# This output was generated with AUGUSTUS (version 3.3.1).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# 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
# Sources of extrinsic information: M RM E W 
# Setting acceptor splice site local malus: 0.1
# Setting donor splice site local malus: 0.1
# Setting exon local malus: 0.985
# Setting CDSpart local malus: 0.985
# Setting UTRpart local malus: 0.985
# reading in the file ../hints/rheMac3.hints.gff ...
# Have extrinsic information about 1 sequences (in the specified range). 
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using species specific transition matrix: /home/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like ../genomes/rheMac3.fa 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 = 220640, name = chr20) -----
#
# Delete group HintGroup , 920-1517, mult= 1, priority= 4 1 features
# Delete group HintGroup , 22770-35055, mult= 1, priority= 4 1 features
# Error: intron hint is too short.
# chr20	b2h	intron	35449	35484	0	.	.	pri=4;src=E "1.00561e+06;0.34;0:0"
# Delete group HintGroup , 35448-35483, mult= 1, priority= 4 1 features
# Delete group HintGroup , 40709-169378, mult= 3, priority= 4 1 features
# Delete group HintGroup , 51699-54175, mult= 1, priority= 4 1 features
# Delete group HintGroup , 65770-178467, mult= 1, priority= 4 1 features
# Delete group HintGroup , 68455-102357, mult= 1, priority= 4 1 features
# Delete group HintGroup , 74190-81004, mult= 14, priority= 4 1 features
# Delete group HintGroup , 77800-78120, mult= 11, priority= 4 1 features
# Delete group HintGroup , 86490-86731, mult= 1, priority= 4 1 features
# Delete group HintGroup , 86523-133371, mult= 1, priority= 4 1 features
# Delete group HintGroup , 87099-196386, mult= 2, priority= 4 1 features
# Delete group HintGroup , 89391-94044, mult= 1, priority= 4 1 features
# Delete group HintGroup , 93545-93598, mult= 2, priority= 4 1 features
# Delete group HintGroup , 96571-182025, mult= 1, priority= 4 1 features
# Delete group HintGroup , 97129-97388, mult= 1, priority= 4 1 features
# Delete group HintGroup , 118743-119080, mult= 1, priority= 4 1 features
# Delete group HintGroup , 122845-125727, mult= 1, priority= 4 1 features
# Delete group HintGroup , 124977-127555, mult= 1, priority= 4 1 features
# Delete group HintGroup , 143776-143879, mult= 1, priority= 4 1 features
# Delete group HintGroup , 144033-144243, mult= 28, priority= 4 1 features
# Delete group HintGroup , 151097-151380, mult= 1, priority= 4 1 features
# Delete group HintGroup , 151376-151417, mult= 1, priority= 4 1 features
# Delete group HintGroup , 153313-153351, mult= 1, priority= 4 1 features
# Delete group HintGroup , 201562-201702, mult= 1, priority= 4 1 features
# Error: intron hint is too short.
# chr20	b2h	intron	207147	207183	0	.	.	mult=6;pri=4;src=E "6.03458e+06;0.34;0:0"
# Delete group HintGroup , 207146-207182, mult= 6, priority= 4 1 features
# Delete group HintGroup , 211493-212259, mult= 1, priority= 4 1 features
# Forced unstranded hint group to the only possible strand for 222 groups.
# Deleted 27 groups because some hint was not satisfiable.
# Predicted genes for sequence number 1 on both strands
# start gene g1
chr20	AUGUSTUS	gene	1	23245	1	-	.	g1
chr20	AUGUSTUS	transcript	1	23245	.	-	.	g1.t1
chr20	AUGUSTUS	tts	1	1	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	exon	1	2043	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	stop_codon	1902	1904	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	CDS	1902	2043	.	-	1	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	CDS	2662	2829	.	-	1	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	exon	2662	2829	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	CDS	3240	3269	.	-	1	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	exon	3240	3269	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	CDS	6126	6214	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	exon	6126	6214	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	CDS	13361	13537	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	exon	13361	13537	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	CDS	19968	20111	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	exon	19968	20111	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	CDS	22184	22291	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	exon	22184	23245	.	-	.	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	start_codon	22289	22291	.	-	0	transcript_id "g1.t1"; gene_id "g1";
