##gff-version 3 # This output was generated with AUGUSTUS (version 2.0.2). # AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mstanke@gwdg.de). # Please cite: Mario Stanke and Stephan Waack (2003) "Gene prediction with a hidden Markov model and # a new intron submodel", Bioinformatics, Vol. 19 Suppl. 2, ii215-ii225 # reading in the file /tmp/bac-submission-temp-C09HBa0067J16-6MpZD/AUGUSTUS_tom_ugs/hints.gff ... # Sources of extrinsic information: M E # Have extrinsic information about 1 sequences (in the specified range). # Initialising the parameters ... # human version. Use default transition matrix. # Looks like /tmp/bac-submission-temp-C09HBa0067J16-6MpZD/AUGUSTUS_tom_ugs/seq_with_defline_removed is in fasta format. # We have hints for 1 sequence and for 1 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 151319, name = C09HBa0067J16.1) ----- # # Set orientation to reverse for hint group HintGroup SGN-U326354, 228-912, priority= 4 7 features # Delete group HintGroup SGN-U318742, 5872-18237, priority= 4 6 features # Set orientation to forward for hint group HintGroup SGN-U318743, 8006-20991, priority= 4 14 features # Set orientation to forward for hint group HintGroup SGN-U336619, 19054-20925, priority= 4 5 features # Set orientation to forward for hint group HintGroup SGN-U313327, 28035-34566, priority= 4 11 features # Delete group HintGroup SGN-U313328, 30863-33976, priority= 4 7 features # Set orientation to forward for hint group HintGroup SGN-U317160, 49922-52492, priority= 4 3 features # Set orientation to reverse for hint group HintGroup SGN-U317105, 80053-83236, priority= 4 5 features # Set orientation to reverse for hint group HintGroup SGN-U329153, 84902-86833, priority= 4 5 features # Set orientation to reverse for hint group HintGroup SGN-U323160, 107346-120954, priority= 4 5 features # Set orientation to forward for hint group HintGroup SGN-U323576, 124183-127871, priority= 4 15 features # Set orientation to forward for hint group HintGroup SGN-U318108, 140186-141556, priority= 4 7 features # Set orientation to forward for hint group HintGroup SGN-U320715, 146104-148958, priority= 4 7 features # Set orientation to forward for hint group HintGroup SGN-U337198, 147766-148809, priority= 4 3 features # Forced unstranded hint group to the only possible strand for 12 groups. # Deleted 2 groups because some hint was not satisfiable. # Constraints/Hints: # Predicted genes for sequence number 1 on both strands ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 220 6065 1 - . ID=g1 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 220 6065 . - . ID=g1.t1;Parent=g1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 220 279 . - 0 ID=g1.t1.cds;Parent=g1.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 493 561 . - 0 ID=g1.t1.cds;Parent=g1.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 636 686 . - 0 ID=g1.t1.cds;Parent=g1.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 772 944 . - 2 ID=g1.t1.cds;Parent=g1.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 6059 6065 . - 0 ID=g1.t1.cds;Parent=g1.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 6063 6065 . - 0 Parent=g1.t1 # protein sequence = [MIDVLLELHLNFITACLRVLVKASQYSLTQSTTSIGRRRPFPTNFSHLRRRIFSSKPDNMADSESKSHETGKNCKPEA # AASEGKQLTPEELEKKKKKEEKAREKELKKLKAAQKAEAAKQ] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 70 # CDS exons: 4/5 # E: 4 # CDS introns: 3/5 # E: 3 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 1 # E: 1 (SGN-U326354) # incompatible hint groups: 0 ### ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 50005 52275 1 + . ID=g2 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 50005 52275 . + . ID=g2.t1;Parent=g2 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 50005 50007 . + 0 Parent=g2.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 50005 50031 . + 0 ID=g2.t1.cds;Parent=g2.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 52060 52275 . + 0 ID=g2.t1.cds;Parent=g2.