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_gingivalis.result/NZ_SGBA010000031.2581.AOI_01.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_SGBA010000031.2581.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.result/NZ_SGBA010000031.2581.AOI_01.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_gingivalis.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_SGBA010000031.2581.AOI_01 Sequence length = 14763 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 -2 433 211 83 348 126 -4.63 0 - - 99 - 0 - 0001 +3 3 48 533 528 483 7.21 99 - - 99 - - - 0002 -3 578 578 333 243 243 -6.27 99 - - - - - 99 -2 775 766 602 171 162 -3.99 0 - - 99 - 0 - -3 839 821 663 174 156 -3.54 0 - - 99 - - 0 0003 +3 606 690 884 276 192 1.61 99 - - 99 - - - -2 1141 898 776 363 120 -10.26 0 99 - - - 0 - 0004 +1 1021 1033 1158 135 123 -0.32 77 77 - - 22 - - 0005 -1 1206 1086 913 291 171 -2.16 61 - - - 61 38 - 0006 +3 1044 1125 1316 270 189 -6.60 99 - - 99 - - - 0007 -2 1567 1516 1388 177 126 -5.80 99 - - - - 99 - 0008 +2 1448 1526 1705 255 177 -4.91 99 - 99 - - - - 0009 -1 1791 1713 1549 240 162 -5.76 99 - - - 99 - - 0010 -2 1891 1774 1622 267 150 -6.20 67 - - - 32 67 - 0011 +2 1718 1745 1918 198 171 -5.79 99 - 99 - - - - +1 1852 2014 2205 351 189 -1.19 0 0 - - - - 99 +3 2076 2136 2363 285 225 3.60 0 - - 0 - - 99 +1 2368 2395 2523 153 126 -3.63 0 0 - 0 - - 99 +3 2364 2400 2555 189 153 -5.92 0 - - 0 - - 99 0012 -3 2582 2567 1821 759 744 6.91 99 - - - - - 99 0013 +1 2524 2569 3105 579 534 -0.53 99 99 - - - - - -2 3307 3193 3047 258 144 -7.91 0 - - - 99 0 - 0014 -1 3510 3492 2572 936 918 4.67 99 - - - 99 - - +2 3248 3377 3556 306 177 -4.69 1 74 1 24 - - - 0015 +3 3375 3492 3617 240 123 -3.63 98 1 - 98 - - - -2 3670 3652 3518 150 132 -8.72 0 99 - - - 0 - 0016 -3 3764 3758 3618 144 138 0.65 93 6 - - - - 93 0017 +1 3106 3625 3915 807 288 -1.74 99 99 - - - - - +1 3919 3928 4095 174 165 -8.85 0 0 0 - - 99 - -1 4230 4191 4048 180 141 -10.18 0 - 0 - 0 99 - +2 3830 4190 4327 495 135 0.92 6 - 6 - - 93 0 0018 -2 4357 4267 3887 468 378 5.95 99 - 0 - - 99 - +2 4730 4760 4888 156 126 -3.05 0 0 0 - 99 0 - 0019 -1 5049 5019 4330 717 687 11.55 99 0 - - 99 - - 0020 +1 4279 4708 5061 780 351 -0.57 99 99 - - - - - 0021 +2 4889 4904 5086 195 180 -3.23 99 - 99 - - - - +1 5092 5104 5238 144 132 -6.14 1 1 48 49 - - - +2 5087 5117 5248 159 129 -4.29 2 - 2 97 - - - 0022 -3 5381 5372 5235 144 135 -2.35 14 85 - 0 - - 14 0023 +3 5076 5184 5429 351 243 -5.29 99 - - 99 - - - +2 5297 5321 5449 150 126 -6.67 0 99 0 - - - - +2 5450 5537 5695 243 156 -6.07 0 99 0 0 0 - - +3 5430 5514 5717 285 201 -8.69 0 99 - 0 0 - - -3 5810 5678 5550 258 126 -4.08 0 99 0 0 0 - 0 0024 +1 5239 5269 5859 618 588 6.88 99 99 - - - - - -1 5895 5739 5365 528 372 -0.23 0 99 - - 0 - - 0025 +3 5724 5856 5981 255 123 -0.89 95 4 - 95 - - - +1 5860 5983 6174 312 189 -0.39 0 0 99 - - - 0 0026 +2 5900 5954 6178 276 222 3.95 99 - 99 - - - 0 -3 6197 6068 5865 330 201 -3.10 7 92 - - - - 7 +3 6120 6135 6269 147 132 -0.65 0 - - 0 - 99 - 0027 -2 6283 6247 6095 186 150 2.61 99 - - - - 99 - 0028 -1 6516 6420 6253 261 165 0.31 99 - - - 99 - - 0029 +2 6350 6383 6679 327 294 -2.73 99 - 99 - - - - 0030 -2 6688 6634 6440 246 192 1.98 99 - 0 - - 99 - -2 7012 6850 6689 321 159 -2.79 0 - - 99 - 0 - +1 6883 6925 7059 174 132 -8.91 0 0 0 99 - - 0 +2 6830 6872 7066 234 192 -11.84 0 - 0 99 - - 0 -2 7165 7153 7013 150 138 -1.50 0 - - 99 - 0 0 +2 7067 7079 7222 153 141 -4.88 0 - 0 99 - - 0 -2 7300 7294 7166 132 126 1.69 0 - - 99 - 0 0 -2 7498 7492 7361 135 129 -3.56 0 - - 99 - 0 0 -1 7587 7527 7402 183 123 -6.75 0 - - 99 0 - 0 -2 7894 7831 7709 183 120 -1.66 0 - 0 99 - 0 0 +2 7871 7898 8074 201 174 -8.39 0 - 0 99 - - 0 +1 8101 8155 8319 216 162 -8.34 0 0 - 99 - - 0 0031 -3 8420 8393 6738 1680 1653 0.41 0 - - 99 - - 0 0032 +3 6516 6525 8579 2061 2052 9.89 99 - - 99 - - - 0033 +2 8495 8564 8764 267 198 -9.14 99 - 99 - - - - -3 8849 8789 8640 207 147 1.64 0 - - 99 - - 0 +1 8878 8896 9021 141 123 -10.77 0 0 - 99 0 - - -2 9223 9223 9086 135 135 -1.71 0 - - 99 - 0 0 0034 +3 8580 8664 9290 708 624 9.85 99 - - 99 - - - -3 9389 9221 9039 348 180 3.32 0 - - 99 - - 0 0035 +2 9191 9227 9403 210 174 -2.91 99 0 99 - - - - +2 9404 9419 9553 147 132 -5.01 0 0 0 - 99 - - -3 9698 9656 9504 192 150 -9.74 0 0 - - 99 - 0 +1 9151 9577 9702 549 123 -1.43 0 0 - - 99 - 0 -2 9754 9727 9602 150 123 -12.23 0 - - - 99 0 - 0036 -1 9777 9774 9355 420 417 3.02 99 - - - 99 - - +2 9617 9635 9781 162 144 -3.75 0 - 0 - 99 - - +3 10038 10098 10256 216 156 -4.61 0 0 - 0 99 - - +1 9898 10096 10308 408 210 0.97 0 0 - - 99 - - +3 10257 10311 10490 231 177 -9.31 0 - - 0 99 - - +2 10466 10640 10789 321 147 -1.70 0 - 0 - 99 0 - -2 10795 10741 10520 273 219 -7.00 0 - 0 - 99 0 - -3 10895 10895 10770 123 123 -9.52 0 0 - - 99 - 0 +2 10949 10973 11098 147 123 1.90 0 0 0 0 99 0 - +1 10900 10996 11127 225 129 -2.78 0 0 - - 99 - - 0037 -1 11145 11145 9979 1164 1164 8.26 99 - - - 99 - - +2 11099 11198 11326 225 126 -4.28 0 0 0 - 99 0 - -3 11558 11555 11433 123 120 -6.35 0 0 0 - 99 - 0 +2 11327 11444 11728 399 282 -4.57 0 0 0 - 99 - - -2 11833 11797 11474 357 321 -7.28 0 0 - - 99 0 - 0038 -1 12168 12159 11164 1002 993 8.10 99 0 - - 99 - - 0039 +1 11155 12202 12354 1197 150 1.54 99 99 - - - - 0 +2 12233 12248 12418 183 168 -5.18 0 - 0 - 99 - - +3 12336 12378 12509 171 129 -6.33 0 0 - 0 99 - - -2 12736 12706 12467 267 237 -10.33 0 0 - - 99 0 - -3 12815 12791 12660 153 129 -5.09 0 0 - - 99 - 0 +2 12746 12752 12880 132 126 -7.42 0 0 0 0 99 - - +3 12675 12711 12896 219 183 -10.65 0 0 - 0 99 - - +1 12355 12445 12939 582 492 -0.35 0 0 - - 99 - - +2 12914 12953 13078 162 123 -6.30 0 0 0 - 99 - - +1 12940 13129 13299 357 168 2.37 0 0 0 - 99 - - +2 13079 13178 13330 249 150 -7.63 0 - 0 - 99 - - +3 13194 13194 13346 150 150 -5.55 0 - - 0 99 - - 0040 -1 13440 13344 12223 1215 1119 4.93 99 - - - 99 - - +3 13473 13629 13793 318 162 0.64 0 - 0 0 - 98 - +1 13732 13747 13887 153 138 -8.33 0 0 1 - - 98 - +2 13586 13604 13948 360 342 1.38 0 - 0 - - 99 - +1 13942 14032 14157 213 123 -4.89 0 0 - 58 - 41 - 0041 -2 14263 13963 13358 903 603 4.34 99 - - - - 99 - 0042 +3 13998 14139 14327 327 186 4.51 99 - - 99 - - - 0043 -1 14448 14385 14185 261 198 -7.48 99 - - - 99 - - 0044 +1 14506 14512 14661 153 147 -6.60 25 25 - - - - 74 0045 -3 14762 14636 14502 258 132 -5.16 92 7 - - - - 92