chr20	AUGUSTUS	tss	23245	23245	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# protein sequence = [MDHLESFIAECDRRTELAKKRLAETQEEISAEVSAKAEKVHELNEEIGKLLAKAEQLGAEGNVDESQKILMEVEKVRA
# KKKEAEEEYRNSMPASSFQQQKLRVCEVCSAYLGLHDNDRRLADHFGGKLHLGFIQIREKLDQLRKTVAEKQEKRNQDRLRRREEREREERLSRRSGS
# RTRDRRRSRSRDRRRRRSRSTSRERRKLSRSRSRDRHRRHRSRSRSHSRGHRRASRDRSAKYKFSRERASREESWESGRSERGPPDWRLESSNGKMAS
# RRSEEKEAGEI]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 7/7
#      W:   7 
# CDS introns: 6/6
#      E:   6 
# 5'UTR exons and introns: 1/1
#      W:   1 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 299
#      E:   6 
#     RM:  11 
#      W: 282 
# incompatible hint groups: 549
#      E:   4 
#      W: 545 
# end gene g1
###
# start gene g2
chr20	AUGUSTUS	gene	51666	87146	1	+	.	g2
chr20	AUGUSTUS	transcript	51666	87146	.	+	.	g2.t1
chr20	AUGUSTUS	tss	51666	51666	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	51666	51700	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	54177	54267	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	69008	69129	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	72864	73164	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	start_codon	72897	72899	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	72897	73164	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	81009	81125	.	+	2	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	81009	81125	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	81500	81691	.	+	2	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	81500	81691	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	82873	83003	.	+	2	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	82873	83003	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	83478	83610	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	83478	83610	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	83805	83934	.	+	2	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	83805	83934	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	84326	84466	.	+	1	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	84326	84466	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	84760	84835	.	+	1	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	84760	84835	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	85068	85223	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	85068	85223	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	85669	85771	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	85669	85771	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	CDS	85866	86077	.	+	2	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	exon	85866	87146	.	+	.	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	stop_codon	86075	86077	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr20	AUGUSTUS	tts	87146	87146	.	+	.	transcript_id "g2.t1"; gene_id "g2";
# protein sequence = [MLDHQDLEAEVHPLKNEERKSQENLGNPSKNEDKLKSTPPQSRLSRCRTVAFFLSLFLCLFVVFVVSFVIPCPDRPAS
# QRMWRIDYNAAVIYDFLAVDDINGDRIQDVLFLYKNTNSSNNFNRSCVDEGFSSPCAFAAAVSGANGSTLWERPVAQDVALVECAVPQPRGSEAPSAC
# ILVGRPGSFIAVDSFTGETLWNHSSSFSRNASILSPLLQVPDVDSDGAPDLLVFTQEQEEVSGHLYSGSTGHQIGLRGGLGVDGESGFLLHVTRTGAH
# YILFPCASSLCGCSVKGLYEKVTGRDGPFKNDPHWESMLNATTRRMLSHSSGAVRYLMHVPGNTGADVLLVGSEGFVLLDGQELTPRWTPKAAHVLRK
# PIFGHYKPDTLAVVVENGTGTNRQILFLDLGTGAVLCSLALPSLPGGPLSASLPTADHRSAFFFWGLHELGSTSETETGEARHSLYMFHPTLPRVLLE
# LANVSTHIVAFDAVLFEPSRHAAYILLTGPADSEAPGLVSVIKHKVRDLVPSSRVVHLGEGEPDSDQAIRDRFSRLRYRREA]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 11/11
#      W:  11 
# CDS introns: 10/10
#      E:  10 
# 5'UTR exons and introns: 7/7
#      E:   3 
#      W:   4 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 206
#      E:  13 
#     RM:  19 
#      W: 174 
# incompatible hint groups: 218
#      E:   1 
#      W: 217 
# end gene g2
###
# start gene g3
chr20	AUGUSTUS	gene	88892	94355	1	-	.	g3
chr20	AUGUSTUS	transcript	88892	94355	.	-	.	g3.t1
