--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/human_augustus_utr-on.gff	Sat Jul 06 10:07:41 2013 -0400
@@ -0,0 +1,77 @@
+##gff-version 3
+# This output was generated with AUGUSTUS (version 2.7).
+# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de)
+# and Oliver Keller (keller@cs.uni-goettingen.de).
+# 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 ...
+# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl
+# Looks like ./examples/example.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 = 9453, name = HS04636) -----
+#
+# Predicted genes for sequence number 1 on both strands
+# start gene g1
+HS04636	AUGUSTUS	gene	836	8857	1	+	.	ID=g1
+HS04636	AUGUSTUS	transcript	836	8857	.	+	.	ID=g1.t1;Parent=g1
+HS04636	AUGUSTUS	transcription_start_site	836	836	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	exon	836	1017	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	start_codon	966	968	.	+	0	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	966	1017	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	CDS	1818	1934	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	1818	1934	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	2055	2198	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	2055	2198	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	2852	2995	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	2852	2995	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	3426	3607	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	3426	3607	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	4340	4423	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	4340	4423	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	4543	4789	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	4543	4789	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	5072	5358	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	5072	5358	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	5860	6007	.	+	0	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	5860	6007	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	CDS	6494	6903	.	+	2	ID=g1.t1.cds;Parent=g1.t1
+HS04636	AUGUSTUS	exon	6494	8857	.	+	.	Parent=g1.t1
+HS04636	AUGUSTUS	stop_codon	6901	6903	.	+	0	Parent=g1.t1
+HS04636	AUGUSTUS	transcription_end_site	8857	8857	.	+	.	Parent=g1.t1
+# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
+# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
+# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
+# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
+# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
+# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
+# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
+# end gene g1
+###
+#
+# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
+#
+# Predicted genes for sequence number 2 on both strands
+# start gene g2
+HS08198	AUGUSTUS	gene	86	2344	1	+	.	ID=g2
+HS08198	AUGUSTUS	transcript	86	2344	.	+	.	ID=g2.t1;Parent=g2
+HS08198	AUGUSTUS	transcription_start_site	86	86	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	exon	86	582	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	start_codon	445	447	.	+	0	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	445	582	.	+	0	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	CDS	812	894	.	+	0	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	812	894	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	1053	1123	.	+	1	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	1053	1123	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	1208	1315	.	+	2	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	1208	1315	.	+	.	Parent=g2.t1
+HS08198	AUGUSTUS	CDS	1587	1688	.	+	2	ID=g2.t1.cds;Parent=g2.t1
+HS08198	AUGUSTUS	exon	1587	1688	.	+	.	Parent=g2.t1
+# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
+# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
+# end gene g2
+###
+# command line:
+# ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa