# 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
# --[0..28]--> unknown_A (30) <--[0..13]--> unknown_B (9) <--[1..3]--> unknown_C (32) <--[0..18]--> unknown_D (21) <--[1..23]--> unknown_E (30) <--[1..14]--> unknown_F (13) <--[0..11]--> unknown_G (22) <--[0..1]--> unknown_H (13) <--[3..12]--> unknown_I (69) <--[0..17]--> unknown_J (26) <--[0..1]--> unknown_K (6) <--[12..88]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2831420180911_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 = 33677, name = Contig28314) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig28314	AUGUSTUS	gene	1196	17402	0.08	-	.	g1
Contig28314	AUGUSTUS	transcript	1196	17402	0.08	-	.	g1.t1
Contig28314	AUGUSTUS	stop_codon	1196	1198	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	intron	1298	4238	0.3	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	intron	4390	4699	0.42	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	intron	4781	6496	0.37	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	intron	6588	9413	0.72	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	intron	9502	13449	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	intron	13598	17289	0.82	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	CDS	1196	1297	0.35	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	CDS	4239	4389	0.59	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	CDS	4700	4780	0.41	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	CDS	6497	6587	0.62	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	CDS	9414	9501	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	CDS	13450	13597	0.92	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	CDS	17290	17402	0.92	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28314	AUGUSTUS	start_codon	17400	17402	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggatggcgatcatgaggatttggagccgtctttacgcagtgttattgaacagaattctctgaaatggctattcgtcg
# gtgggaaaggaggtgtcgggaaaacaacgacaagttgctgtttagccacacagttggctaaagtccgtgaaagcgttctcatcatttcaaccgatcca
# gcgcataacatctctgatgccttcagccagaagttttcaaaagtaccgtctcttgtgaaaggtttcaaaaacttatatgccatgacatttgacatggc
# atgggaacagttgttcagagtcctcagtgcttttccaggaattgatgaagccatgagctttgcagaagtcatgaacatgatgagcatggggaaagcag
# ttgtttcagagctcctcagtgcttttccaggaattgatgaagccatgagctttgcagaagtcatgaaagaagcactgggccagtttttaggaaacttg
# aaaattctttttaaaatcatcactgctgagccagggccaaggtcactcagactggtgaatggcatgaacttttcctgtgtggtttttgatacggcccc
# cacagggcacaccctcaggttgttatcatttccctccgtcatagaaaaaggtctgggtaaaatcctgagactgaaaaacagaatcggaccatttgtat
# cccaggggaggatgagtgaggagtggaatggtaggggaggaatgagtgaggatgatatgatggaggcgaggatgagtgaggatggagatgatgagggg
# aggaattga]
# protein sequence = [MDGDHEDLEPSLRSVIEQNSLKWLFVGGKGGVGKTTTSCCLATQLAKVRESVLIISTDPAHNISDAFSQKFSKVPSLV
# KGFKNLYAMTFDMAWEQLFRVLSAFPGIDEAMSFAEVMNMMSMGKAVVSELLSAFPGIDEAMSFAEVMKEALGQFLGNLKILFKIITAEPGPRSLRLV
# NGMNFSCVVFDTAPTGHTLRLLSFPSVIEKGLGKILRLKNRIGPFVSQGRMSEEWNGRGGMSEDDMMEARMSEDGDDEGRN]
# end gene g1
###
# start gene g2
Contig28314	AUGUSTUS	gene	21151	24174	0.22	-	.	g2
Contig28314	AUGUSTUS	transcript	21151	24174	0.22	-	.	g2.t1
Contig28314	AUGUSTUS	stop_codon	21151	21153	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	intron	21389	21933	1	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	intron	22128	22478	0.95	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	intron	22832	23232	0.4	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	intron	23401	23801	0.93	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	CDS	21151	21388	1	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	CDS	21934	22127	1	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	CDS	22479	22831	0.53	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	CDS	23233	23400	0.74	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	CDS	23802	24174	0.67	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig28314	AUGUSTUS	start_codon	24172	24174	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaagtgttgtcttaaaaattgtggaaaggacgtagatatacaaaatgaatctaggatagaagtgaaaactgttttac
