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1 # This output was generated with AUGUSTUS (version 2.7).
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2 # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
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3 # and Oliver Keller (keller@cs.uni-goettingen.de).
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4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
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5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
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6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
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7 # No extrinsic information on sequences given.
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8 # Initialising the parameters ...
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9 # human version. Using default transition matrix.
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10 # Looks like /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat is in fasta format.
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11 # We have hints for 0 sequences and for 0 of the sequences in the input set.
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12 #
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13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
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14 #
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15 # Constraints/Hints:
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16 # (none)
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17 # Predicted genes for sequence number 1 on both strands
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18 # start gene g1
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19 HS04636 AUGUSTUS gene 966 6903 1 + . g1
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20 HS04636 AUGUSTUS transcript 966 6903 . + . g1.t1
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21 HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "g1.t1"; gene_id "g1";
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22 HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "g1.t1"; gene_id "g1";
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23 HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "g1.t1"; gene_id "g1";
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24 HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "g1.t1"; gene_id "g1";
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25 HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "g1.t1"; gene_id "g1";
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26 HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "g1.t1"; gene_id "g1";
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27 HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "g1.t1"; gene_id "g1";
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28 HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "g1.t1"; gene_id "g1";
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29 HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "g1.t1"; gene_id "g1";
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30 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
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31 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
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32 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
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33 HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
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34 HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
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35 HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
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36 HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
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37 HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
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38 HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
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39 HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1";
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40 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
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41 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
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42 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
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43 # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
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44 # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
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45 # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
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46 # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
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47 # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
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48 # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
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49 # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
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50 # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
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51 # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
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52 # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
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53 # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
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54 # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
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55 # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
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56 # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
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57 # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
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58 # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
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59 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
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60 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
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61 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
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62 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
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63 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
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64 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
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65 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
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66 # end gene g1
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67 ###
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68 #
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69 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
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70 #
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71 # Constraints/Hints:
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72 # (none)
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73 # Predicted genes for sequence number 2 on both strands
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74 # start gene g2
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75 HS08198 AUGUSTUS gene 445 1848 1 + . g2
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76 HS08198 AUGUSTUS transcript 445 1848 . + . g2.t1
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77 HS08198 AUGUSTUS intron 583 811 . + . transcript_id "g2.t1"; gene_id "g2";
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78 HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "g2.t1"; gene_id "g2";
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79 HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "g2.t1"; gene_id "g2";
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80 HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "g2.t1"; gene_id "g2";
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81 HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "g2.t1"; gene_id "g2";
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82 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
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83 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
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84 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
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85 HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
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86 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
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87 HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "g2.t1"; gene_id "g2";
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88 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
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89 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
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90 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
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91 # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
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92 # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
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93 # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
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94 # ggcgtggtga]
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95 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
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96 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
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97 # HVLDGECTAGASMAAW]
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98 # end gene g2
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99 ###
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100 # command line:
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101 # augustus --strand=both --noInFrameStop=false --gff3=off --protein=on --introns=on --start=off --stop=off --cds=on --codingseq=on --singlestrand=false /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat --UTR=off --genemodel=complete --species=human
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