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Augustus Extrinsic Configuration and Hints File Formats

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Gemy Kaithakottil edited this page Apr 22, 2024 · 1 revision

Augustus extrinsic configuration file:

# source of extrinsic information:
# M manual anchor (required)
# P protein database hit
# E EST/cDNA database hit
# C combined est/protein database hit
# D Dialign
# R retroposed genes
# T transMapped refSeqs
# W wiggle track coverage info from RNA-Seq

[SOURCES]
M RM F E P W

#
# individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set
# and the whole hint group is disregarded when one hint in it is unsatisfiable.
# 1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for
# hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby.
#
[SOURCE-PARAMETERS]
M individual_liability
F individual_liability
E individual_liability
P individual_liability
W individual_liability

#   feature        bonus         malus   gradelevelcolumns
#		r+/r-
#
# the gradelevel colums have the following format for each source
# sourcecharacter numscoreclasses boundary    ...  boundary    gradequot  ...  gradequot
#

[GENERAL]
      start      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
       stop      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
        tss      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
        tts      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
        ass      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
        dss      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
   exonpart      1  .992       M    1  1e+100  RM  1     1    F 1    1e4  E 1    1e2  P 1    1      W 1    1.005
       exon      1     1       M    1  1e+100  RM  1     1    F 1    1e8  E 1    1e4  P 1    1      W 1    1
 intronpart      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
     intron      1  0.01       M    1  1e+100  RM  1     1    F 1    1e8  E 1    1e4  P 1    1e4    W 1    1
    CDSpart      1     1 .985  M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1e2    W 1    1
        CDS      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1e4    W 1    1
    UTRpart      1     1 .985  M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
        UTR      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
     irpart      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1
nonexonpart      1     1       M    1  1e+100  RM  1     10   F 1    1    E 1    1    P 1    1      W 1    1
  genicpart      1     1       M    1  1e+100  RM  1     1    F 1    1    E 1    1    P 1    1      W 1    1

Augustus hints file formats

1. Repeats

1.1 Raw input file format (RepeatMasker)

scaffold1	RepeatMasker	similarity	35029	35172	33.4	-	.	Target "Motif:TpSIREcon" 5777 5917
scaffold1	RepeatMasker	similarity	36295	36433	25.7	-	.	Target "Motif:TpSIREcon" 36 177
scaffold1	RepeatMasker	similarity	42778	42839	18.0	+	.	Target "Motif:Copia-15_Cia-I" 509 571

Augustus hints GFF file format

scaffold1	repeats_SRMP1	nonexonpart	35029	35172	33.4	.	.	src=RM;grp=RM_int_1;pri=1;
scaffold1	repeats_SRMP1	nonexonpart	36295	36433	25.7	.	.	src=RM;grp=RM_int_2;pri=1;
scaffold1	repeats_SRMP1	nonexonpart	42778	42839	18.0	.	.	src=RM;grp=RM_int_3;pri=1;

1.2 Raw input file format (Any other pipeline)

Chr3	repeat	match	1066691	1066745	14	+	.	ID=Chr3:hit:481:1.3.0.5;Name=Chr3:hit:481:1.3.0.5;Note=species:%28TCATTTT%29n|genus:Simple_repeat;Target=species:%28TCATTTT%29n|genus:Simple_repeat%201%2055%20+
Chr3	repeat	match_part	1066691	1066745	14	+	.	ID=Chr3:hsp:481:1.3.0.5;Parent=Chr3:hit:481:1.3.0.5;Target=species:%2528TCATTTT%2529n|genus:Simple_repeat 1 55 +
Chr3	repeat	match	1073302	1073342	14	+	.	ID=Chr3:hit:482:1.3.0.5;Name=Chr3:hit:482:1.3.0.5;Note=species:A-rich|genus:Low_complexity;Target=species:A-rich|genus:Low_complexity%201%2040%20+
Chr3	repeat	match_part	1073302	1073342	14	+	.	ID=Chr3:hsp:482:1.3.0.5;Parent=Chr3:hit:482:1.3.0.5;Target=species:A-rich|genus:Low_complexity 1 40 +
Chr3	repeat	match	1074028	1074054	13	+	.	ID=Chr3:hit:483:1.3.0.5;Name=Chr3:hit:483:1.3.0.5;Note=species:%28TCT%29n|genus:Simple_repeat;Target=species:%28TCT%29n|genus:Simple_repeat%201%2028%20+
Chr3	repeat	match_part	1074028	1074054	13	+	.	ID=Chr3:hsp:483:1.3.0.5;Parent=Chr3:hit:483:1.3.0.5;Target=species:%2528TCT%2529n|genus:Simple_repeat 1 28 +