# cgtctcgctttagtagtgaaaacttccttgtgtcatggagcgaagatggtgaagcaaagtttcacacggactgttggcaacgcctgttaaacatgaga
# acagccattattagaaaagtcgggacaaaaagaagtcaatcaaattcccaagactttataaccaaacaagagaaagctctgatcagggaggcgaaaaa
# gacggcagaatactttgattccgtagaacaaattaaacacgaagcgagtcgagttgcagagatgctgaagtcagcaaaacactgtgtggcattcacag
# gagctggaatctccactgctgcaggtattggggactacagaggcaagagtggaaaatggacagaaatggaccaaagccaagtcacggacaagatcgag
# cagatttttgatattcaggggccttccccaagcaaaaaacattgtccaggagaagagtcttctgacaaagagggagttgattatgaggagttaaggcc
# tacccttactcacgaagctttgtgtttcctgattgacatgaaactgatgaagcatgtgatcagtcagaatggcgatggccttcacggtctgtcaggaa
# tttcccaggaaaatctttcagagctccacggaaatgtattccatgagaagtgtgagaaatgtggccataggtatgaccgctccttctatgtgatggac
# gatgagagcagtcagtactatgaggatgtagaggattatgggaaatcggaagtaaagaaaccaaggcatgctaagcggtgtgaaacatgtggattatc
# tcacagaacgggcaggaagtgtgaacagaagggctgcagtggattcttgatggacactattattaactttggggataatttagaggaggacatactgt
# ccagagccttcagccaggcctacgaatgtgacctgatgatcggtctaggcaccactcttacggtaacccctgccaacgagctggtggaagttatcaaa
# aaaccgcaacgccttgtcatatgtaatagacaaaagacggattatgataaagactgcctcaggaaactcccgggagccgatcagagtgtgggcaggaa
# actcccgggagccgatcagagtgtgggcagtcgtgtgcacggagattgtgacgttttcatgcgggaggtgctcaagaacatcgtaggagaggaaaaac
# tgaagagctgggagagggacagacaaacgagaatgatcagctataacaagcagcgccaacagactagttaa]
# protein sequence = [MKCCLKNCGKDVDIQNESRIEVKTVLPSRFSSENFLVSWSEDGEAKFHTDCWQRLLNMRTAIIRKVGTKRSQSNSQDF
# ITKQEKALIREAKKTAEYFDSVEQIKHEASRVAEMLKSAKHCVAFTGAGISTAAGIGDYRGKSGKWTEMDQSQVTDKIEQIFDIQGPSPSKKHCPGEE
# SSDKEGVDYEELRPTLTHEALCFLIDMKLMKHVISQNGDGLHGLSGISQENLSELHGNVFHEKCEKCGHRYDRSFYVMDDESSQYYEDVEDYGKSEVK
# KPRHAKRCETCGLSHRTGRKCEQKGCSGFLMDTIINFGDNLEEDILSRAFSQAYECDLMIGLGTTLTVTPANELVEVIKKPQRLVICNRQKTDYDKDC
# LRKLPGADQSVGRKLPGADQSVGSRVHGDCDVFMREVLKNIVGEEKLKSWERDRQTRMISYNKQRQQTS]
# end gene g2
###
# start gene g3
Contig28314	AUGUSTUS	gene	24507	33482	0.06	+	.	g3
Contig28314	AUGUSTUS	transcript	24507	33482	0.06	+	.	g3.t1
Contig28314	AUGUSTUS	start_codon	24507	24509	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	24651	25718	0.96	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	25747	26559	0.74	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	26634	26697	0.41	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	26741	27566	0.37	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	27666	28139	0.92	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	28328	28657	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	28791	29062	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	29239	29463	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	29585	29715	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	29869	30505	0.78	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	30661	30954	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	31067	31234	0.8	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	31401	32031	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	32221	32628	0.99	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	32853	33131	0.92	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	intron	33263	33425	0.34	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	24507	24650	0.98	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	25719	25746	1	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	26560	26633	0.45	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	26698	26740	0.41	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	27567	27665	0.91	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	28140	28327	1	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	28658	28790	1	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	29063	29238	1	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	29464	29584	1	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	29716	