chr20	AUGUSTUS	tts	88892	88892	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	88892	90276	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	stop_codon	90162	90164	.	-	0	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	90162	90276	.	-	1	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	90396	90478	.	-	0	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	90396	90478	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	92556	92694	.	-	1	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	92556	92694	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	92777	92864	.	-	2	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	92777	92864	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	93043	93158	.	-	1	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	93043	93158	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	93252	93365	.	-	1	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	93252	93365	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	93458	93519	.	-	0	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	93458	93519	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	93599	93671	.	-	1	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	93599	93671	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	CDS	94276	94319	.	-	0	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	exon	94276	94355	.	-	.	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	start_codon	94317	94319	.	-	0	transcript_id "g3.t1"; gene_id "g3";
chr20	AUGUSTUS	tss	94355	94355	.	-	.	transcript_id "g3.t1"; gene_id "g3";
# protein sequence = [MNSISHTWFPSDSHYRGPASNCSPPVPFQTKRADFYKQEIEYCRRALGRTRVKSSVCLEAYLSFCGQRGPHDPLVSGC
# LPSNPWISDDAAYWVMNAPTVVAPTKLRVERWGFSFRELLEDPVGRAHFMDFLGKEFSGENLSFWEACEELRYGAQAQVPTLVDAVYQQFLAPGAARW
# VNIDSRTMERTLEGLRQPHRYVLDDAQLHIYMLMKKDSYPRFLKSDMYKGLLAEAGIPLETKKRVFPFSRRPRHSSPSPALLPTPVEPTAAGGPGGGD
# GVA]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 84.2
# CDS exons: 8/9
#      W:   8 
# CDS introns: 6/8
#      E:   6 
# 5'UTR exons and introns: 1/1
#      W:   1 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 139
#      E:   6 
#      W: 133 
# incompatible hint groups: 86
#      W:  86 
# end gene g3
###
# start gene g4
chr20	AUGUSTUS	gene	94426	97445	1	-	.	g4
chr20	AUGUSTUS	transcript	94426	97445	.	-	.	g4.t1
chr20	AUGUSTUS	tts	94426	94426	.	-	.	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	exon	94426	95655	.	-	.	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	stop_codon	95418	95420	.	-	0	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	CDS	95418	95655	.	-	1	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	CDS	95842	95918	.	-	0	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	exon	95842	95918	.	-	.	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	CDS	96122	96235	.	-	0	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	exon	96122	97161	.	-	.	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	start_codon	96233	96235	.	-	0	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	exon	97356	97445	.	-	.	transcript_id "g4.t1"; gene_id "g4";
chr20	AUGUSTUS	tss	97445	97445	.	-	.	transcript_id "g4.t1"; gene_id "g4";
# protein sequence = [MLWGRAELAPLQAVPVLLAIYLAKKNIRKQGTLVDYEKECYDRLHTKINHAWDLVLMQAREQLRAAKQRRKGDRLVIA
# CQEQTYWLVNRPPVSPPAVRVWGHWPAQGSVCFPDRCSQDHRFEPVEGPALEILVGAGRSCFVT]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 3/3
#      W:   3 
# CDS introns: 2/2
#      E:   2 
# 5'UTR exons and introns: 3/3
#      E:   1 
#      W:   2 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 177
#      E:   3 
#      W: 174 
# incompatible hint groups: 18
#      W:  18 
# end gene g4
###
# start gene g5
chr20	AUGUSTUS	gene	105886	107444	1	+	.	g5
chr20	AUGUSTUS	transcript	105886	107444	.	+	.	g5.t1
chr20	AUGUSTUS	tss	105886	105886	.	+	.	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	exon	105886	106106	.	+	.	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	start_codon	105923	105925	.	+	0	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	CDS	105923	106106	.	+	0	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	CDS	106283	106359	.	+	2	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	exon	106283	106359	.	+	.	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	CDS	107112	107264	.	+	0	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	exon	107112	107444	.	+	.	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	stop_codon	107262	107264	.	+	0	transcript_id "g5.t1"; gene_id "g5";
chr20	AUGUSTUS	tts	107444	107444	.	+	.	transcript_id "g5.t1"; gene_id "g5";
# protein sequence = [MAGAWAWRAGSGGAGGKPSRGGGGILQTSSFSSDPSLPNVQVTRLTLLSEQAPGPVVMDLTGDLAVLKDQVFVLKEGV
# DYRVKITFKEYEFVTPVEEAPRGALVRGPYLVVSLFTDDDRTHHLSWEWGLRISQDWKD]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 85.7
# CDS exons: 3/3
#      W:   3 
# CDS introns: 1/2
#      E:   1 
# 5'UTR exons and introns: 1/1
#      W:   1 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 40
#      E:   1 
#      W:  39 
# incompatible hint groups: 10
#      E:   1 
#      W:   9 
# end gene g5
###
# start gene g6
chr20	AUGUSTUS	gene	107516	111253	1	+	.	g6