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs stop_codon 52273 52275 . + 0 Parent=g2.t1 # protein sequence = [MDFEDHDNVKNMAKDVEVKGFNPGLIVLIVVGGLLLTFLVGNYLLYMYAQKTLPPKKKKPVSKKKMKKERLKQGVSAP # GE] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 2/2 # E: 2 # CDS introns: 1/1 # E: 1 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 2 # E: 2 (SGN-U317160,SGN-U317159) ### ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 80244 83129 1 - . ID=g3 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 80244 83129 . - . ID=g3.t1;Parent=g3 C09HBa0067J16.1 AUGUSTUS_tom_ugs stop_codon 80244 80246 . - 0 Parent=g3.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 80244 80477 . - 0 ID=g3.t1.cds;Parent=g3.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 81390 81592 . - 2 ID=g3.t1.cds;Parent=g3.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 82841 83129 . - 0 ID=g3.t1.cds;Parent=g3.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 83127 83129 . - 0 Parent=g3.t1 # protein sequence = [MANTDESNPLLPNQQSEVKDEKNPNKPISSTTPVPPFPADPVKPLSAVVPMGWTVEGVPMGHGVVVDPIMNRAQWDSG # LCACFGRTDEFCSSDIEVCLLGSMAPCVLYGSNAERLGSAPGTFANHCLPYTGLFLIGQSFFGSNCVAPCFTYPSRTAIRRKFNLEGSCEAFNRSSGC # CGSFIEDEVQREQCESVCDFATHFFCHPCALCQEGRELRRRLPHPGFKAQQVLVMIPPNEQTMGR] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 3/3 # E: 3 # CDS introns: 2/2 # E: 2 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 1 # E: 1 (SGN-U317105) ### ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 85131 86735 1 - . ID=g4 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 85131 86735 . - . ID=g4.t1;Parent=g4 C09HBa0067J16.1 AUGUSTUS_tom_ugs stop_codon 85131 85133 . - 0 Parent=g4.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 85131 85151 . - 0 ID=g4.t1.cds;Parent=g4.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 85958 86118 . - 2 ID=g4.t1.cds;Parent=g4.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 86672 86735 . - 0 ID=g4.t1.cds;Parent=g4.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 86733 86735 . - 0 Parent=g4.t1 # protein sequence = [MKLKCNFIVIFFLLLLASPSSGKMDLSKVNASEIYEIDYRGPETHTKMPPQRVGRHNNHHRGTLFHPNATKPGKNGKK # NHG] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 3/3 # E: 3 # CDS introns: 2/2 # E: 2 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 1 # E: 1 (SGN-U329153) ### ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 101740 104149 1 - . ID=g5 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 101740 104149 . - . ID=g5.t1;Parent=g5 C09HBa0067J16.1 AUGUSTUS_tom_ugs stop_codon 101740 101742 . - 0 Parent=g5.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 101740 101858 . - 2 ID=g5.t1.cds;Parent=g5.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 102357 102612 . - 0 ID=g5.t1.cds;Parent=g5.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 103745 104149 . - 0 ID=g5.t1.cds;Parent=g5.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 104147 104149 . - 0 Parent=g5.t1 # protein sequence = [MCMMSAGKSEINRLNTTMDETAKAVEELKAELSRKKVAHNLCASKNEVDMDEKNNRECRIHVIAENNNENRNIYRALD # LQVAEEGECASSVITEEPQPEVMEMDQLEAELESELLKLPWCATEVMDLNGGRDPCQDEFLEKEFNQADDRNAETYLCNGVLPSELDQKLCHLLIEQQ # EGQIVELESELRQTHSKLHEKEAELQALKDCVRRLTEFSLGNASDEETDGKMEDEIIVGGDQEKKIEPEVGKSIIGMKRSMIF] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 0 # CDS exons: 0/3 # CDS introns: 0/2 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 0 ### ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 123192 130206 1 + . ID=g6 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 123192 130206 . + . ID=g6.t1;Parent=g6 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 123192 123194 . + 0 Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 123192 123262 . + 0 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 124107 124203 . + 1 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 124298 124378 . + 0 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 124466 124695 . + 0 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 125413 125607 . + 1 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 125792 125882 . + 1 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 126931 127053 . + 0 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 127232 127382 . + 0 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 127510 127614 . + 2 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 129206 130206 . + 2 ID=g6.t1.cds;Parent=g6.