# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /augustus/config/ ...
# Using protein profile unknown
# --[2..905]--> unknown_A (8) <--[1..2]--> unknown_B (20) <--[0..453]--> unknown_C (22) <--[8..49]--> unknown_E (23) <--[4..17]--> unknown_F (18) <--[0..5]--> unknown_G (28) <--[18..40]--> unknown_J (9) <--[8..12]--> unknown_K (17) <--[0..6]--> unknown_L (22) <--[0..6]--> unknown_M (9) <--[0..3]--> unknown_N (10) <--[0..1]--> unknown_O (23) <--[4..7]--> unknown_P (29) <--[0..24]--> unknown_Q (21) <--[4..6]--> unknown_R (11) <--[1..3]--> unknown_S (86) <--[0..46]--> unknown_T (26) <--[0..2]--> unknown_U (40) <--[2..57]--> unknown_V (38) <--[1..7]--> unknown_W (14) <--[0..2]--> unknown_X (22) <--[3..13]--> unknown_Y (13) <--[4..161]--> unknown_Z (20) <--[2..64]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig508620180911_busco_2432604931_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 18813, name = Contig5086) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig5086	AUGUSTUS	gene	2399	15927	0.05	-	.	g1
Contig5086	AUGUSTUS	transcript	2399	15927	0.05	-	.	g1.t1
Contig5086	AUGUSTUS	stop_codon	2399	2401	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	2563	8902	0.24	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	9071	9982	0.53	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	10140	10236	0.67	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	10579	11013	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	11616	11741	0.71	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	11880	12092	0.7	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	12231	12525	0.8	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	intron	12555	12658	0.91	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	2399	2562	0.67	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	8903	9070	0.53	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	9983	10139	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	10237	10578	0.67	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	11014	11615	0.98	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	11742	11879	0.71	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	12093	12230	0.87	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	12526	12554	0.83	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	CDS	12659	15927	0.63	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5086	AUGUSTUS	start_codon	15925	15927	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcttgatattgacgagcagatattgcgaactggattggagttgtcggataggttcattggcagctttaagagaaaca
# aaatgaagtatgcagagtatccagatttgtactcaaaggaaaagtcattgcagctatgctctagatatcaacataagtacaaacactgtaaagtcacg
# attgaaacgtcccacggggcagtatgcacagtgctggatgaaaaagacaaagtcaaaacgatagaaatatctggcaggtcaaaatgtgggaaggttta
# taacgaagatgaagttgtagtagagattttaaacgaacgccccgaagtagatgttattccacgtctaaacaaagttatcaatgcaagacctcaaaacg
# acgaaaaactgtatggccaagtggttggaataacaaagagaacacgtttcgctgcggtcaaaaatccggtatttctgtgcacatttgatgatttcgaa
# acacatttgacgaagccactatgcaagactgtcccaaaaattagtattctgcacaacaattgtcagaataagtttcaagtggagacatacaggtatga
