# 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
# No extrinsic information on sequences given.
# Sources of extrinsic information: M RM 
# Initializing the parameters using config directory /home/mario/augustus/git/Augustus/config/ ...
# human version. Using default transition matrix.
# Looks like ../genomes/rn6.fa 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 = 99944, name = chr10) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
chr10	AUGUSTUS	gene	1	24304	1	+	.	g1
chr10	AUGUSTUS	transcript	1	24304	.	+	.	g1.t1
chr10	AUGUSTUS	CDS	18938	19112	.	+	2	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	19196	19403	.	+	1	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	19575	19702	.	+	0	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	19898	19976	.	+	1	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	21007	21097	.	+	0	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	21178	21301	.	+	2	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	21543	21679	.	+	1	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	22359	22537	.	+	2	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	22614	22760	.	+	0	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	23602	23718	.	+	0	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	CDS	24008	24304	.	+	0	transcript_id "g1.t1"; gene_id "g1";
chr10	AUGUSTUS	stop_codon	24302	24304	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# protein sequence = [AGLVSEHFSQAPQKLSFYSWYGSTRLFHFRVPPDTVLLRWLLHVSQGGPSCADVEITVHFRYGAPPVINPLGTSFPDD
# TLTHASFHIKTLLSTMLLGNTSVNISHPAPGDWFLVAHLPPSSQKIQVKGFVPTCAYIFQPDMLVMRVVEVSILEPDIPLPQTLLSHPSYLKIFVPEY
# TQELRLELQGCVSSVSPGCPSEVTNGTSVAACVNVASPFLSFNASLNCTTAFFQGYPMFLSASSHMANLIIPYPETDNWYLSLQLVCPESPEDCEQAA
# VRVETVLYLVPCLNDCGPYGQCLLLRRYGYLYAGCSCKAGWRGWSCTDNSTAQTAAQQRAAALLLTLSNLMFLAPIAISVHRSFLVEASVYFYTMFFS
# TFYHACDQPGEAVLCILSYDTLQYCDFLGSGASTWVTILCMARLKTILKQVLLVLGLLVIAMSLQMDRRGIWNLMGPCVFAFVIMAFMWIYRCGHRRQ
# CYPTSWQRWVFYLLPGISMAFVGIAMYTSMMTSDNYYYTHSIWHILLAGSVAFLLPPREEKAGSWACLQKFPCHYQICRNDRDELYTVT]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/11
# CDS introns: 0/11
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 50
#     RM:  50 
# incompatible hint groups: 0
# end gene g1
###
# start gene g2
chr10	AUGUSTUS	gene	25614	28225	1	+	.	g2
chr10	AUGUSTUS	transcript	25614	28225	.	+	.	g2.t1
chr10	AUGUSTUS	start_codon	25614	25616	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr10	AUGUSTUS	CDS	25614	25901	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr10	AUGUSTUS	CDS	27374	27508	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr10	AUGUSTUS	CDS	27592	27678	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr10	AUGUSTUS	CDS	28115	28225	.	+	0	transcript_id "g2.t1"; gene_id "g2";
chr10	AUGUSTUS	stop_codon	28223	28225	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# protein sequence = [MPLHRYPVHLWQKLRLQQGICARLPSHFLRSLEEERTPTPVHYKPHGAKFKINPKNGQRERVEDVPIPVHYPPESQQE
# LWGGEGLILGYRYANNDKTPEEDLCSKFGMDLKRGMLLRLARQDPQLHPDNPERRAAIYDKYRNFVIPEAEAEWVGLTLEEALEKQRLLEEKDPVPLF
# KVYVEELVQRLQEQALSRPAVVQKRAGDHV]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/4
# CDS introns: 0/3
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 1
#     RM:   1 
# incompatible hint groups: 0
# end gene g2
###
# start gene g3
chr10	AUGUSTUS	gene	68941	99944	1	+	.	g3
chr10	AUGUSTUS	transcript	68941	99944	.	+	.	g3.t1
chr10	AUGUSTUS	start_codon	68941	68943	.	+	0	transcript_id "g3.t1"; gene_id "g3";
chr10	AUGUSTUS	CDS	68941	69001	.	+	0	transcript_id "g3.t1"; gene_id "g3";
chr10	AUGUSTUS	CDS	69887	69957	.	+	2	transcript_id "g3.t1"; gene_id "g3";
chr10	AUGUSTUS	CDS	74706	74804	.	+	0	transcript_id "g3.t1"; gene_id "g3";
chr10	AUGUSTUS	CDS	83972	84082	.	+	0	transcript_id "g3.t1"; gene_id "g3";
chr10	AUGUSTUS	CDS	85220	85363	.	+	0	transcript_id "g3.t1"; gene_id "g3";
chr10	AUGUSTUS	CDS	91728	91904	.	+	0	transcript_id "g3.t1"; gene_id "g3";
chr10	AUGUSTUS	CDS	96090	96119	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# protein sequence = [MSAQAQMRALLDQLMGTARDGSVYLCLPTSICKGVAEKPHVHRARMDLGECTKIHDLALRADYEIASKERDLFFELDA
# MDHLESFIAECDRRTELAKKRLAETQEEISAEVSAKAEKVHELNEEIGKLLAKAEQLGAEGNVDESQKILMEVEKVRSKKKEAEEEYRNSMPASSFQQ
# QKLRVCEVCSAYLGLHDNDRRLADHFGGKLHLGFIQIREKLDQLRVWIKNPRSEE]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/7
# CDS introns: 0/7
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 0/0
# hint groups fully obeyed: 106
#     RM: 106 
# incompatible hint groups: 0
# end gene g3
###
# command line:
# augustus --species=human ../genomes/rn6.fa --softmasking=1
