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_macacae.result/NZ_UGTI010000011.110.AOI_01.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_macacae.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_macacae.result/NZ_UGTI010000011.110.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_macacae.result/NZ_UGTI010000011.110.AOI_01.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Porphyromonadaceae/Porphyromonas_macacae.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_UGTI010000011.110.AOI_01 Sequence length = 21128 ----- 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 34 216 213 180 13.24 99 99 - - - - - +2 299 311 439 138 126 -0.19 0 - 0 - - 99 - -3 578 575 405 171 168 -5.82 0 - - - - 99 0 +1 481 499 639 156 138 1.47 1 1 - - - 98 - 0002 -2 760 757 179 579 576 5.14 99 - - - - 99 - 0003 +3 603 615 782 177 165 4.90 99 - - 99 - - - 0004 -3 920 899 678 240 219 -5.22 99 - - - - - 99 +2 857 881 1030 171 147 2.81 0 - 0 - - 99 - +3 1128 1128 1370 240 240 1.42 0 - - 0 - 99 - +2 1148 1436 1582 432 144 5.10 8 - 8 - - 91 - +3 1494 1494 1715 219 219 4.81 0 - - 0 - 99 - -1 1842 1806 1651 189 153 2.82 0 - - - 0 99 - 0005 +1 1735 1744 1923 186 177 3.84 68 68 - - - 31 - +1 1924 1930 2130 204 198 -4.10 0 0 - - - 99 - 0006 +3 2229 2241 2405 174 162 4.84 98 - - 98 - 1 - 0007 -2 2548 2344 761 1785 1581 6.93 99 - - - - 99 - 0008 -1 2586 2535 2407 177 126 -2.08 64 - - - 64 35 - -1 2805 2805 2587 216 216 2.82 0 - 99 - 0 - - -2 2863 2851 2681 180 168 -1.38 0 - 99 - - 0 - +1 2734 2836 3063 327 225 -4.20 0 0 99 - - - - -2 3208 3175 3023 183 150 -1.51 0 - 99 - - 0 - +3 3213 3216 3341 126 123 0.74 0 - 99 0 0 - - -1 3390 3339 3172 216 165 1.46 0 - 99 - 0 - - -2 3412 3394 3260 150 132 0.91 0 - 99 - 0 0 - 0009 +2 2444 2456 3475 1029 1017 7.30 99 - 99 - - - - +1 3691 3781 3903 210 120 0.37 0 0 - 99 - - 0 -3 4007 3977 3495 510 480 1.25 0 - - 99 - - 0 0010 +3 3486 3519 4367 879 846 11.98 99 - - 99 - - - 0011 -3 4460 4391 4008 450 381 -2.10 99 - - - - - 99 -1 4653 4545 4399 252 144 -4.74 0 99 - - 0 - - -1 4974 4926 4792 180 132 -5.43 0 99 - - 0 - - -3 5033 4982 4854 177 126 3.57 4 95 - - - - 4 0012 +2 5003 5018 5158 153 138 6.44 41 49 41 - 8 - - -3 5183 5180 5052 129 126 -2.92 0 95 - - 4 - 0 -1 5217 5175 4975 240 198 4.00 0 99 - - 0 - - -1 5613 5595 5428 183 165 0.55 0 99 - - 0 - - 0013 +2 5543 5564 5701 156 135 -0.02 67 32 67 - - - - -3 5909 5891 5682 225 207 1.61 1 98 - - - - 1 0014 +1 4339 4339 5928 1587 1587 4.03 99 99 - - - - - -3 6038 6035 5913 123 120 0.28 0 - - 99 0 - 0 0015 -1 6144 6015 5824 318 189 -2.27 99 - - - 99 - - 0016 +3 5874 5925 7049 1173 1122 5.75 99 - - 99 - - - 0017 -1 7203 7128 6844 357 282 -0.94 99 - - - 99 - - +3 7095 7104 7292 195 186 3.50 0 99 - 0 - - 0 0018 -3 7469 7412 7050 417 360 5.91 99 - - - - - 99 -1 7617 7611 7486 129 123 3.21 0 99 - - 0 - - 0019 +1 7108 7108 7767 657 657 11.98 99 99 - - - - - -1 7917 7818 7678 237 138 -0.92 0 - - - 0 99 - 0020 -2 7951 7909 7538 411 369 -0.28 99 - - - - 99 - -3 8153 8015 7881 270 132 -0.66 0 - - 99 - - 0 -1 8418 8289 8164 252 123 -3.14 0 - - 99 0 - 0 -3 8699 8318 8154 543 162 1.99 0 - - 99 - - 0 +1 8683 8704 8826 141 120 1.30 0 0 - 99 - - 0 0021 +3 7755 7758 8942 1185 1182 9.43 99 - - 99 - - - 0022 +2 8750 8906 9028 276 120 1.86 99 - 99 - - - - -2 9214 9208 9017 195 189 3.47 0 - - 99 - 0 - -3 9311 9266 9099 210 165 3.55 0 - - 99 - - 0 +1 9187 9217 9360 171 141 -0.66 0 0 - 99 - - - 0023 -2 9526 9418 9293 231 123 9.36 23 - - 76 - 23 - -1 9615 9501 9325 288 174 -3.33 0 - - 98 0 1 - -2 9682 9670 9527 153 141 0.36 0 - - 99 - 0 0 -3 