$ gth -v -frompos 1 -topos 200000 -inverse -force -o arab_mapping.txt -cdna CeresTigr.gz -species arabidopsis -genomic NC_003070.fna.gz 
$ d=-, compute chains for bucket 368/377 (matches in bucket=1)
$ d=-, compute chains for bucket 369/377 (matches in bucket=1)
$ d=-, compute chains for bucket 370/377 (matches in bucket=1)
$ d=-, compute chains for bucket 371/377 (matches in bucket=1)
$ d=-, compute chains for bucket 372/377 (matches in bucket=1)
$ d=-, compute chains for bucket 373/377 (matches in bucket=9)
$ d=-, compute chains for bucket 374/377 (matches in bucket=1)
$ d=-, compute chains for bucket 375/377 (matches in bucket=2)
$ d=-, compute chains for bucket 376/377 (matches in bucket=2)
$ d=-, compute chains for bucket 377/377 (matches in bucket=1)
$ sort global chains according to reference sequence coverage
$ calculate spliced alignment for every chain
$ d=-, compute spliced alignment, genseq=-, chain=1/5, refseq=+
$ d=-, compute spliced alignment, genseq=-, chain=2/5, refseq=+
$ d=-, compute spliced alignment, genseq=-, chain=3/5, refseq=+
$ d=-, compute spliced alignment, genseq=-, chain=4/5, refseq=+
$ d=-, compute spliced alignment, genseq=-, chain=5/5, refseq=+
$ output spliced alignments
$ compute predicted gene locations
$ output predicted gene locations
