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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 # arabidopsis version. Using default transition matrix.
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9 # We have hints for 0 sequences and for 0 of the sequences in the input set.
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10 #
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11 # ----- prediction on sequence number 1 (length = 2066, name = arabidopsis) -----
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12 #
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13 # Constraints/Hints:
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14 # (none)
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15 # Predicted genes for sequence number 1 on both strands
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16 # start gene g1
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17 arabidopsis AUGUSTUS gene 775 1851 0 + . g1
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18 arabidopsis AUGUSTUS transcript 775 1851 . + . g1.t1
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19 arabidopsis AUGUSTUS start_codon 775 777 . + 0 transcript_id "g1.t1"; gene_id "g1";
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20 arabidopsis AUGUSTUS CDS 775 1851 0.99 + 0 transcript_id "g1.t1"; gene_id "g1";
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21 arabidopsis AUGUSTUS stop_codon 1849 1851 . + 0 transcript_id "g1.t1"; gene_id "g1";
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22 # protein sequence = [MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVTPSDVGKLNRLVIPKQHA
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23 # ERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKGWSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFG
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24 # FNFNFPTTSQYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNIVGSEPLVIDSVPVVPGRLTPVMLPPLP
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25 # PPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRGEIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP]
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26 # end gene g1
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27 ###
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28 # start gene g2
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29 arabidopsis AUGUSTUS gene 841 1661 . - . g2
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30 arabidopsis AUGUSTUS transcript 841 1661 . - . g2.t1
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31 arabidopsis AUGUSTUS stop_codon 841 843 . - 0 transcript_id "g2.t1"; gene_id "g2";
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32 arabidopsis AUGUSTUS intron 1024 1101 0.75 - . transcript_id "g2.t1"; gene_id "g2";
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33 arabidopsis AUGUSTUS intron 1193 1325 0.03 - . transcript_id "g2.t1"; gene_id "g2";
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34 arabidopsis AUGUSTUS intron 1416 1512 0.85 - . transcript_id "g2.t1"; gene_id "g2";
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35 arabidopsis AUGUSTUS CDS 841 1023 0.87 - 0 transcript_id "g2.t1"; gene_id "g2";
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36 arabidopsis AUGUSTUS CDS 1102 1192 0.78 - 1 transcript_id "g2.t1"; gene_id "g2";
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37 arabidopsis AUGUSTUS CDS 1326 1415 0.05 - 1 transcript_id "g2.t1"; gene_id "g2";
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38 arabidopsis AUGUSTUS CDS 1513 1661 0.35 - 0 transcript_id "g2.t1"; gene_id "g2";
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39 # protein sequence = [SLPHSIFTPKSLSLFPAVEGGGGSGGNITGVNLPGTTGTESITNGSDPTMNVGDFRCLSPGESGRSYILAMDEICWNI
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40 # EKDNVSCIELFLFDETAPSFGHNVALARVPIRREIPLSVLFRDHESVEFSDVAWCYHFVEHVFFLRRWNHHHRKVVVVSAGTGAAACSDVGG]
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41 # end gene g2
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42 ###
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43 #
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44 # ----- prediction on sequence number 2 (length = 1802, name = arabidopsis2) -----
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45 #
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46 # Constraints/Hints:
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47 # (none)
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48 # Predicted genes for sequence number 2 on both strands
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49 # start gene g3