chr20	AUGUSTUS	transcript	107516	111253	.	+	.	g6.t1
chr20	AUGUSTUS	tss	107516	107516	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	107516	107793	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	start_codon	107598	107600	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	107598	107793	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	108785	108991	.	+	2	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	108785	108991	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	109057	109190	.	+	2	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	109057	109190	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	109272	109409	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	109272	109409	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	109478	109594	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	109478	109594	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	109706	109831	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	109706	109831	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	109938	110135	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	109938	110135	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	110391	110511	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	110391	110511	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	110592	110773	.	+	2	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	110592	110773	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	110870	110980	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	110870	110980	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	CDS	111103	111147	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	exon	111103	111253	.	+	.	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	stop_codon	111145	111147	.	+	0	transcript_id "g6.t1"; gene_id "g6";
chr20	AUGUSTUS	tts	111253	111253	.	+	.	transcript_id "g6.t1"; gene_id "g6";
# protein sequence = [MSRQLLPVLLLLLRASCPWGQEQGPKSPSEEPPEEEIPKEDGILVLSRHTLGLALREHPALLVEFYAPWCGHCKALAP
# EYSKAAALLAAESTAVTLSKVDGPAQPELAEEFGVTEYPTLKFFRSGNRTHPEEYTGPREAEGIAEWLRRRVGPSALRLEDEAAAQALIDGRDLVVIG
# FFQDLQDEDVATFLALARDALDMTFGLTDRPRLFEQFGLTKDTVVLFKKFDEGRADFPVDEELGLDLGDLSRFLVTHSMHLVTEFNSQTSPKIFAARI
# LNHLLLFVNQTLAAHRELLAGFGEAAPHFRGQVLFVVVDVAADNEHVLQYFGLKAEAAPTLRFINVETTKKYAPVDGGPVTAASVTAFCHAVLNGQVK
# PYLLSQEVPPDWDQRPVKTLVGKNFEQVAFDETKNVFVKFYAPWCTHCKEMAPAWEALAEKYQDHEDIIIAQLDATANELDAFAVHSFPTLKYFPAGP
# GRKVIEYKSARDLETLSKFLDNGGAVPTEEPTEEPAAPFPEPRANSTVGSKEEL]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 39.1
# CDS exons: 6/11
#      W:   6 
# CDS introns: 3/10
#      E:   3 
# 5'UTR exons and introns: 0/1
# 3'UTR exons and introns: 0/1
# hint groups fully obeyed: 3
#      E:   3 
# incompatible hint groups: 72
#      W:  72 
# end gene g6
###
# start gene g7
chr20	AUGUSTUS	gene	111468	115225	1	-	.	g7
chr20	AUGUSTUS	transcript	111468	115225	.	-	.	g7.t1
chr20	AUGUSTUS	tts	111468	111468	.	-	.	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	exon	111468	112260	.	-	.	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	stop_codon	112134	112136	.	-	0	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	CDS	112134	112260	.	-	1	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	CDS	113467	113634	.	-	1	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	exon	113467	113634	.	-	.	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	CDS	115080	115198	.	-	0	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	exon	115080	115225	.	-	.	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	start_codon	115196	115198	.	-	0	transcript_id "g7.t1"; gene_id "g7";
chr20	AUGUSTUS	tss	115225	115225	.	-	.	transcript_id "g7.t1"; gene_id "g7";
# protein sequence = [MELSETEYVRPEGPPGPAHPAQASQARSHGRAAVLGPELRTRSQRKAGGGSAQPCDSIVVAYYFCGEPIPYRTLVRGR
# AVTLGQFKELLTKKGSYRYYFKKVSDEFDCGVVFEEVREDEAVLPVFEEKIIGKVEKVD]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 85.7
# CDS exons: 3/3
#      W:   3 
# CDS introns: 1/2
#      E:   1 
# 5'UTR exons and introns: 1/1
#      W:   1 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 89
#      E:   1 
#      W:  88 
# incompatible hint groups: 45
#      W:  45 
# end gene g7
###
# start gene g8
chr20	AUGUSTUS	gene	116332	122545	1	-	.	g8
chr20	AUGUSTUS	transcript	116332	122545	.	-	.	g8.t1
