Mercurial > repos > bgruening > glimmer_build_icm
view test-data/glimmer_w_icm_trans-table-11_genomic.dout @ 1:15ad71e21010 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author | iuc |
---|---|
date | Tue, 30 Oct 2018 18:46:17 -0400 |
parents | 9c195b26a5ac |
children | cc51783dc93c |
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Command: glimmer3 -o 50 -g 90 -t 30 -z 11 -A atg,gtg,ttg -l /tmp/tmpubrxoL/files/000/dataset_1.dat /tmp/tmpubrxoL/files/000/dataset_2.dat glimmer_output Sequence file = /tmp/tmpubrxoL/files/000/dataset_1.dat Number of sequences = 1 ICM model file = /tmp/tmpubrxoL/files/000/dataset_2.dat Excluded regions file = none List of orfs file = none Input is NOT separate orfs Independent (non-coding) scores are used Circular genome = false Truncated orfs = false Minimum gene length = 90 bp Maximum overlap bases = 50 Threshold score = 30 Use first start codon = false Translation table = 11 Start codons = atg,gtg,ttg Start probs = 0.333,0.333,0.333 Stop codons = taa,tag,tga GC percentage = 70.9% Ignore score on orfs longer than 1738 >gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence Sequence length = 147347 ----- Start ----- --- Length ---- ------------- Scores ------------- ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC +1 289 316 417 126 99 -12.44 0 0 0 0 - 0 0 99 +1 418 706 894 474 186 -12.50 0 0 0 72 - 0 0 26 +2 203 755 907 702 150 -7.78 0 - 0 4 - 0 5 89 -2 934 478 245 687 231 -16.05 0 - 0 0 - 0 0 99 -1 1005 960 808 195 150 -10.87 0 - - 0 0 - 0 99 +1 895 904 1029 132 123 -21.92 0 0 - 0 - - 0 99 +2 1211 1316 1450 237 132 -9.27 0 0 0 0 0 0 99 0 -2 1513 1462 1295 216 165 -13.99 0 0 - 0 0 0 99 0 -1 1587 1506 1006 579 498 -11.27 0 - - 0 0 - 1 98 +1 1132 1774 2016 882 240 -10.77 0 0 0 0 0 0 99 0 -2 2221 1633 1514 705 117 -17.27 0 0 0 0 - 0 0 99 +2 1451 2192 2287 834 93 -3.86 2 0 2 11 0 - 5 80 +2 2288 2414 2524 234 108 -14.85 0 0 0 0 0 0 98 0 +1 2386 2521 2676 288 153 -10.44 0 0 0 0 - 0 99 0 -2 2704 2332 2222 480 108 -8.27 0 - - 83 0 0 7 9 +1 2677 2713 2865 186 150 -16.16 0 0 0 42 - 0 4 53 0001 +3 174 183 2918 2742 2733 -2.60 0 - - 0 - - 99 0 +2 2525 2828 2947 420 117 -8.18 0 - 0 - - 0 0 99 0002 -3 3062 2777 144 2916 2631 -1.16 0 0 - - 0 - 0 99 -2 3301 2845 2705 594 138 -6.29 0 0 0 62 - 0 0 37 +2 2948 3149 3352 402 201 -10.20 0 0 0 0 0 - - 99 +1 2866 3262 3363 495 99 -8.25 0 0 - 13 0 - 3 83 -1 3396 3171 2995 399 174 -6.74 0 0 0 - 0 0 - 99 -2 3403 3400 3302 99 96 -10.07 0 - - 95 0 0 1 2 -3 3419 3407 3195 222 210 -5.41 0 - - 1 - - 0 98 -1 3810 3810 3553 255 255 -10.41 0 - 0 0 0 - 99 0 +3 3102 3750 3866 762 114 0.43 0 0 0 0 - 0 98 0 +3 3867 4098 4313 444 213 -6.66 0 0 0 0 - 38 0 60 -3 4343 3824 3420 921 402 -0.79 4 - 0 0 - - 4 95 +2 3353 3869 4357 1002 486 1.19 5 0 5 - - 94 - 0 +1 3754 4183 4413 657 228 -5.38 0 0 - - 0 0 - 99 -1 4416 4254 4105 309 147 -9.43 0 27 0 0 0 10 0 60 -2 4438 4081 3641 795 438 -3.03 0 - 0 - - 0 0 99 +1 4516 4519 4635 117 114 -13.75 0 0 - 0 0 0 1 98 +1 4636 4651 4755 117 102 -11.88 0 0 - 51 2 0 0 45 +1 4756 4789 4884 126 93 -12.88 0 0 - 57 0 - 6 35 +1 4885 5017 5109 222 90 -13.07 0 0 0 99 - 0 0 0 -2 5323 5050 4859 462 189 -13.21 0 - - 83 0 0 0 16 +1 5110 5227 5376 264 147 -10.43 0 0 - 17 