29868	1	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	30506	30660	1	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	30955	31066	1	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	31235	31400	0.8	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	32032	32220	0.99	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	32629	32852	1	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	33132	33262	0.7	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	CDS	33426	33482	0.34	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig28314	AUGUSTUS	stop_codon	33480	33482	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgccaacgggaagcaaaatattttcaggatatcgagcacttggttttgttagcgatcatgtgcctcttgcatctcgat
# acaacaagagactaaaagataattacgtaatcacaagcgtggggaaggccttccacacttacaactgttccaagttaggaataaccaacataagtgat
# cgacacccagacaacataagctgtatcgccgttaccaatagatacgtgttcactgggtgtggtaaagagaaaatgaaagccagtgattcgattgttgt
# catagtgatgaaaggacacacaaatgaagttcacctccttcttccatttggaagccatcttatctccgtggacattcacagtaatctgaagatttggg
# atgttgaaaatggaggtgtgtacctggagatggagtttagtaactccacattccacattacggccattatgcaccccagcacgtatctaaacaaagtc
# gtcctcgggagcaagcagggcacgcttcaactgtggaacatcctgaaagacaagatgctgtattccttcgatggctggagtagctcagtcacagttct
# acagcagtctcctgctgttgacgttattgctgtaggattgtctgacggaaggacgattttacacaacattaaatatgatgagacgataatgcactttc
# agcaagactggggaccagtgtcagccatttcattcagaacagatggtcaccctatcatggctacaggaagtacagcgggacacatcgctctttggaat
# ttggaggagaaaaagctccagagtcagatcagacacgcccatcagagcacagtgtcgggaatgaattgtctcccttcagaaccactaatggtcacatc
# agctgcagacaattcactcaaagtatggatctttgatttacctgatggaggaggtcggttactacgacaacgatcaggtcacagtgcaccaccgaaca
# ccattcatcactatgacaacaatggcaaaaatatcttaagtgcaggccaggacagcgtacttcgctcgttttccaccattcacgactctgagagcaaa
# agtttgggaagggccagctacaacaagtcagagacgaagaaggcgggacttctccgtgacagacatatgatgcctaccaatgcaccagtgttcgctgc
# ggatatcgcccgggccagtgactgggataacatcgtggcttgtcacaggggactggctcaagtaaccacgtggaattatcagaggggcaccatgggaa
# aattccgtctgtgtcacccgcgatttcaggagaaacaataccaatcagccacagcccagtgtgttgatatcagcagctgtggcaacttttgtgtgatt
# ggctacagctctggtcatgtggacaagtacaacctacagtctgggattcacaggggcgccattggggaccgagctcacgaatgctgtgtggtaggggt
# ggcagtggacggtatgaaccaggtcctcgtaacggcagggctgaacggagaaatccgcttctggggtttcaaaaagcaccagaaaatcgacagcatgc
# acactgagaactacatctcgaaaatcttactacacagagagagttccatgatggctgtagcaatggaaaatttccagatcattgtggtggatctcgac
# actcggcgggtggtgagaaagtttcaaggtcacagtaacaagttgaccgggctgtccttcagtcctgatgctcgctggctcatctcgtccgccatgga
# ttgtacagtcaggacctgggacttgccctcgggaaggttgattgactgtttcgccgtggagatggctgtgacctcactctcgatgtcgcccactgcgg
# actttctggtgaccagccacgtggacagtgtgggggtgtacacctggtacaataacaccctcctctcccacgtctcactggcccccctctccgacgac
# taccagccacaggaagtggaactcccagacactcgctccacgggagcagacgacagtcaggaagacaacaacgctacagatccagaggcatcggagga
# ttacgcgtctccggaacaattatcgtctgagctggtgaccctgtcgcttctcccgaactctcgctggcagaacctccttaacctggacattatcaagt
# ttgcagtgtttttcttgagtattgatatccccacaaatctaaatccttcaaagtag]
# protein sequence = [MPTGSKIFSGYRALGFVSDHVPLASRYNKRLKDNYVITSVGKAFHTYNCSKLGITNISDRHPDNISCIAVTNRYVFTG
# CGKEKMKASDSIVVIVMKGHTNEVHLLLPFGSHLISVDIHSNLKIWDVENGGVYLEMEFSNSTFHITAIMHPSTYLNKVVLGSKQGTLQLWNILKDKM
# LYSFDGWSSSVTVLQQSPAVDVIAVGLSDGRTILHNIKYDETIMHFQQDWGPVSAISFRTDGHPIMATGSTAGHIALWNLEEKKLQSQIRHAHQSTVS
# GMNCLPSEPLMVTSAADNSLKVWIFDLPDGGGRLLRQRSGHSAPPNTIHHYDNNGKNILSAGQDSVLRSFSTIHDSESKSLGRASYNKSETKKAGLLR
# DRHMMPTNAPVFAADIARASDWDNIVACHRGLAQVTTWNYQRGTMGKFRLCHPRFQEKQYQSATAQCVDISSCGNFCVIGYSSGHVDKYNLQSGIHRG
# AIGDRAHECCVVGVAVDGMNQVLVTAGLNGEIRFWGFKKHQKIDSMHTENYISKILLHRESSMMAVAMENFQIIVVDLDTRRVVRKFQGHSNKLTGLS
# FSPDARWLISSAMDCTVRTWDLPSGRLIDCFAVEMAVTSLSMSPTADFLVTSHVDSVGVYTWYNNTLLSHVSLAPLSDDYQPQEVELPDTRSTGADDS
# QEDNNATDPEASEDYASPEQLSSELVTLSLLPNSRWQNLLNLDIIKFAVFFLSIDIPTNLNPSK]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370H3E.prfl --predictionStart=0  --predictionEnd=33677  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2831420180911_busco_2432604931_.temp