 1 98 - +2 11531 11543 11686 153 141 -7.58 0 98 0 - - 0 - 0019 +1 11410 11464 11697 285 231 -6.58 99 99 - - - 0 - 0020 -2 11710 11368 11240 468 126 -5.71 99 - - 0 - 99 - +2 11834 11912 12076 240 162 -3.20 0 - 0 - 99 0 - -3 12452 12422 12276 174 144 -12.48 0 0 - - 99 - 0 +1 11959 12064 12486 525 420 2.00 0 0 - - 99 - - +2 12602 12611 12742 138 129 -6.61 0 0 0 - 99 - - +1 12487 12553 12873 384 318 1.74 0 0 - - 99 - - +1 12874 13252 13407 531 153 0.34 0 0 - - 99 - 0 -3 13607 13265 13107 498 156 -17.33 0 0 - - 99 0 0 +2 13586 13619 13747 159 126 1.10 0 0 0 - 99 - - +1 13408 13546 13848 438 300 -1.84 0 0 - - 99 - - +2 13748 13748 13870 120 120 4.15 0 - 0 - 99 0 - +3 13827 13836 13991 162 153 -16.94 0 - - 0 99 0 - +1 13849 13906 14187 336 279 -1.80 0 0 - - 99 0 - -2 14245 13894 13664 579 228 -12.99 0 - - - 99 0 - +2 14456 14462 14629 171 165 -1.97 0 0 0 - 99 - - +1 14188 14236 14808 618 570 4.12 0 0 - - 99 - - 0021 -1 14913 14790 11659 3252 3129 19.74 99 - - - 99 - - +3 14658 14811 14999 339 186 1.90 0 - - 0 - - 99 -2 15022 14992 14864 156 126 -18.02 0 0 - 0 - 0 99 +1 14848 14893 15069 219 174 -2.18 0 0 - - - - 99 +2 15086 15095 15232 144 135 -11.84 0 - 0 0 - - 99 -2 15454 15310 15176 276 132 -17.22 0 - - 0 - 0 99 +3 15099 15240 15458 357 216 6.18 0 - - 0 - 0 99 -1 15741 15717 15514 225 201 -18.86 0 - - - 0 - 99 +2 15617 15626 15763 144 135 -11.19 0 - 0 0 - - 99 0022 -3 16076 15905 14805 1269 1098 7.52 99 - - - - - 99 -1 16503 16080 15910 591 168 -20.64 0 - 0 - 0 99 0 -1 16902 16800 16660 240 138 -20.67 0 - 0 - 0 99 - +3 16944 17022 17198 252 174 -4.54 0 - 0 0 0 99 0 -1 17232 17163 16903 327 258 -19.39 0 - 0 - 0 99 - 0023 -2 17473 17449 15902 1569 1545 18.03 99 - 0 - - 99 - -3 17534 17489 17211 321 276 -11.10 0 - 99 - - - 0 0024 -1 17604 17586 17446 156 138 -4.97 99 - 0 - 99 - - 0025 +2 15869 15968 17629 1758 1659 -0.31 99 - 99 - - - - 0026 -2 17722 17620 17474 246 144 -5.21 72 - 27 0 - 72 - 0027 +3 17478 17595 17759 279 162 -10.32 99 - - 99 - - - 0028 -1 17802 17769 17617 183 150 -10.67 99 - - - 99 - -