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##gff-version 2
# exonerate output in gff2 format; not gff3 because
# - 'similarity' is not a Sequence Ontology term
# - attributes' name/values are separated by space ' ' not equals '='
##source-version exonerate:protein2genome:local 2.2.0
##date 2015-01-16
##type DNA
#
# exonerate run with --showtargetgff generates 'features on the target' i.e. mappings to the query
# tab-delimited
# seqname source feature start end score strand frame attributes
#
seq1 exonerate:protein2genome:local gene 8 11 3652 - . gene_id 0 ; sequence seq2 ; gene_orientation .
seq1 exonerate:protein2genome:local cds 9 11 . - .
seq1 exonerate:protein2genome:local exon 9 11 . - . insertions 3 ; deletions 6
#seq1 exonerate:protein2genome:local similarity 8 11 3652 - . alignment_id 0 ; Query seq2 ; Align 11 1 3
seq1 exonerate:protein2genome:local similarity 9 11 3652 - . alignment_id 0 ; Query seq2 ; Align 11 1 3
#
# appending FASTA sequences is strictly a GFF3 format feature
# but Jalview is able to handle this mixture of GFF2 / GFF3 :-)
#
##FASTA
>seq1
ACTACGACACGACGACGACGACG
>seq2
CDEQEATGTQDAQEQAQC
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