Augustus hints GFF file format

Chr3	repeats_SRMP1	nonexonpart	1066691	1066745	14	.	.	src=RM;grp=Chr3:hit:481:1.3.0.5;pri=1;
Chr3	repeats_SRMP1	nonexonpart	1073302	1073342	14	.	.	src=RM;grp=Chr3:hit:482:1.3.0.5;pri=1;
Chr3	repeats_SRMP1	nonexonpart	1074028	1074054	13	.	.	src=RM;grp=Chr3:hit:483:1.3.0.5;pri=1;

2. RNA-Seq expression (BAM)

Raw input file format

SRR5956436.88984066	133	Chr3	1066438	0	*	=	1066438	0	TAATGCTGCAAGACAAATGAAGGGTCAGAAGAAGAAAGTTTTTATGGTTGCCCTCAGAAACAACTCTACAAGGCTTCGTGTTGGTCTCCATTACACGAGAA	#####################################################################################################	YT:Z:UP
SRR5956436.88984066	89	Chr3	1066438	60	2S9M15742N90M	=	1066438	0	CGCACTTGAATCGTGGTGCAAAGAAGGTTGTTATCTCTGCCCCCAGCAAAGACGCTCCAATGTTTGTTGTTGGTGTCAACGAGCACGAATACAAGTCCGAC	######################B0B07<0<<'<'<BBBB<7'''<'7<<<<B7'0''0FFB77'BBB7<7B<BBBBFBFBF0BBBFBFFB<<FBB<FBBBB	AS:i:-7	ZS:i:-19	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:9G7C81	YT:Z:UP	XS:A:+	NH:i:1
SRR5956436.56142548	81	Chr3	1066722	60	1S9M16307N91M	=	1082976	0	TTATTTTGAGCGACAAGTTTGTGAAATTGGTGTCATGGTACGACAACGAATGGGGTTACAGTTCCCGTGTGGTCGACTTGATCGTCCACATGTCAAAGGCC	###############BBFFFFBBBB<BB7FFBBB<B<<0B<BBB07FIFFB<BBFFBF<BFBFFBFIIIFIFFB<0IIFFBFFIFFFBFBFFFFFFFFBBB	AS:i:-2	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:100	YT:Z:UP	XS:A:+	NH:i:1
SRR5956436.35469335	99	Chr3	1066765	60	101M	=	1066810	146	GGGTACTAACTTAGTTGAATAGTGGTCTCTTTACGTAATTTAGGAATGGTATTTTGTACTTTTAGCACTTATTTCCTCCTCTTTCTTTATATTCCTCTACT	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIIBFFFIIIFIIIIIIIIIIIIIIIIIIFFIIIIIFFFFFFFFFFFFFFFFFFF	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:101	YS:i:0	YT:Z:CP	XS:A:-	NH:i:1
SRR5956436.35469335	147	Chr3	1066810	60	101M	=	1066765	-146	ATGGTATTTTGTACTTTTAGCACTTATTTCCTCCTCTTTCTTTATATTCCTCTACTTTATAAAGATAAAGATATGGGTATGGATCCTTCTATTAAGAAAAT	BFFFFFFFFFFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIFBIIFFIIIIIIIIIIIIIIFIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:101	YS:i:0	YT:Z:CP	XS:A:-	NH:i:1
SRR5956436.87667436	99	Chr3	1067244	60	2S99M	=	1067505	364	GGCGTTTTATTTGTTGAATTCTGCTTGTTAGAAATAAACCAACAGTAGATTGAGTGTGAACGAAATAATCTTATATCCACATAGTCTATATAAAGCTATAT	BBBFFFFFFFFFFIIIIIIIIIIIIIIIIFIIIIIIIIIIFIIIIFIIIIIIIIIIIFFFFIIIIIIIIIIIFFFFFFFFFFFFFFFFFFBFFFFFFFFFB	AS:i:-2	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:99	YS:i:0	YT:Z:CP	XS:A:-	NH:i:1
SRR5956436.16706501	99	Chr3	1067425	60	101M	=	1067493	169	AAATGGGTGGGCGTGTAAAAGGTCATAAATCAAAGTAGTTCAGTTTTATATGACAGGGCCGCTCATCTAACGTATAAGTTCCAAACTATAATACCTTTGAC	BBBFFFFBFFFFFFFFIIIIIIFFIIIIIIIIIIIFIIFIIIIIIIIIIIIIIIIIIIIIFFFFBFFFFFFFBBFBFBFFFFFFFFFFFFBFFFFFFFFFB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:101	YS:i:0	YT:Z:CP	XS:A:-	NH:i:1
SRR5956436.77111845	99	Chr3	1067481	60	101M	=	1067571	191	GGCCGCTCATCTAACGTATAAGTTCCAAACTATAATACCTTTGACTGGTCAAACCTCATCTCTTAAGTCTATTTTGCATACACTTATCTTCGACTTTTTCA	BBBFFFFFFFFFFIIIFIIIIIIIIIIIIIIIIIIIIFFIIIIIIIIIFFIIIIIIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFF<	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:101	YS:i:0	YT:Z:CP	XS:A:-	NH:i:1
SRR5956436.16706501	147	Chr3	1067493	60	101M	=	1067425	-169	AACGTATAAGTTCCAAACTATAATACCTTTGACTGGTCAAACCTCATCTCTTAAGTCTATTTTGCATACACTTATCTTCGACTTTTTCATTTTATTTTTTC	FFFFFFFFFFFBFFFFFFFFFFFBBFFFFFFFFIIIFIFFBIIIIIIIIIFIIIIIIIIIIIIIIIIFFFIIIIIIIIIFFIIIIIIIFFFFFFFFFFBBB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:101	YS:i:0	YT:Z:CP	XS:A:-	NH:i:1
SRR5956436.87667436	147	Chr3	1067505	60	101M	=	1067244	-364	CCAAACTATAATACCTTTGACTGGTCAAACCTCATCTCTTAAGTCTATTTTGCATACACTTATCTTCGACTTTTTCATTTTATTTTTTCTTTTGATCTACA	BFFFFFFFFFBB<FFBFFFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIFBFFIIIIIIIIIFBIIIIIIIIIIIIIIFIIIIFFFFFFFFFFBBB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:101	YS:i:-2	YT:Z:CP	XS:A:-	NH:i:1