chr20	AUGUSTUS	tts	116332	116332	.	-	.	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	exon	116332	117578	.	-	.	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	stop_codon	117269	117271	.	-	0	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	CDS	117269	117578	.	-	1	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	CDS	121067	121237	.	-	1	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	exon	121067	121237	.	-	.	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	CDS	121645	122198	.	-	0	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	exon	121645	122545	.	-	.	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	start_codon	122196	122198	.	-	0	transcript_id "g8.t1"; gene_id "g8";
chr20	AUGUSTUS	tss	122545	122545	.	-	.	transcript_id "g8.t1"; gene_id "g8";
# protein sequence = [MVLLVPTQEEEGEDGDPSSGLPGPCHKLPPAPAWHHFPPRCVDVGCAGLRDAHEENPESILDEHVQRVLRTPGRQSPG
# PGHRSPDSGHMAKMPVALGSAASGHGKHAPKSGVKLDAAGLHHHRHVHHHVHHSTARPKEQVEAEAARRAQSSFAWGPEPHSHGAKSRGYSESVGAAP
# NASDGLAHSGKAGMACKRNAKKAESGKSASAEVPGASEDAEKNQKIMQWIIEGEKEISRHRRTGHGSSGTRKPQPHENSRPLSLERPAAVHPWAGPQL
# RTSVQPSHLFIQDPTMPPHPAPNPLTQLEEARRRLEEEEKRASRAPSKQRYGRIVGWGGSWELPQHHSWG]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 3/3
#      W:   3 
# CDS introns: 2/2
#      E:   2 
# 5'UTR exons and introns: 1/1
#      W:   1 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 179
#      E:   2 
#     RM:   4 
#      W: 173 
# incompatible hint groups: 21
#      W:  21 
# end gene g8
###
# start gene g9
chr20	AUGUSTUS	gene	124424	180505	1	-	.	g9
chr20	AUGUSTUS	transcript	124424	180505	.	-	.	g9.t1
chr20	AUGUSTUS	tts	124424	124424	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	exon	124424	124796	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	exon	127422	128891	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	stop_codon	128808	128810	.	-	0	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	CDS	128808	128891	.	-	0	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	CDS	129055	129192	.	-	0	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	exon	129055	129192	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	CDS	135293	135389	.	-	1	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	exon	135293	135389	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	CDS	139001	139141	.	-	1	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	exon	139001	139141	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	CDS	175212	176089	.	-	0	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	exon	175212	176170	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	start_codon	176087	176089	.	-	0	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	exon	180270	180505	.	-	.	transcript_id "g9.t1"; gene_id "g9";
chr20	AUGUSTUS	tss	180505	180505	.	-	.	transcript_id "g9.t1"; gene_id "g9";
# protein sequence = [MNIQEQGFPLDLGASFTEDAPRPPVPGEEGELVSTDPRPASYSFCSGKGVGIKAETSTATPRRSDLDLGYEPEGSASP
# TPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKLEPCDSNEEKRLKLARAIYRKYILDNNGIVSRQTKPATKSFIKGCIMKQL
# IDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTRTGSESPKVCSDQSSGSGTGKGISGYLPTLNEDEEWKCDQDMDEDDGRDAAPPGRLPQKLLLE
# TAAPRASSSRRYSEGREFRYGSWREPVNPYYVNAGYALAPATSANDSEQQSLSSDADTLSLTDSSVDGIPPYRIRKQHRREMQESVQVNGRVPLPHIP
# RTYRVPKEVRVEPQKFAEELIHRLEAVQRTREAEEKLEERLKRVRMPSPSSGWDVQRPHPTLRGPETHLGHPH]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 66.7
# CDS exons: 5/5
#      W:   5 
# CDS introns: 2/4
#      E:   2 
# 5'UTR exons and introns: 1/3
#      W:   1 
# 3'UTR exons and introns: 2/3
#      W:   2 
# hint groups fully obeyed: 198
#      E:   2 
#     RM:  33 
#      W: 163 
# incompatible hint groups: 67
#      W:  67 
# end gene g9
###
# start gene g10
chr20	AUGUSTUS	gene	194467	197185	1	-	.	g10
chr20	AUGUSTUS	transcript	194467	197185	.	-	.	g10.t1
chr20	AUGUSTUS	tts	194467	194467	.	-	.	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	exon	194467	194861	.	-	.	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	stop_codon	194754	194756	.	-	0	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	CDS	194754	194861	.	-	0	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	CDS	195400	195486	.	-	0	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	exon	195400	195486	.	-	.	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	CDS	195573	195707	.	-	0	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	exon	195573	195707	.	-	.	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	CDS	196134	196190	.	-	0	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	exon	196134	196286	.	-	.	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	start_codon	196188	196190	.	-	0	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	exon	196950	197185	.	-	.	transcript_id "g10.t1"; gene_id "g10";
