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_fragilis.result/NZ_JACFSY0100000151.8433.AOI_01.fna /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/GLIMMER.icm /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_JACFSY0100000151.8433.AOI_01 Sequence file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.result/NZ_JACFSY0100000151.8433.AOI_01.fna Number of sequences = 1 ICM model file = /data/pg-molgen/USERS/Vicky/Results_BAGEL4_Peregrine/Results_Bacteroidaceae//Bacteroides_fragilis.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_JACFSY0100000151.8433.AOI_01 Sequence length = 21515 ----- Start ----- --- Length ---- ----------- Scores ------------ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 0001 +1 100 142 501 399 357 1.92 99 99 - - - - - 0002 -1 540 513 187 351 324 11.40 99 - - - 99 - - 0003 +2 398 437 727 327 288 -9.04 99 - 99 - - - - +1 670 868 1002 330 132 1.15 0 0 - - - - 99 0004 -3 1124 1112 510 612 600 10.15 99 - - - - - 99 0005 -3 1253 1247 1125 126 120 -9.48 99 - - - - - 99 +3 1161 1161 1373 210 210 -0.52 0 - 0 0 - 99 - -3 1661 1523 1323 336 198 -6.24 0 - - - - 99 0 +2 1493 1580 1810 315 228 -1.70 0 - 0 - - 99 - 0006 -2 1861 1840 1157 702 681 11.14 99 - - - - 99 - -3 1898 1880 1662 234 216 -7.48 0 - - 99 - - 0 0007 +3 1602 1743 2033 429 288 -3.77 99 - - 99 - - - +1 1858 1948 2073 213 123 -4.37 0 0 0 - 99 - - -3 2144 2117 1986 156 129 -8.08 0 - 0 - 99 - 0 +3 2034 2052 2231 195 177 -13.52 0 - 0 0 99 - - +2 1820 2105 2323 501 216 -1.67 0 0 0 - 99 - - +3 2232 2265 2390 156 123 -13.80 0 0 - 0 99 0 - +2 2324 2327 2449 123 120 3.42 0 0 0 - 99 0 - +3 2601 2625 2753 150 126 -13.76 0 0 - 0 99 - - +1 2074 2644 2775 699 129 0.58 0 0 - - 99 - - +3 2754 2859 2996 240 135 -14.15 0 0 0 0 99 - - +2 2816 3059 3211 393 150 -3.00 0 - 0 - 99 - - +1 3076 3157 3306 228 147 -3.88 0 0 - - 99 - 0 -3 3455 3260 3135 318 123 -8.65 0 0 - - 99 - 0 +2 3254 3269 3472 216 201 -0.13 0 - 0 - 99 - - +1 3391 3466 3630 237 162 0.79 0 0 - - 99 - - +1 3712 3718 3855 141 135 -3.61 0 0 0 0 99 - - +3 3600 3720 3896 294 174 -12.36 0 - 0 0 99 - - +2 3554 3569 3985 429 414 2.91 0 - 0 - 99 - - +2 4142 4163 4327 183 162 -2.27 0 0 0 - 99 - - +3 4593 4638 4760 165 120 -14.73 0 0 - 0 99 - - 0008 +1 4054 4252 4824 768 570 -3.35 0 0 0 - 99 - - +2 4667 4787 4993 324 204 -0.73 0 - 0 - 99 - - +1 4825 4849 5031 204 180 0.36 0 0 - - 99 - - +3 4890 4935 5060 168 123 -9.20 0 - - 0 99 0 - +3 5157 5160 5339 180 177 -8.71 0 0 0 0 99 - - +1 5032 5191 5523 489 330 -3.40 0 0 0 - 99 - - +2 5141 5420 5578 435 156 -1.16 0 - 0 - 99 - - +2 5807 5828 5962 153 132 -3.36 0 0 0 - 99 - 0 -3 5966 5960 5808 156 150 -8.45 0 0 0 - 99 