Augustus hints GFF file format

# Forward Strand
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077319	1077328	9.000	+	.	src=W;pri=3;mult=9;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077329	1077338	22.800	+	.	src=W;pri=3;mult=22;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077339	1077348	32.500	+	.	src=W;pri=3;mult=32;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077349	1077358	37.000	+	.	src=W;pri=3;mult=37;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077359	1077368	43.100	+	.	src=W;pri=3;mult=43;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077369	1077378	55.600	+	.	src=W;pri=3;mult=55;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077379	1077388	58.800	+	.	src=W;pri=3;mult=58;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077389	1077398	66.100	+	.	src=W;pri=3;mult=66;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077399	1077408	75.800	+	.	src=W;pri=3;mult=75;
Chr3	SRR5956436_hisat_Forward_SWP3	exonpart	1077409	1077418	79.100	+	.	src=W;pri=3;mult=79;

# Reverse Strand
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067818	1067827	7.000	-	.	src=W;pri=3;mult=7;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067828	1067837	7.000	-	.	src=W;pri=3;mult=7;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067838	1067847	7.900	-	.	src=W;pri=3;mult=7;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067848	1067857	11.600	-	.	src=W;pri=3;mult=11;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067858	1067867	16.000	-	.	src=W;pri=3;mult=16;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067868	1067877	16.000	-	.	src=W;pri=3;mult=16;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067878	1067887	16.000	-	.	src=W;pri=3;mult=16;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067888	1067897	16.000	-	.	src=W;pri=3;mult=16;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067898	1067907	16.700	-	.	src=W;pri=3;mult=16;
Chr3	SRR5956436_hisat_Reverse_SWP3	exonpart	1067908	1067917	14.800	-	.	src=W;pri=3;mult=14;

