# 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 using config directory /augustus/config/ ...
# Using protein profile unknown
# --[0..243]--> unknown_A (24) <--[0..8]--> unknown_B (25) <--[0..15]--> unknown_C (30) <--[8..20]--> unknown_D (14) <--[0..15]--> unknown_E (12) <--[19..168]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig1785520180911_busco_2432604931_.temp 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 = 31186, name = Contig17855) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig17855	AUGUSTUS	gene	6488	32021	0.01	-	.	g1
Contig17855	AUGUSTUS	transcript	6488	32021	0.01	-	.	g1.t1
Contig17855	AUGUSTUS	exon	6488	6625	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	exon	7636	7869	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	stop_codon	7664	7666	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	intron	7870	21846	0.02	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	intron	22010	26096	0.54	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	intron	26361	31884	0.51	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	CDS	7664	7869	0.03	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	CDS	21847	22009	0.82	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	exon	21847	22009	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	CDS	26097	26360	0.52	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	exon	26097	26360	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	CDS	31885	31908	0.51	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	exon	31885	32021	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	start_codon	31906	31908	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	tss	32021	32021	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	protein_match	21878	21913	5.58	-	0	target "unknown_E[1..12]"; target_start 128; transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	protein_match	21935	21976	5.08	-	0	target "unknown_D[1..14]"; target_start 107; transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	protein_match	26100	26189	8.79	-	0	target "unknown_C[1..30]"; target_start 65; transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	protein_match	26193	26267	10.2	-	0	target "unknown_B[1..25]"; target_start 39; transcript_id "g1.t1"; gene_id "g1";
Contig17855	AUGUSTUS	protein_match	26268	26339	11	-	0	target "unknown_A[1..24]"; target_start 15; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtccgctaaattcggacagtcgactgtggggcgtagctctaagatgttgcagcacatcaactacaggatgcgatgca
# ccctgcaagatggccgcacctttataggaacattcaaagcttttgataaacacatgaacttgatcctcggagattgtgacgagttcaggaaaataaaa
# ccgaaaagttcaaaacagggagaaagagaggagaagcgagttctagggcttgtgttactgcgaggtgaacatcttgtctctatgacagtggaaggacc
# ccctccagctgaggagggagttgctagagtgccattatctggagctggcccgggacaaggaatcggccgtgctgctgggcggggcatctctggaccgg
# gaggctctgggggaccgggattacaaggaccggcccgcggagtgggcggaccttcacaacaaatgatggctcctggagaaattgattcctccaccctg
# cggaccaggacgatgacgtccccccacaccccacctgccacctcccccgccacacacaacgggcaccactaccagaagatatccggggtcccctgccc
# tgctaccccgactcgctacactgccccagtgcacatcgatgtcggaggggtcatttacacctcgtcattggaaaccctcacaaagtaa]
# protein sequence = [MSAKFGQSTVGRSSKMLQHINYRMRCTLQDGRTFIGTFKAFDKHMNLILGDCDEFRKIKPKSSKQGEREEKRVLGLVL
# LRGEHLVSMTVEGPPPAEEGVARVPLSGAGPGQGIGRAAGRGISGPGGSGGPGLQGPARGVGGPSQQMMAPGEIDSSTLRTRTMTSPHTPPATSPATH
# NGHHYQKISGVPCPATPTRYTAPVHIDVGGVIYTSSLETLTK]
# sequence of block unknown_E   128 [GPGLQGPARGVG] 140
# sequence of block unknown_D   107 [GPGQGIGRAAGRGI] 121
# sequence of block unknown_C    65 [GEREEKRVLGLVLLRGEHLVSMTVEGPPPA] 95
# sequence of block unknown_B    39 [AFDKHMNLILGDCDEFRKIKPKSSK] 64
# sequence of block unknown_A    15 [MLQHINYRMRCTLQDGRTFIGTFK] 39
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09371675.prfl --predictionStart=6217  --predictionEnd=46342  --species=fly ./tmp/Contig1785520180911_busco_2432604931_.temp