0 0 +1 5524 5662 6003 477 339 0.86 0 0 - - 99 - - -3 6164 6137 6000 162 135 -11.43 0 - - - 99 0 0 -2 6199 6142 5957 240 183 -10.70 0 - - - 99 0 - +1 6016 6097 6243 225 144 -2.62 0 0 0 - 99 - - 0009 -1 6252 6168 1849 4401 4317 11.55 99 - - - 99 - - 0010 +2 6095 6143 6319 222 174 1.48 99 - 99 - - - - -3 6659 6620 6495 162 123 -14.75 0 - - - 99 - 0 +2 6545 6677 6802 255 123 -1.01 0 0 0 - 99 - - +1 6526 6862 7026 498 162 -8.61 0 0 - 0 99 - - +3 6819 6912 7085 264 171 -15.30 0 - - 0 99 0 - +1 7027 7030 7188 159 156 -2.11 0 0 - - 99 0 - -3 7379 7310 7173 204 135 -4.90 0 - - - 99 - 0 +1 7297 7582 7740 441 156 0.13 0 0 - - 99 - - +2 7646 7670 7813 165 141 -5.04 0 - 0 - 99 0 - +1 8041 8119 8385 342 264 -3.49 0 0 - - 99 - - 0011 -1 8415 8397 6253 2160 2142 11.01 99 - - - 99 - - 0012 -2 8458 8455 8321 135 132 3.36 96 - 0 3 - 96 - 0013 +2 8216 8231 8536 318 303 -5.02 99 - 99 - - - - 0014 +3 8268 8373 8606 336 231 -3.98 99 - - 99 - - - +2 8621 8666 8794 171 126 -12.94 0 - 0 0 - - 99 -2 8959 8926 8798 159 126 -8.13 0 - - 0 - 0 99 +3 8670 8760 9008 336 246 0.70 0 - - 0 - - 99 0015 -3 9104 9083 8427 675 654 8.83 99 - - - - - 99 0016 +1 8959 9067 9342 381 273 1.43 99 99 - - - - - -2 9547 9532 9404 141 126 -4.82 0 - - - - 0 99 +1 9499 9604 9732 231 126 -1.03 0 0 - 0 - - 99 +3 9579 9582 9779 198 195 1.39 0 - - 0 - - 99 0017 -3 9977 9956 9105 870 849 8.37 99 - - - - - 99 0018 +2 9971 9971 10093 120 120 -6.58 99 - 99 - - - - +2 10301 10403 10561 258 156 0.32 0 - 0 - 99 - - +2 10832 10838 10966 132 126 -6.31 0 - 0 - 99 - - +2 10967 11135 11287 318 150 -1.29 0 - 0 - 99 - - +2 11333 11357 11488 153 129 -5.21 0 - 0 - 99 - - 0019 -1 11571 11517 9997 1572 1518 7.91 99 - - - 99 - - 0020 +2 11627 11627 11767 138 138 0.33 99 - 99 - - - - 0021 +3 11793 11796 11948 153 150 -5.22 99 - - 99 - - - 0022 -3 12029 11966 11808 219 156 -0.73 99 - - - - - 99 0023 +3 12132 12141 12275 141 132 0.01 69 - 30 69 - - - -2 12427 12421 12215 210 204 -0.90 0 - 99 - - 0 - 0024 +2 12023 12095 12439 414 342 4.08 99 - 99 - - - - -2 12766 12703 12563 201 138 -11.01 0 99 - - 0 0 - +2 12572 12686 12820 246 132 -6.61 0 99 0 - 0 - - -3 12953 12893 12735 216 156 1.65 0 99 - - 0 - 0 0025 -1 13083 12648 12436 645 210 1.55 99 - - - 99 - - +3 12927 13029 13151 222 120 -15.24 0 99 - 0 - - 0 -3 13196 13082 12954 240 126 1.85 0 99 - 0 0 - 0 -1 13269 13254 13096 171 156 -3.73 0 99 - - 0 - - -3 13331 13331 13200 129 129 -6.91 0 99 - - - - 0 0026 +1 12481 12487 13395 912 906 10.07 99 99 - - - - - 0027 -2 13594 13495 13328 264 165 2.62 99 - - - - 99 - 0028 +3 13434 13461 13655 219 192 -5.90 99 - - 99 - - - +3 13716 13734 13856 138 120 -5.03 0 99 - 0 - - - 0029 +1 13732 13756 13917 183 159 -2.31 99 99 - - - - - 0030 +3 13905 13929 14054 147 123 3.64 48 - - 48 - - 51 0031 -3 14069 14045 13914 153 129 4.76 69 - - 30 - - 69 -1 14505 14484 14098 405 384 2.55 0 - 99 - 0 - - -1 14652 14652 14518 132 132 -4.05 0 - 99 - 0 0 - -2 14902 14893 14732 168 159 0.17 0 - 99 - - 0 0 -3 14930 14906 14727 201 177 -9.20 0 - 99 - - - 0 -1 15327 14934 14803 522 129 -2.00 0 - 99 - 0 - 0 -1 15594 15579 15328 264 249 0.82 0 - 99 - 0 - - 0032 +2 14048 14072 15670 1620 1596 11.83 99 - 99 - - - - 0033 +2 15731 15746 15871 138 123 3.50 95 - 95 - - 4 - 0034 -2 15943 15712 15443 498 267 -5.39 99 - - - - 99 - -2 16105 16093 15944 159 147 -4.30 0 - - 99 - 0 0 -3 16427 16271 16119 306 150 1.68 0 - - 99 - - 0 -1 16494 16431 16282 210 147 -14.07 0 - - 99 0 - 0 0035 +3 15825 15840 16520 693 678 9.62 99 - - 99 - - - -1 16734 16680 16534 198 144 -0.03 0 - 99 - 0 0 - +1 16540 16540 16740 198 198 -8.31 0 0 99 - - 0 - -2 16759 16513 16391 366 120 -0.98 0 - - 99 - 0 - -1 16992 16938 16735 255 201 1.96 0 - 99 - 0 - - -2 17125 17080 16799 324 279 -4.32 0 0 99 - - 0 - -1 17256 17241 17017 237 222 3.68 0 0 99 - 0 - - 0036 +1 16741 16789 17682 939 891 -9.06 0 0 99 - - - - -1 17760 17754 17611 147 141 0.56 0 - 99 - 0 0 - 0037 +2 16499 16517 18046 1545 1527 10.67 99 - 99 - - - - 0038 -2 18103 18049 17570 531 477 -1.12 99 - - - - 99 - -1 18141 17997 17848 291 147 -2.23 0 - 99 - 0 0 - -1 18597 18543 18409 186 132 -3.34 0 - 0 99 0 - 0 +2 18296 18341 18610 312 267 -8.52 0 - 0 99 - - - -2 18673 18643 18485 186 156 -2.59 0 - - 99 - 0 - -2 18979 18925 18731 246 192 -1.34 0 - 0 99 - 0 0 -3 19106 18707 18570 534 135 3.21 0 - - 99 - - 0 +2 18620 18935 19162 540 225 -5.70 0 - 0 99 - - - 0039 +3 18174 18198 19385 1209 1185 10.39 99 - - 99 - - - 0040 -1 19416 19407 19258 156 147 -3.87 31 - - - 31 5 63 0041 -2 19465 19456 19250 213 204 -2.85 95 - - - - 95 4 -3 19589 19328 19107 480 219 -0.11 0 - - 99 - - 0 +3 19611 19626 19748 135 120 -5.75 0 99 - 0 - - - 0042 +1 19561 19798 19959 396 159 1.05 99 99 - - 0 - - 0043 -1 19983 19797 19660 321 135 -1.75 52 47 - - 52 - - 0044 +2 19817 19856 20005 186 147 -6.35 99 - 99 - - - - -1 20175 20136 20014 159 120 -1.75 0 - 99 - 0 0 - +3 20247 20268 20393 144 123 -8.28 0 - 99 0 0 0 - -1 20508 20445 20236 270 207 3.89 0 - 99 - 0 0 - +3 20460 20517 20672 210 153 -9.08 0 0 99 0 - 0 - +1 20506 20545 20745 237 198 -13.32 0 0 99 - - 0 - -1 20865 20772 20641 222 129 -1.29 0 - 99 - 0 0 - +3 20859 20862 21014 153 150 -2.50 0 - 99 0 - 0 - 0045 -2 21031 20170 19988 1041 180 0.09 99 - - - - 99 - -3 21263 21251 21114 147 135 -7.25 0 - 99 - - 0 0 -2 21514 21163 21032 480 129 1.47 0 - 99 - - 0 -