3. RNA-Seq Junctions (Portcullis)

Raw input file format

Chr3	Reat_Portcullis_Pass_Junctions	match	1068053	1068618	1.000	-	.	ID=All_portcullis_pass_69584;Name=All_portcullis_pass_69584;Note=1.000
Chr3	Reat_Portcullis_Pass_Junctions	match_part	1068053	1068180	1.000	-	.	ID=All_portcullis_pass_69584.exon1;Parent=All_portcullis_pass_69584
Chr3	Reat_Portcullis_Pass_Junctions	match_part	1068486	1068618	1.000	-	.	ID=All_portcullis_pass_69584.exon2;Parent=All_portcullis_pass_69584
Chr3	Reat_Portcullis_Pass_Junctions	match	1068542	1068925	1.000	-	.	ID=All_portcullis_pass_69585;Name=All_portcullis_pass_69585;Note=1.000
Chr3	Reat_Portcullis_Pass_Junctions	match_part	1068542	1068675	1.000	-	.	ID=All_portcullis_pass_69585.exon1;Parent=All_portcullis_pass_69585
Chr3	Reat_Portcullis_Pass_Junctions	match_part	1068786	1068925	1.000	-	.	ID=All_portcullis_pass_69585.exon2;Parent=All_portcullis_pass_69585
Chr3	Reat_Portcullis_Pass_Junctions	match	1068871	1069201	0.928	-	.	ID=All_portcullis_pass_69586;Name=All_portcullis_pass_69586;Note=0.928
Chr3	Reat_Portcullis_Pass_Junctions	match_part	1068871	1069003	0.928	-	.	ID=All_portcullis_pass_69586.exon1;Parent=All_portcullis_pass_69586
Chr3	Reat_Portcullis_Pass_Junctions	match_part	1069108	1069201	0.928	-	.	ID=All_portcullis_pass_69586.exon2;Parent=All_portcullis_pass_69586

Augustus hints GFF file format

# Gold set
Chr3	Portcullis_pass_gold_SEP6	intron	1068181	1068485	1.000	-	.	src=E;grp=All_portcullis_pass_69584;pri=6;
Chr3	Portcullis_pass_gold_SEP6	intron	1068676	1068785	1.000	-	.	src=E;grp=All_portcullis_pass_69585;pri=6;

# Silver set
Chr3	Portcullis_pass_silver_SEP4	intron	1069004	1069107	0.928	-	.	src=E;grp=All_portcullis_pass_69586;pri=4;

4. Transcript Assemblies (Mikado output)

Raw input file format

Chr3	Mikado_permissive_loci	gene	1083763	1086277	16	+	.	ID=mikado.Chr3G314;Name=mikado.Chr3G314;multiexonic=True;superlocus=Mikado_permissive_superlocus:Chr3+:1081002-1086277
Chr3	Mikado_permissive_loci	mRNA	1083763	1086277	16.0	+	.	ID=mikado.Chr3G314.1;Parent=mikado.Chr3G314;Name=mikado.Chr3G314.1;rpkm=0.1327;alias=SRR7947123.hisat.scallop_SRR7947123_SCLP.387.179.0;canonical_junctions=1,2;canonical_number=2;canonical_proportion=1.0;cds_padded=False;cov=1.8603;exon=3;padded=True;primary=True
Chr3	Mikado_permissive_loci	exon	1083763	1084000	.	+	.	ID=mikado.Chr3G314.1.exon1;Parent=mikado.Chr3G314.1
Chr3	Mikado_permissive_loci	five_prime_UTR	1083763	1084000	.	+	.	ID=mikado.Chr3G314.1.five_prime_UTR1;Parent=mikado.Chr3G314.1
Chr3	Mikado_permissive_loci	exon	1084105	1084935	.	+	.	ID=mikado.Chr3G314.1.exon2;Parent=mikado.Chr3G314.1
Chr3	Mikado_permissive_loci	five_prime_UTR	1084105	1084135	.	+	.	ID=mikado.Chr3G314.1.five_prime_UTR2;Parent=mikado.Chr3G314.1
Chr3	Mikado_permissive_loci	CDS	1084136	1084935	.	+	0	ID=mikado.Chr3G314.1.CDS1;Parent=mikado.Chr3G314.1
Chr3	Mikado_permissive_loci	CDS	1085057	1085096	.	+	1	ID=mikado.Chr3G314.1.CDS2;Parent=mikado.Chr3G314.1
Chr3	Mikado_permissive_loci	exon	1085057	1086277	.	+	.	ID=mikado.Chr3G314.1.exon3;Parent=mikado.Chr3G314.1
Chr3	Mikado_permissive_loci	three_prime_UTR	1085097	1086277	.	+	.	ID=mikado.Chr3G314.1.three_prime_UTR1;Parent=mikado.Chr3G314.1

