# 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
# --[11..174]--> unknown_B (18) <--[0..28]--> unknown_C (30) <--[10..24]--> unknown_E (9) <--[0..11]--> unknown_F (40) <--[0..11]--> unknown_G (24) <--[0..7]--> unknown_H (23) <--[1..4]--> unknown_I (14) <--[0..2]--> unknown_J (15) <--[10..41]--> unknown_K (28) <--[10..47]--> unknown_L (25) <--[0..6]--> unknown_M (17) <--[5..644]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig7832820180911_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 = 5668, name = Contig78328) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig78328	AUGUSTUS	gene	1546	2825	0.01	-	.	g1
Contig78328	AUGUSTUS	transcript	1546	2825	0.01	-	.	g1.t1
Contig78328	AUGUSTUS	tts	1546	1546	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	exon	1546	2825	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	stop_codon	1702	1704	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	CDS	1702	2784	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	start_codon	2782	2784	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	tss	2825	2825	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	1753	1803	4.24	-	0	target "unknown_M[1..17]"; target_start 327; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	1804	1878	2.85	-	0	target "unknown_L[1..25]"; target_start 302; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	1939	2022	2.32	-	0	target "unknown_K[1..28]"; target_start 254; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2062	2106	2.54	-	0	target "unknown_J[1..15]"; target_start 226; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2107	2148	5.93	-	0	target "unknown_I[1..14]"; target_start 212; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2152	2220	5.37	-	0	target "unknown_H[1..23]"; target_start 188; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2221	2292	4.07	-	0	target "unknown_G[1..24]"; target_start 164; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2299	2418	4.27	-	0	target "unknown_F[1..40]"; target_start 122; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2431	2457	4.51	-	0	target "unknown_E[1..9]"; target_start 109; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2506	2595	5.85	-	0	target "unknown_C[1..30]"; target_start 63; transcript_id "g1.t1"; gene_id "g1";
Contig78328	AUGUSTUS	protein_match	2611	2664	4.31	-	0	target "unknown_B[1..18]"; target_start 40; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacgtggtctgttttatctcgacttttgcattgccgcacaagatgtcttttgagacactatgcaacttttaataagt
# tggatcattatgaggcggtgttggagagatttcctgggggaatacaaatggcatttgcctatggttctggtgtatttaaacagatgggtcaaagtgat
# gctcaagtacaaagcaatatgatcgatttgatattcgttgttgatgattcatacagatggcatcagcaaaatatgaaacaaaatgggaaacactattc
# ttttcttaagtatttgggagcaaaacgagttgcgaaaattcaggaaaattcaggtgctgctgtgtatttcaacactaaggtgcagtgtgcaggacgcg
# aaattaagtatggagtgattagcacaaagcaagtaataatagacttactggattggaacagtttgtatgtaagtggaagaatgcacaaaccaatcaga
# attctcattccacccacaaaagtagaactgtgctcagcgattcaaatcaatctggaaaatgctgtacatgctgctctgcttttgcttcctgaaacttt
# caccgaggaagaattgtatcagcaaattgctgccctctcttatgatggcgattttagaatgaagtttggcgaagacaaaaacaaaatttctaacattg
# tcacacctaatatggcatacttcaggaatctgtatgaacagattttgttgaaagacgaacatgtgaaatggaacatgaaacaaggtattttggagcag
# tatccaaatcatgtgtctcagtttcatcatttgaaccttcttccaaaaacagttcaattaaatttactatcttcaatgcacagaagaccaggcaaata
# tccagacctggaggaaattatcagacagctagcttttgacagtaactgtgcagattatgtaagaaaaggcattgcagaaattgtaagaagttctagtg
# taggccaaagtataaaaagcatatttactgctggcttagtcaaatctgtgctttacagcagtaggaaagttcaaaagatgatggatagtaaaaagaaa
# gagaaaaatgtagtacaaccatag]
# protein sequence = [MTWSVLSRLLHCRTRCLLRHYATFNKLDHYEAVLERFPGGIQMAFAYGSGVFKQMGQSDAQVQSNMIDLIFVVDDSYR
# WHQQNMKQNGKHYSFLKYLGAKRVAKIQENSGAAVYFNTKVQCAGREIKYGVISTKQVIIDLLDWNSLYVSGRMHKPIRILIPPTKVELCSAIQINLE
# NAVHAALLLLPETFTEEELYQQIAALSYDGDFRMKFGEDKNKISNIVTPNMAYFRNLYEQILLKDEHVKWNMKQGILEQYPNHVSQFHHLNLLPKTVQ
# LNLLSSMHRRPGKYPDLEEIIRQLAFDSNCADYVRKGIAEIVRSSSVGQSIKSIFTAGLVKSVLYSSRKVQKMMDSKKKEKNVVQP]
# sequence of block unknown_M   327 [IFTAGLVKSVLYSSRKV] 344
# sequence of block unknown_L   302 [NCADYVRKGIAEIVRSSSVGQSIKS] 327
# sequence of block unknown_K   254 [QYPNHVSQFHHLNLLPKTVQLNLLSSMH] 282
# sequence of block unknown_J   226 [MAYFRNLYEQILLKD] 241
# sequence of block unknown_I   212 [GEDKNKISNIVTPN] 226
# sequence of block unknown_H   188 [TFTEEELYQQIAALSYDGDFRMK] 211
# sequence of block unknown_G   164 [VELCSAIQINLENAVHAALLLLPE] 188
# sequence of block unknown_F   122 [GREIKYGVISTKQVIIDLLDWNSLYVSGRMHKPIRILIPP] 162
# sequence of block unknown_E   109 [GAAVYFNTK] 118
# sequence of block unknown_C    63 [SNMIDLIFVVDDSYRWHQQNMKQNGKHYSF] 93
# sequence of block unknown_B    40 [IQMAFAYGSGVFKQMGQS] 58
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DYK.prfl --predictionStart=0  --predictionEnd=22688  --species=fly ./tmp/Contig7832820180911_busco_2432604931_.temp