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50 arabidopsis2 AUGUSTUS gene 97 1600 . - . g3
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51 arabidopsis2 AUGUSTUS transcript 97 1600 . - . g3.t1
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52 arabidopsis2 AUGUSTUS stop_codon 97 99 . - 0 transcript_id "g3.t1"; gene_id "g3";
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53 arabidopsis2 AUGUSTUS intron 349 521 0.73 - . transcript_id "g3.t1"; gene_id "g3";
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54 arabidopsis2 AUGUSTUS intron 1210 1333 0.36 - . transcript_id "g3.t1"; gene_id "g3";
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55 arabidopsis2 AUGUSTUS intron 1452 1560 0.54 - . transcript_id "g3.t1"; gene_id "g3";
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56 arabidopsis2 AUGUSTUS CDS 97 348 0.73 - 0 transcript_id "g3.t1"; gene_id "g3";
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57 arabidopsis2 AUGUSTUS CDS 522 1209 0.6 - 1 transcript_id "g3.t1"; gene_id "g3";
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58 arabidopsis2 AUGUSTUS CDS 1334 1451 0.44 - 2 transcript_id "g3.t1"; gene_id "g3";
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59 arabidopsis2 AUGUSTUS CDS 1561 1600 0.42 - 0 transcript_id "g3.t1"; gene_id "g3";
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60 arabidopsis2 AUGUSTUS start_codon 1598 1600 . - 0 transcript_id "g3.t1"; gene_id "g3";
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61 # protein sequence = [MVKLVFSDLSCAFASANSTASSTNSSIFFSIDFSSASFASLFSIKYFFNAAIGITELIGISQGVSSESISLTFNQGWT
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62 # FSSSSSSDSFFSDFPDLQDIHTVNMNTRHPKCRTFLPNLGVRSGSQVRHPNGPQVILDNKDNRQFIESSHVETLEELSVVTSSISEKGDSDIITILFQ
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63 # DFPPVLGAKGSTSGDRNAFTNKSKATKHVVFFGEHVHGSTLASAASSNLAEELAHNSTSRDTFAEGMDMVTVGTNDRVRLGKELDKASRNSLLAIVQV
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64 # NKTKHLASAGIIGGLLLLDNFLDRDDGRSTGGVGVIESAKGEGTGGSEERRRRSQSDREQETILMGSMQRNRGSELSGSESRRHCYQWKPQ]
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65 # end gene g3
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66 ###
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67 # start gene g4
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68 arabidopsis2 AUGUSTUS gene 121 1582 0 + . g4
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69 arabidopsis2 AUGUSTUS transcript 121 1582 . + . g4.t1
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70 arabidopsis2 AUGUSTUS start_codon 121 123 . + 0 transcript_id "g4.t1"; gene_id "g4";
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71 arabidopsis2 AUGUSTUS intron 352 434 0.97 + . transcript_id "g4.t1"; gene_id "g4";
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72 arabidopsis2 AUGUSTUS intron 1213 1304 1 + . transcript_id "g4.t1"; gene_id "g4";
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73 arabidopsis2 AUGUSTUS CDS 121 351 0.72 + 0 transcript_id "g4.t1"; gene_id "g4";
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74 arabidopsis2 AUGUSTUS CDS 435 1212 0.97 + 0 transcript_id "g4.t1"; gene_id "g4";
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75 arabidopsis2 AUGUSTUS CDS 1305 1582 1 + 2 transcript_id "g4.t1"; gene_id "g4";
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76 arabidopsis2 AUGUSTUS stop_codon 1580 1582 . + 0 transcript_id "g4.t1"; gene_id "g4";
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77 # protein sequence = [MATAFAPTKLTATVPLHGSHENRLLLPIRLAPPSSFLGSTRSLSLRRLNHSNATRRSPVVSVQEVVKEKQSTNNTSLL
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78 # ITKEEGLELYEDMILGRSFEDMCAQMYYRGKMFGFVHLYNGQEAVSTGFIKLLTKSDSVVSTYRDHVHALSKGVSARAVMSELFGKVTGCCRGQGGSM
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79 # HMFSKEHNMLGGFAFIGEGIPVATGAAFSSKYRREVLKQDCDDVTVAFFGDGTCNNGQFFECLNMAALYKLPIIFVVENNLWAIGMSHLRATSDPEIW
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80 # KKGPAFGMPGVHVDGMDVLKVREVAKEAVTRARRGEGPTLVECETYRFRGHSLADPDELRDAAEKAKYAARDPIAALKKYLIENKLAKEAELKSIEKK
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81 # IDELVEEAVEFADASPQPGRSQLLENVFADPKGFGIGPDGRYRCEDPKFTEGTAQV]
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82 # end gene g4
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83 ###
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84 # command line:
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85 # ./bin/augustus --species=arabidopsis --UTR=off --singlestrand=true --mea=1 /home/bag/projects/github/galaxytools/augustus/test-data/arabidopsis_augustus.fa
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