##gff-version 3
#
#Alignments
#
#Nucleotide to genome, and protein to genome alignments are a little
#tricky because they involve two coordinate systems, the coordinates
#of the alignment on the genome (known as the "source" coordinates),
#and the coordinates of the cDNA, EST or protein (known as the
#"target" coordinates). In GFF3, the target coordinates are specified
#using the Target tag.

#This example shows three different alignment features of type
#"EST_match". Each alignment has a distinct ID, and all the
#discontinuous parts of the alignment have the same ID, as described
#earlier. In addition to the ID and Name tags, each segment also has a
#Target tag whose value has the format "<target seqid> <target start>
#<target end>." For example, the very first line indicates that the
#EST named agt830.5 aligns to genomic contig ctg123 such that
#positions 1 through 451 of agt830.5 aligns to bases 1050-1500 of
#ctg123.

#Using the ##FASTA section of the GFF3 file, you can specify the
#sequence of the ESTs as well as of the contig, and GBrowse will
#display the DNA and/or protein sequences in the appropriate contexts.

#See the GFF3 specification for instructions on how to represent
#gapped alignments.

ctg123	est	EST_match	1050	1500	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5	1	451
ctg123	est	EST_match	3000	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5	452	654

ctg123	est	EST_match	5410	5500	.	-	.	ID=Match2;Name=agt830.3;Target=agt830.3	505	595
ctg123	est	EST_match	7000	7503	.	-	.	ID=Match2;Name=agt830.3;Target=agt830.3	1	504

ctg123	est	EST_match	1050	1500	.	+	.	ID=Match3;Name=agt221.5;Target=agt221.5	1	451
ctg123	est	EST_match	5000	5500	.	+	.	ID=Match3;Name=agt221.5;Target=agt221.5	452	952
ctg123	est	EST_match	7000	7300	.	+	.	ID=Match3;Name=agt221.5;Target=agt221.5	953	1253