# tgagaatgcaaatgatctaaaatttgaaggattgaaggcaattgatccggctaaccgcaaaggatatctgtgccttgtttgtcttatcggttggaatg
# agctttatcctgtaggagcagttctctccatacacagctatagtgacaacacaaattccagtttgaaagtgttgtgtcttcaaaaccaaataccgact
# cattacaatgaagatactgttcagttgacaaatgatatagttcagaatccccttttagaaagcgcagaggagatcagagaaaacattgctgacgatca
# catggtctttacaatcgaccccccaggatccaaagatttagacgatgcactgagtgtgaaaaagataggagaggatcgctacgaaattggagtgcaca
# ttgctgacgtagcaagtatagttatgaaaggtgatgcaatcgataaagaagctcaggaaagatcaagaaccttttatccaggagaaggttatcgacct
# catcatatgttgccagagcctcttagcacacatatttgcagccttttgccaaacgaaagcaggcatgcactttctgtattttttgttgccacgtcttc
# aggagatgtgttgaacatgtcaaaaccaacaattaaaagaacagtggttaagtcgtgccgacaattaacgtaccaacaggcccaatcaattatatcta
# atcagcatgcaaacaaagagccagaattagaccaacagattcatgttttaaatgcgattgcaaaggaacggcgaaagaaacgtcttggaaataaacgt
# tttgctttcccatttgagcctgattacatgggaagtaacgacagctattactctgcagaagatgctcacaaccttgtggaggaatacatgattctgac
# aaatcatgtaattgctaactttttgttgggtaaattcccacattgtgtgccactccgggttcaggaagaaccttcagcagagacagtaagagaatgga
# tggagtcatacccggtcattgggaattttgttcttggaattcagcatttgcgtttaccagacaaaacggcaattgaagtgcagaaagtgcgacaattg
# agatggaataaaatatttccgattcagcttcatgtatggaaaaaaatgacctcggatttgatggaatcaaactttgacgatgtacagcgtattgttgg
# aacagatgcaattcatccacagcaggcgctagcattagaagcatggatttcttttcaggagtccgcaaaatataaatgttctggaaatttgggaagaa
# gaggcaattgtcttcacttttcccttggaattcgcccatacactcactgtacttctcctattcgcagatactcggatatcatagtccagagattgatt
# catgcagcacttgatgaaagaaattctccgtacaaaaaggaggaggtggaaagagtatgtgaaaacattaacgatatcacaaaacgagagaaagcgtt
# tgaaaaacagtgttttgctcttcatttcggaaagaaactttcgaaaaaaccagttttgtgcaatgccatggtccaagacgtctctgagaaagaagtgt
# cgttgcatttcccaggaatgaggaaacttccaaaagactgtaaagatattccttatcacatgttaaaagtcagtgctaagccattggtgaagcctggt
# gaagattcaaaaccatttgcttcgttatcgtggcaacaacgactatactcgtttacaggatacgcccccaaaatacggcttttgaacaaaggactccc
# ggtgcgaattgatccgcatcaacgagtaacctatcaacaattgccaaaatggcagaaaatcctgaaggccatattggacagtaagcattcccagctta
# aaggggcattctttggaacggatcaccctgatgtgaatatgagtcaatctgtacctgcatgcttcaacacagaagctgacgttagctcggaggttaga
# gacggcaacatcatacaacaatgttgcgatttcagcatgagtttgagtcatggtcagatcctagcagtgcagttgatggcagaacctaaaaagggagt
# tatggtaccctcagtccaaatggtagaagttacaaacaatgtgaaattatgtcttcagcacattgcggatccggtgaagtgttttgcaagttatttta
# caaaaacagttccagacaaaatcaagtctcctgtcgagtacacgagaatatggctgaacatctttcgtatggaatcggctgtgaaaatggcccaaagt
# atgcctgttgtcatcaatgatttaccgattcaattttctggagggccagacaacagtgattgtgtctttgtattacgaaattcattctgtctgaaaag
# agacatagaatttggatgtttgtcacagaaaatgataatcttcggtgaggaaaataacgacgaagaagaaaaagagtcgcattatctgttgagttcag
# actgtgtctgtatcagatgcgacctcgtgaaaggaattccttctcgtgttacaaatgatacgtcaccaaatgacagatacatatgggttggtcatgga
# gaagtcagcatcttgcaaaaagggaaaaagaacggcaaaatgaaaatacacattcgtttgcacaaggacagtccaagaccaactgcagaaatgtgttc
# caatccaccacctcgatgtagcgttgaactccttcaaaaagctgatgcagacaagcgtgttgaagctactttgagttgccttgacaaggatcattttg
# acctgtcccagaaaatagaagcagatgtgacaatttgtagattagcaccaaacaacattcaacagttgaaagcgattaaatgtgctttgagtaatcga
# ttcagcctaattcaaggaccaccaggtacggggaaaacttacactggaataaagctcatctatctgtttgtgaaaattaatgacattttacgaaagga
# agggggagaacacaagcaagttgtattttgtggtccatccaacaaatctgtggacttggtcgctcgctggatgctgaacaaattcgaagatcgtacgc
# ccaatattgtgcgcatgtacggcagttccttggaaaacgctgtttttcatattcctggaagagattataccagtaaaacctcgtgcaaagataacaga
# ccagatcctgaattagcaagtatctcgttacatcatcgtattcgtgaagagggcaaaccgtatgctgaagaattaaggaactacgataacatgttcaa
# gaataacccaagcttctctgatcacagcgaaataggaaattataagaaagtatgcagtaaagcttgccaggaagaattaaaacattatgatgtcatat
# tctgcaccactgctgttgctacaaatgcaaggtttttgaaggcaacaaaaggaaaaattgatcagttgattattgatgaagctggtatgtgcactgaa
# ccggaaacccttgcaccaatcattgccaccagagcagaacaggttgttcttattggagaccacaagcagcttcagcctgttgtcctttgcaaagaggc
# agcattgcttgggttggaaaaatctttgtttgaacgatatgctagtcgagctgtgttcctcaactgccaatacagaatgaatccgagaatatgcgatt
# tcccgtccgaacagttttaccagaataagttggaaacaatgccttccatagcatggagggtgaaggaacccttgtcactgtggaatgttcctatggta
# ccgcacttgttttgtcatgttgaaggtgaagaggaatgccttagtgtcactacagaggaaggaaatcntatagcatggagggtgaaggaacccttatc
# actgtggaatgttcccatggtaccgcacttgttttgtcatgtggaaggtgaagaggactgccttagtgtcactacagaggaaggaaatcagcaatcaa
# aaagcaataaagccgaagtagagcaagtggttcgaatctaccgtgatctggttattcgtgaaaaagtcggtcacaaacaaatcaacatcatctcgcag
# tacaacgcccagtgttatgctattaaaagagaactaaaacagcaaaaattcatcaatttcaacgtcaacactgttgtggcaagtcaaggtggcgagtg
# ggattacgtgatattcagcaccgtcagatctctccccgagtatagaatagagcccaacccaaccctgggatggtgtaaacaaaacctcgggtttatca
# cggaccaacaccagatcaacgttgccctcacacgggcaagaaaaggactcataatcataggaaacaaacgtctgatgaagtgcgacaaagtttggaac
# aacttactaacgcactacagcagaaaaggctgcgttgtggacgcggaatctgtgtcatccaagcgccaaaagaagccgaggaagacccgagaggccac
# agaggaagaattcaatgctttaacttaa]
# protein sequence = [MLDIDEQILRTGLELSDRFIGSFKRNKMKYAEYPDLYSKEKSLQLCSRYQHKYKHCKVTIETSHGAVCTVLDEKDKVK
# TIEISGRSKCGKVYNEDEVVVEILNERPEVDVIPRLNKVINARPQNDEKLYGQVVGITKRTRFAAVKNPVFLCTFDDFETHLTKPLCKTVPKISILHN
# NCQNKFQVETYRYDENANDLKFEGLKAIDPANRKGYLCLVCLIGWNELYPVGAVLSIHSYSDNTNSSLKVLCLQNQIPTHYNEDTVQLTNDIVQNPLL
# ESAEEIRENIADDHMVFTIDPPGSKDLDDALSVKKIGEDRYEIGVHIADVASIVMKGDAIDKEAQERSRTFYPGEGYRPHHMLPEPLSTHICSLLPNE
# SRHALSVFFVATSSGDVLNMSKPTIKRTVVKSCRQLTYQQAQSIISNQHANKEPELDQQIHVLNAIAKERRKKRLGNKRFAFPFEPDYMGSNDSYYSA
# EDAHNLVEEYMILTNHVIANFLLGKFPHCVPLRVQEEPSAETVREWMESYPVIGNFVLGIQHLRLPDKTAIEVQKVRQLRWNKIFPIQLHVWKKMTSD
# LMESNFDDVQRIVGTDAIHPQQALALEAWISFQESAKYKCSGNLGRRGNCLHFSLGIRPYTHCTSPIRRYSDIIVQRLIHAALDERNSPYKKEEVERV
# CENINDITKREKAFEKQCFALHFGKKLSKKPVLCNAMVQDVSEKEVSLHFPGMRKLPKDCKDIPYHMLKVSAKPLVKPGEDSKPFASLSWQQRLYSFT
# GYAPKIRLLNKGLPVRIDPHQRVTYQQLPKWQKILKAILDSKHSQLKGAFFGTDHPDVNMSQSVPACFNTEADVSSEVRDGNIIQQCCDFSMSLSHGQ
# ILAVQLMAEPKKGVMVPSVQMVEVTNNVKLCLQHIADPVKCFASYFTKTVPDKIKSPVEYTRIWLNIFRMESAVKMAQSMPVVINDLPIQFSGGPDNS
# DCVFVLRNSFCLKRDIEFGCLSQKMIIFGEENNDEEEKESHYLLSSDCVCIRCDLVKGIPSRVTNDTSPNDRYIWVGHGEVSILQKGKKNGKMKIHIR
# LHKDSPRPTAEMCSNPPPRCSVELLQKADADKRVEATLSCLDKDHFDLSQKIEADVTICRLAPNNIQQLKAIKCALSNRFSLIQGPPGTGKTYTGIKL
# IYLFVKINDILRKEGGEHKQVVFCGPSNKSVDLVARWMLNKFEDRTPNIVRMYGSSLENAVFHIPGRDYTSKTSCKDNRPDPELASISLHHRIREEGK
# PYAEELRNYDNMFKNNPSFSDHSEIGNYKKVCSKACQEELKHYDVIFCTTAVATNARFLKATKGKIDQLIIDEAGMCTEPETLAPIIATRAEQVVLIG
# DHKQLQPVVLCKEAALLGLEKSLFERYASRAVFLNCQYRMNPRICDFPSEQFYQNKLETMPSIAWRVKEPLSLWNVPMVPHLFCHVEGEEECLSVTTE
# EGNXIAWRVKEPLSLWNVPMVPHLFCHVEGEEDCLSVTTEEGNQQSKSNKAEVEQVVRIYRDLVIREKVGHKQINIISQYNAQCYAIKRELKQQKFIN
# FNVNTVVASQGGEWDYVIFSTVRSLPEYRIEPNPTLGWCKQNLGFITDQHQINVALTRARKGLIIIGNKRLMKCDKVWNNLLTHYSRKGCVVDAESVS
# SKRQKKPRKTREATEEEFNALT]
# end gene g1
###
# start gene g2
Contig5086	AUGUSTUS	gene	16001	18353	0.16	-	.	g2