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs stop_codon 130204 130206 . + 0 Parent=g6.t1 # protein sequence = [MHNIHVSGSNIPSPLLNFSELRSRYECRSYLLRNLAKLGFKEPTPIQRQTIPVLLSGRECFACAPTGSGKTFAFVFPV # LMKLKHTSKDGVRAVILSPTKELAAQTTRECKKLARKKFYIRLMTKQLAKSGDFSKLRCDVLISTPLRLKFAIQKRKLDLSRVEYLVLDESDKLFEPG # MLEQVDFVVKACTNPSILRSLFSATLPDIVEDRARTIMHDAVRVIIGRKNSASETIEQKLVYVGSEEGKLLALRQSFAESLNPPVLVFVQNKERAKEL # YDELKLEDIRADVIHSDLSQIQRENAIDNFRAGKTWVLIATDVVARGMDFKGVNCVINYDFPDAAAAYIHRIGRSGRAGRSGQAITFYTEADIPFLRN # IANVITSSGAYVLTHPRIEIYDEAKDVSSWPKPSEIPYQAKVANSVNLVGFVQTPVHFETSSDGKYCASTVVAHENSDDNSVLMIPVVFAGDLAHVVA # CHVKENDCVYVYGKFSMEPLSCEFMDEYQSCFHIVAENVNFVQGLKRNVSLKGNVKSVYPKGKNFVLDDSDNQHSDYLVKQKDRLSGLEYDDSVNLGG # SKSEEGVTGGDDWRDLIKNSKQWWDCRKAKLDGIVKARHPDFKKKDSSTSLWIENAPRWVLEGLEGLEFDAYAPKPKGIGKDVDCWKDLLENPDKWWD # NRVSKLNQKAPDFKHKNTGIGLWVGSSPDWVLSRLPPLRDQRAASSDK] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 73.7 # CDS exons: 7/10 # E: 7 # CDS introns: 7/9 # E: 7 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 1 # E: 1 (SGN-U323576) ### ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 139400 142045 1 + . ID=g7 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 139400 142045 . + . ID=g7.t1;Parent=g7 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 139400 139402 . + 0 Parent=g7.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 139400 139474 . + 0 ID=g7.t1.cds;Parent=g7.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 140030 140356 . + 0 ID=g7.t1.cds;Parent=g7.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 140506 140727 . + 0 ID=g7.t1.cds;Parent=g7.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 140971 141090 . + 0 ID=g7.t1.cds;Parent=g7.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 141338 142045 . + 0 ID=g7.t1.cds;Parent=g7.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs stop_codon 142043 142045 . + 0 Parent=g7.t1 # protein sequence = [MEKKGSWFSSVKKALSPDPKEKVDKKASKSKKKWFGKEKHTLVDSSTAVTATASPPHPVPVLPVEEVKLEEVEEEQTK # HAYSVAVATAAAAEAAVAAAHAAAEVVRLTTVNQFSGKSQEEVAAIRVQTAFRGYLARRALRALRGLVRLKSLVDGPTAKRQTTNALKCMQTLSRMQS # QISSRRIRMLEENRTLQRQLMQKHVKELESLRRGEEWDDSLQSKERVEASLLSKYEAAIRRERALAYSYSHQQTWKKSSRSTNLLFMDPTNPQWGWSW # LERWTGARPWESQSMSEKQLKTDQMSVRSVSIAGGEIAKSFARHQLNSELPSSPSRQKPSHPSRYHSPTTPSKPTTSVAAARKLKPASPRISAMNQDD # DNRSMLSVQSERNRRHSIAGSSIRDDESLASSPSVPSYMASTQSAKAKTRLQNPLGMENGKPEKGSAGSVKKRLSYPPSPARTRRHSGPPKFDNTSLN # TSIAEDHVNGVVN] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 77.8 # CDS exons: 4/5 # E: 4 # CDS introns: 3/4 # E: 3 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 1 # E: 1 (SGN-U318108) # incompatible hint groups: 1 # E: 1 (SGN-U324722) ### ### C09HBa0067J16.1 AUGUSTUS_tom_ugs gene 147707 148612 1 + . ID=g8 C09HBa0067J16.1 AUGUSTUS_tom_ugs transcript 147707 148612 . + . ID=g8.t1;Parent=g8 C09HBa0067J16.1 AUGUSTUS_tom_ugs start_codon 147707 147709 . + 0 Parent=g8.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 147707 147864 . + 0 ID=g8.t1.cds;Parent=g8.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs CDS 148456 148612 . + 1 ID=g8.t1.cds;Parent=g8.t1 C09HBa0067J16.1 AUGUSTUS_tom_ugs stop_codon 148610 148612 . + 0 Parent=g8.t1 # protein sequence = [MAIAAAAYASRYGIQAWQAFKARPPTVRMRKFYEGGFQPKMNRREAALILGVRENTEANKVREAHRKVMVANHPDAGG # SHYLASKINEAKDTLLGQTKNNGSAF] # Evidence for and against this transcript: # % of transcript supported by hints (any source): 100 # CDS exons: 2/2 # E: 2 # CDS introns: 1/1 # E: 1 # 5'UTR exons and introns: 0/0 # 3'UTR exons and introns: 0/0 # hint groups fully obeyed: 0 # incompatible hint groups: 2 # E: 2 (SGN-U320715,SGN-U337198) ### # command line: # /usr/bin/augustus.real --species=human --hintsfile=/tmp/bac-submission-temp-C09HBa0067J16-6MpZD/AUGUSTUS_tom_ugs/hints.gff --extrinsicCfgFile=extrinsic.ME.cfg --gff3=on /tmp/bac-submission-temp-C09HBa0067J16-6MpZD/AUGUSTUS_tom_ugs/seq_with_defline_removed