0 - 0 81 +3 4314 5430 5606 1290 174 -8.42 0 - - 0 - 0 0 99 -3 5699 4442 4344 1353 96 -16.33 0 - - 3 - 0 0 96 -2 5710 5560 5339 369 219 -19.46 0 - - 0 - 0 0 99 +3 5607 5631 5786 177 153 -14.74 0 0 0 0 0 - - 99 -3 5876 5849 5715 159 132 -13.78 0 6 0 - 0 - 0 92 +2 5540 5840 5956 414 114 -7.11 0 99 0 0 0 0 - 0 -3 6170 6080 5922 246 156 -12.41 0 6 - - 0 - 0 93 +1 5596 5833 6183 585 348 -1.28 1 1 - - 0 - - 98 +2 5957 6044 6196 237 150 -13.96 0 - 0 0 41 - - 58 -1 6366 5805 5617 747 186 -4.60 0 0 0 - 0 - - 99 +1 6247 6304 6399 150 93 -15.50 0 0 0 0 - 66 - 33 -3 6500 6494 6354 144 138 -8.37 0 - 0 0 - 0 0 99 +2 6197 6200 6559 360 357 -9.78 0 - 0 0 - - - 99 +3 6036 6426 6566 528 138 -12.55 0 - - 0 0 0 - 99 -2 6571 6460 6230 339 228 -6.11 0 - 0 0 - 0 - 99 +2 6560 6632 6760 198 126 -4.57 0 0 0 0 0 0 0 99 -1 6828 6486 6367 459 117 -11.09 0 - 2 0 0 0 0 97 +3 6567 6870 7016 447 144 -17.36 0 0 - 0 0 - 0 99 -3 7055 6722 6591 462 129 -6.81 0 0 0 0 0 0 0 99 -1 7155 7107 6829 324 276 -3.23 0 0 - 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99 +3 8343 8673 8771 426 96 -17.17 0 0 2 0 - 0 0 97 -3 8885 8798 8451 432 345 -11.88 0 - 0 - - 0 0 99 +2 8279 8861 8965 684 102 -18.08 0 0 0 0 0 0 - 99 +1 8830 8896 9006 174 108 -15.65 0 0 - - 0 0 - 99 -2 9076 8263 7994 1080 267 -0.85 1 - 83 0 - 1 0 14 -1 9483 8790 8686 795 102 -12.36 0 - 0 - 0 0 0 99 -2 9571 9427 9290 279 135 -9.65 0 0 57 0 0 0 6 36 +3 9081 9201 9602 519 399 -0.17 22 0 0 22 - - 31 45 0004 -3 9656 9575 9039 615 534 0.16 70 0 0 - - - 70 29 +2 8966 9524 9664 696 138 -7.28 0 0 0 - 0 - - 99 +2 9665 9719 9829 162 108 -12.97 0 4 0 0 32 - - 63 -3 9887 9875 9753 132 120 -8.52 0 0 - 0 0 - 0 98 +1 9007 9685 9906 897 219 -3.64 0 0 - - 35 - - 64 -1 9912 9651 9484 426 165 -8.05 0 0 0 - 0 - 0 99 +3 9723 9807 9938 213 129 -6.37 0 - - 0 - - - 99 -2 9982 9958 9821 159 135 -2.76 2 - - - - 2 - 97 -3 10040 9986 9888 150 96 -9.57 0 - 0 - - 84 0 15 +2 9830 9929 10084 252 153 -13.60 0 3 0 - 0 - - 96 -1 10209 10197 9913 294 282 -9.64 0 0 - - 0 - - 99 -2 10222 10159 10067 153 90 -5.61 0 0 - 0 0 0 0 99 -3 10340 10181 10041 297 138 -10.51 0 0 - 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96 3 +1 19078 19150 19245 165 93 -12.66 0 0 - 14 0 0 0 85 0012 +3 18666 19242 19361 693 117 0.51 62 0 - 62 1 0 0 35 +1 19246 19252 19371 123 117 -8.89 0 0 - - 3 0 0 96 +2 19499 19514 19621 120 105 -12.19 0 0 0 0 1 - 0 97 -3 19694 19097 18996 696 99 -4.82 0 - 0 0 - - 0 99 +3 19494 19758 19883 387 123 0.69 0 0 - 0 99 - - 0 -3 19994 19988 19809 183 177 -9.69 0 0 - - 98 - 0 0 +1 19372 19906 20079 705 171 -1.39 5 5 0 0 42 0 - 52 -1 20205 19140 19024 1179 114 -12.42 0 - 6 0 0 - 58 35 -2 20275 20083 19874 399 207 -8.43 0 - - - 64 0 - 35 +3 19884 20343 20444 558 99 -7.90 0 - 20 0 0 0 45 34 +3 20478 20589 20702 222 111 -7.21 0 0 0 0 0 0 3 95 +1 20593 20650 20754 159 102 -12.16 0 0 1 - 0 0 98 0 +1 20785 20800 20892 105 90 -8.04 0 0 89 0 - 0 0 10 -3 21473 20153 19995 1476 156 -9.30 0 - 0 0 3 0 0 96 +3 20703 21399 21503 798 102 -11.04 0 63 0 0 0 4 - 31 0013 +2 19910 20378 21781 1869 1401 1.14 99 - 99 - - 0 - 0 +2 21920 21977 22099 177 120 -8.11 0 99 0 - 0 0 0 0 +2 22142 22316 22531 387 213 -2.03 0 99 0 - 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