9764 9764 9435 327 327 -1.05 0 - - 99 - - 0 +1 9604 9625 9768 162 141 -0.83 0 0 - 99 - - 0 0024 +3 8952 8955 9974 1020 1017 11.03 99 - - 99 - - - 0025 -2 10033 10012 9818 213 192 0.98 99 - - - - 99 - 0026 -3 10100 10100 9936 162 162 -0.45 99 - - - - - 99 +1 10168 10183 10323 153 138 -3.27 0 0 - 99 - - - -2 10498 10495 10358 138 135 -0.85 0 - - 99 - 0 0 -3 10568 10514 10332 234 180 1.74 0 - - 99 - - 0 -2 10666 10645 10523 141 120 -2.11 0 - - 99 - 0 - +1 10624 10624 10764 138 138 -1.81 0 0 - 99 - - 0 -3 10823 10805 10569 252 234 -0.21 0 - - 99 - - 0 -3 11009 10988 10824 183 162 2.95 0 - - 99 - - 0 0027 +3 9975 9993 11159 1182 1164 10.22 99 - - 99 - - - 0028 -2 11218 11197 11021 195 174 9.10 99 - - - - 99 - 0029 -1 11325 11325 11122 201 201 1.45 99 - - - 99 - - 0030 +1 11191 11203 11388 195 183 2.95 99 99 - - - - - +2 11792 11801 11926 132 123 0.73 0 0 0 - 99 - - +3 11826 11835 11984 156 147 -2.04 0 0 - 0 99 - - +1 11602 11881 12015 411 132 1.34 0 0 - - 99 - - 0031 -1 12087 12069 11326 759 741 8.70 99 - - - 99 - - 0032 +2 11927 11966 12127 198 159 4.87 99 - 99 - - - - -3 13094 13070 12924 168 144 -3.89 0 - 99 - - - 0 0033 +2 12914 12950 13408 492 456 8.17 99 - 99 - - - - 0034 +2 13409 13445 13603 192 156 3.26 99 - 99 - - - - -2 13807 13783 13562 243 219 -0.02 0 - - 99 - 0 - -3 13946 13943 13773 171 168 -0.86 0 0 - 99 - - 0 +1 13777 13798 13953 174 153 -2.22 0 0 - 99 - - - -2 14032 13993 13871 159 120 -0.64 0 - - 99 - 0 - -3 14246 14195 13980 264 213 -5.14 0 - - 99 - - 0 0035 +3 13485 13500 14270 783 768 8.56 99 - - 99 - - - 0036 -2 14842 14623 14135 705 486 -0.11 99 - - - - 99 - -1 14955 14859 14584 369 273 5.16 0 - 99 - 0 - - -2 15163 15133 14885 276 246 -2.51 0 - 99 - - 0 - 0037 +2 14258 14264 15175 915 909 11.07 99 - 99 - - - - -3 15380 15377 15144 234 231 -0.53 0 99 - - - - 0 -1 15582 15459 15196 384 261 0.11 0 99 - - 0 - - +3 15297 15348 15596 297 246 -6.03 0 99 - 0 - - - -3 15761 15716 15471 288 243 5.62 0 99 - - - - 0 -1 15828 15774 15583 243 189 -3.14 0 99 - - 0 - - 0038 +1 15139 15172 15864 723 690 10.24 99 99 - - - - - -3 16262 16181 16005 255 174 2.81 0 - - 99 - - 0 -3 16559 16487 16263 294 222 -0.39 0 - - 99 - - 0 -1 17070 17070 16897 171 171 -10.04 0 - - 99 0 - 0 -3 17096 17078 16560 534 516 1.91 0 - - 99 - - 0 -3 17393 17309 17157 234 150 4.88 0 - - 99 0 - 0 0039 +3 15939 15951 17501 1560 1548 11.00 99 - - 99 - - - 0040 -1 17616 17610 17149 465 459 0.47 99 - - - 99 - - -2 17713 17683 17555 156 126 -2.34 0 99 - - - 0 - -1 17853 17787 17617 234 168 -1.21 0 99 - - 0 - - -3 18296 18185 17991 303 192 4.47 0 99 - - - - 0 0041 +1 17488 17494 18504 1014 1008 9.76 99 99 - - - - - 0042 -3 18752 18749 18453 297 294 6.05 99 - - - - - 99 -2 19429 19180 19019 408 159 -7.93 0 99 - - 0 0 - -3 19481 19481 19350 129 129 3.43 0 99 - - 0 - 0 0043 +1 18505 18508 19524 1017 1014 9.86 99 99 - - - - - 0044 -1 19569 19527 19321 246 204 1.77 99 - - - 99 - - +1 19618 19660 19785 165 123 -4.54 0 0 86 - - 13 - -2 19915 19783 19622 291 159 4.99 0 0 99 - - 0 - +3 19779 19809 19931 150 120 -6.62 0 - 99 0 - - - -3 20390 20375 20253 135 120 5.25 0 - 99 - 0 0 0 -1 20424 20406 20239 183 165 5.75 0 - 99 - 0 0 - -2 20539 20353 20216 321 135 0.70 0 - 99 - - 0 - 0045 +2 19556 19610 20602 1044 990 10.42 99 - 99 - - - - 0046 -1 20733 20700 20536 195 162 -1.15 99 - - - 99 - - -3 20762 20759 20610 150 147 -2.82 0 - - 99 - 0 0 -2 20770 20713 20576 192 135 -6.06 0 - - 99 0 0 - -3 21056 21050 20814 240 234 0.90 0 - - 99 - - 0 -1 21084 21045 20836 246 207 -2.64 0 - 0 99 0 - 0 -2 21106 21088 20921 183 165 3.20 0 - - 99 0 0 -