chr20	AUGUSTUS	tss	197185	197185	.	-	.	transcript_id "g10.t1"; gene_id "g10";
# protein sequence = [MRTLDLIDEAYGFDFYILKTPKEDLCSKFGMDLKRGMLLRLARQDPQLHPEDPERRAAIYDKYKEFAIPEEEAEWVGL
# TLEEAIEKQRLLEEKDPVPLFKIYVAELIQRLQQQALSEPVVVQKRASGQ]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 100
# CDS exons: 4/4
#      W:   4 
# CDS introns: 3/3
#      E:   3 
# 5'UTR exons and introns: 3/3
#      E:   1 
#      W:   2 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 78
#      E:   4 
#      W:  74 
# incompatible hint groups: 25
#      W:  25 
# end gene g10
###
# start gene g11
chr20	AUGUSTUS	gene	198183	208425	1	-	.	g11
chr20	AUGUSTUS	transcript	198183	208425	.	-	.	g11.t1
chr20	AUGUSTUS	tts	198183	198183	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	198183	199608	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	stop_codon	199312	199314	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	199312	199608	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	199932	200048	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	199932	200048	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	201331	201477	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	201331	201477	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	201537	201715	.	-	2	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	201537	201715	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	202070	202206	.	-	1	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	202070	202206	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	202446	202569	.	-	2	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	202446	202569	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	202657	202747	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	202657	202747	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	203436	203755	.	-	2	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	203436	203755	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	203844	204112	.	-	1	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	203844	204112	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	204307	204434	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	204307	204434	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	204648	204855	.	-	1	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	204648	204855	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	204940	205117	.	-	2	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	204940	205117	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	CDS	205226	205304	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	205226	206751	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	start_codon	205302	205304	.	-	0	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	exon	207548	208425	.	-	.	transcript_id "g11.t1"; gene_id "g11";
chr20	AUGUSTUS	tss	208425	208425	.	-	.	transcript_id "g11.t1"; gene_id "g11";
# protein sequence = [MAEDWLRGQRVAVTFTKVRVGVPRAAEVGLVSEHFSQAPQRLSFYSWYGSARLFRFRVPPDTVLLRWLLQVSREGGTA
# CTDAEITVHFRSGAPPVINPLGTSFPDDTSVQPSFQVRVPLSAAPLSNASVNVSHPAPGDWFVAAHLPPSSQKIELKGLAPTCAYVFQPDLLVTRVVE
# ISVMEPDVPLPHTLVSHPSYLKVFVPDYTRELLLELRDCVSSGSLGCPVRLTVGPVTLPSNFQKVLTCTSAPWPCRLLLPSPPWDRWLQVTAESLVGP
# LGTVTFSAVAALTACRPQSVTIQPLLQSSQNQSFNASTGLPSLSPDHQYLGRSGSVDRSPFCLTNYPVMREDMDVVSVHFQLLDRVSVRVCPNTPSMM
# RLRLNTGMDSGGSLTISLRANKTEMRNETVIVACVNAASPFLGFNSSLNCTTAFFQGYPLSLSAWSLRANLIIPYPETDNWYLSLQLMCPENAEECEQ
# AVVHVETTLYLVPCLNDCGPYGQCLLLRRHSYLYAGCSCKAGWRGWSCTDNSTAQTVAQQRAAALLLTLSNLMFLAPITVSVQRFFLVEASVYAYTMF
# FSTFYHACDQPGEAVLCILNYDTLQYCDFLGSGAAIWVTILCMARLKAVLKYVLFLLGTLVIAMSLQLDRRGIWNMLGPCLFAFVIMASMWTYRCGHR
# RQCYPTSWQRWAFYLLPGISMASVGVAIYTSMMTSDNYYYTHSIWHVLLAGSAALLLPPPDEHAEPWACSQKFPCHYQICKNDREELYTVT]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 89.7
# CDS exons: 12/13
#      W:  12 
# CDS introns: 11/12
#      E:  11 
# 5'UTR exons and introns: 2/3
#      W:   2 
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 276
#      E:  11 
#     RM:   2 
#      W: 263 
# incompatible hint groups: 240
#      W: 240 
# end gene g11
###
# command line:
# augustus --species=human ../genomes/rheMac3.fa --hintsfile=../hints/rheMac3.hints.gff --UTR=on --allow_hinted_splicesites=atac --extrinsicCfgFile=extrinsic.M.RM.E.W.cfg --softmasking=on --alternatives-from-evidence=off