Contig5086	AUGUSTUS	transcript	16001	18353	0.16	-	.	g2.t1
Contig5086	AUGUSTUS	stop_codon	16001	16003	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	intron	16468	16652	0.95	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	intron	16711	16814	0.89	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	intron	16935	17030	0.96	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	intron	17115	17514	0.28	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	intron	17731	18296	0.7	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	CDS	16001	16467	0.88	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	CDS	16653	16710	0.95	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	CDS	16815	16934	0.92	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	CDS	17031	17114	0.29	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	CDS	17515	17730	0.32	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	CDS	18297	18353	0.7	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig5086	AUGUSTUS	start_codon	18351	18353	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaaccctagcttgatgtggaatgatgttttaacaaatcatggaataaacttggctgggaaattgaagattatccgag
# aagtgaggtcaatcattgatgagtataacaacgcagatgatgtaaatgcctggtactcgatctataggagagaaatacagacctcctacagaatgttg
# ttgggtatctacggtgcagataaactaaacgaggatctcattctacgtgaagttctgcaatacgatatcggcaatggatggaaactgctgaataacct
# ctgggcgcatgctcttgagcagcgtggaatgctggacgtggccatcaacaaggccgagaatgccatagctatggcgggagcgaatcacgacttgtcgt
# cctttgagggtttactaaatagactgaaaatggatgctgtcaaaatgcaccaagattctctgaaagcaaatcagggtaccgcgactgtcaaaggagct
# gagaagggtataccgaatgtgaaaaaacaagaacaaaaaaagaaagaacgaaaacgtggaaaagtcaagaaactgggaaaagaagacaatgatctaga
# ggaactggacaaagaaagtgaaggtgttgaatcagattgtccaagagatgatggattacgtgatacgatagagcctgaactggtgtccaacttgagag
# atgactccccaaagacctggaaagacgtaacagaatttgacttgcccatcagcaggccaggacgaaaacgacgacgtcatcgcactggtgattcgggt
# ttgtcctctaacggaaatggaacagcaactatagaagtggaaagcgaggtgaattccggaggatccggcattttctctaacatgcactcagtagaatc
# agatgaaagtgaggatgaataccgaccactaccttccggtccatcaaacaatctccagttcatggatcaaacatcgaattctaattcacgtttaatca
# acgaagcaaacgaagaggatgatctccatcaaagaggatga]
# protein sequence = [MNPSLMWNDVLTNHGINLAGKLKIIREVRSIIDEYNNADDVNAWYSIYRREIQTSYRMLLGIYGADKLNEDLILREVL
# QYDIGNGWKLLNNLWAHALEQRGMLDVAINKAENAIAMAGANHDLSSFEGLLNRLKMDAVKMHQDSLKANQGTATVKGAEKGIPNVKKQEQKKKERKR
# GKVKKLGKEDNDLEELDKESEGVESDCPRDDGLRDTIEPELVSNLRDDSPKTWKDVTEFDLPISRPGRKRRRHRTGDSGLSSNGNGTATIEVESEVNS
# GGSGIFSNMHSVESDESEDEYRPLPSGPSNNLQFMDQTSNSNSRLINEANEEDDLHQRG]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CAV.prfl --predictionStart=0  --predictionEnd=35315  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig508620180911_busco_2432604931_.temp