Augustus hints GFF file format

# In Augustus Run1 and Run2
Chr3	Mikado_short_and_long_gold_SMP10	exonpart	1083763	1084000	.	+	.	src=M;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SMP10	exon	1084105	1084935	.	+	.	src=M;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SMP10	exonpart	1085057	1086277	.	+	.	src=M;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SMP10	intron	1084001	1084104	.	+	.	src=M;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SMP10	intron	1084936	1085056	.	+	.	src=M;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;

# In Augustus Run3
Chr3	Mikado_short_and_long_gold_SEP10	exonpart	1083763	1084000	.	+	.	src=E;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SEP10	exon	1084105	1084935	.	+	.	src=E;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SEP10	exonpart	1085057	1086277	.	+	.	src=E;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SEP10	intron	1084001	1084104	.	+	.	src=E;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;
Chr3	Mikado_short_and_long_gold_SEP10	intron	1084936	1085056	.	+	.	src=E;grp=Mikado_short_and_long_gold.Chr3G314.1;pri=10;

5. Protein Alignments

Raw input file format

Chr3	BrapaFPsc_run3_spaln	match	1178718	1180537	2213.7	+	.	ID=Brara.E03498.1.v1.3.m2;Prev_Parent=Brara.E03498.1.v1.3.g2;Name=Brara.E03498.1.v1.3.m2;Note=Brara.E03498.1.v1.3|cov:100.00|id:85.50|cds_id:97.1|cds_exon_f1:57.14|cds_junction_f1:80.00|cds_ccode:j|min_ef1:0.00|max_ef1:100.00|avg_ef1:34.00|min_jf1:0.00|max_jf1:100.00|avg_jf1:28.02;cds_id=97.1;cds_exon_f1=57.14;cds_junction_f1=80.00;cds_ccode=j;min_ef1=0.00;max_ef1=100.00;avg_ef1=34.00;min_jf1=0.00;max_jf1=100.00;avg_jf1=28.02
Chr3	BrapaFPsc_run3_spaln	match_part	1178718	1178819	68.75	+	0	ID=Brara.E03498.1.v1.3.m2.exon1;Parent=Brara.E03498.1.v1.3.m2
Chr3	BrapaFPsc_run3_spaln	match_part	1179106	1180254	88.51	+	0	ID=Brara.E03498.1.v1.3.m2.exon2;Parent=Brara.E03498.1.v1.3.m2
Chr3	BrapaFPsc_run3_spaln	match_part	1180340	1180537	75.0	+	0	ID=Brara.E03498.1.v1.3.m2.exon3;Parent=Brara.E03498.1.v1.3.m2

Augustus hints GFF file format

# In Augustus run1 and run2
Chr3	BrapaFPsc_spaln_protein_SPP4	CDSpart	1178718	1178819	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=4;
Chr3	BrapaFPsc_spaln_protein_SPP4	CDS	1179106	1180254	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=4;
Chr3	BrapaFPsc_spaln_protein_SPP4	CDSpart	1180340	1180537	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=4;
Chr3	BrapaFPsc_spaln_protein_SPP4	intron	1178820	1179105	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=4;
Chr3	BrapaFPsc_spaln_protein_SPP4	intron	1180255	1180339	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=4;

# In Augustus run3
Chr3	BrapaFPsc_spaln_protein_SPP9	CDSpart	1178718	1178819	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=9;
Chr3	BrapaFPsc_spaln_protein_SPP9	CDS	1179106	1180254	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=9;
Chr3	BrapaFPsc_spaln_protein_SPP9	CDSpart	1180340	1180537	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=9;
Chr3	BrapaFPsc_spaln_protein_SPP9	intron	1178820	1179105	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=9;
Chr3	BrapaFPsc_spaln_protein_SPP9	intron	1180255	1180339	68.75	+	0	src=P;grp=Brara.E03498.1.v1.3.m2;pri=9;
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