##gff-version 3
##sequence-region C12HBa0079F24.1 1 21211
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	match	9551	13928	0.993	+	0	ID=SGN-E300172_alignment_1;Target=SGN-E300172 1 584 +
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	match_part	9551	9709	0.987	+	0	ID=GTH_SGN_E_tom_potato_match_part_1;Target=SGN-E300172 1 157 +;Parent=SGN-E300172_alignment_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	match_part	9787	9943	0.994	+	0	ID=GTH_SGN_E_tom_potato_match_part_2;Target=SGN-E300172 158 313 +;Parent=SGN-E300172_alignment_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	match_part	13658	13928	0.996	+	0	ID=GTH_SGN_E_tom_potato_match_part_3;Target=SGN-E300172 314 584 +;Parent=SGN-E300172_alignment_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	gene	9551	13928	.	+	0	ID=GTH_SGN_E_tom_potato_gene_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	mRNA	9551	13928	.	+	0	ID=GTH_SGN_E_tom_potato_gene_1_AGS_1;Parent=GTH_SGN_E_tom_potato_gene_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	exon	9551	9709	0.987	+	0	ID=GTH_SGN_E_tom_potato_exon_1;Parent=GTH_SGN_E_tom_potato_gene_1_AGS_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	exon	9787	9943	0.994	+	0	ID=GTH_SGN_E_tom_potato_exon_2;Parent=GTH_SGN_E_tom_potato_gene_1_AGS_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato_potato	exon	13658	13928	0.996	+	0	ID=GTH_SGN_E_tom_potato_exon_3;Parent=GTH_SGN_E_tom_potato_gene_1_AGS_1
C12HBa0079F24.1	RepeatMasker	nucleotide_motif	569	613	251	+	0	ID=Gypsy00178_alignment_1;Target=Gypsy00178 6528 6572 +
C12HBa0079F24.1	RepeatMasker	nucleotide_motif	614	630	251	-	0	ID=Copia00181_alignment_1;Target=Copia00181 1784 1848 -
C12HBa0079F24.1	RepeatMasker	nucleotide_motif	4700	4783	290	+	0	ID=Gypsy00071_alignment_1;Target=Gypsy00071 4059 4139 +
C12HBa0079F24.1	RepeatMasker	nucleotide_motif	7347	7410	275	-	0	ID=Unknown00034_alignment_1;Target=Unknown00034 5145 5207 -
C12HBa0079F24.1	RepeatMasker	nucleotide_motif	12001	12198	491	+	0	ID=Unknown00043_alignment_1;Target=Unknown00043 5535 5732 +
C12HBa0079F24.1	RepeatMasker	nucleotide_motif	20048	20374	583	-	0	ID=Unknown00043_alignment_2;Target=Unknown00043 519 8813 -
C12HBa0079F24.1	RepeatMasker	nucleotide_motif	20384	20495	289	-	0	ID=Unknown00043_alignment_3;Target=Unknown00043 8286 8396 -
C12HBa0079F24.1	BLAST_tomato_bacs	match	968	3854	5291	+	0	ID=C12HBa0004A15.3_rev_alignment_1;blast_gaps=13;Target=clone-C12HBa0004A15.3 5685 8558 -;blast_match_length=2886;blast_percent_identity=99.55;blast_mismatches=0;blast_evalue=0.0
C12HBa0079F24.1	Contigs	contig	1	3854	.	.	0	ID=contig1_1;length=3854
C12HBa0079F24.1	Contigs	contig	3955	21211	.	.	0	ID=contig2_1;length=17257
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_end	30	175	266	+	0	ID=C12HBa0079F24.1-LE_HBa0079F24_SP6_19870_1;blast_gaps=1;Target=LE_HBa0079F24_SP6_19870 1 145 +;is_problematic=0;blast_percent_identity=98.63;blast_mismatches=1;blast_evalue=4e-68
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_end	607	820	367	+	0	ID=C12HBa0079F24.1-LE_HBa0079F24_SP6_19870_2;blast_gaps=1;Target=LE_HBa0079F24_SP6_19870 571 783 +;is_problematic=0;blast_percent_identity=99.53;blast_mismatches=0;blast_evalue=2e-98
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_start	4110	4253	270	-	0	ID=C12HBa0079F24.1-SL_MboI0107F10_T7_300919_1;blast_gaps=0;Target=SL_MboI0107F10_T7_300919 44 187 +;is_problematic=0;blast_percent_identity=98.61;blast_mismatches=2;blast_evalue=3e-69
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_start	4110	4253	285	-	0	ID=C12HBa0079F24.1-SL_MboI0132M15_T7_190371_1;blast_gaps=0;Target=SL_MboI0132M15_T7_190371 46 189 +;is_problematic=0;blast_percent_identity=100.00;blast_mismatches=0;blast_evalue=4e-74
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_start	8878	9337	854	-	0	ID=C12HBa0079F24.1-LE_HBa0220M08_T7_385160_1;blast_gaps=1;Target=LE_HBa0220M08_T7_385160 286 744 +;is_problematic=0;blast_percent_identity=99.78;blast_mismatches=0;blast_evalue=0.0
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_start	8895	9337	821	-	0	ID=C12HBa0079F24.1-LE_HBa0108M03_T7_96197_1;blast_gaps=1;Target=LE_HBa0108M03_T7_96197 287 728 +;is_problematic=0;blast_percent_identity=99.77;blast_mismatches=0;blast_evalue=0.0
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_end	8896	9337	819	-	0	ID=C12HBa0079F24.1-LE_HBa0004A15_SP6_796_1;blast_gaps=1;Target=LE_HBa0004A15_SP6_796 271 711 +;is_problematic=0;blast_percent_identity=99.77;blast_mismatches=0;blast_evalue=0.0
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_start	9358	9596	458	-	0	ID=C12HBa0079F24.1-LE_HBa0108M03_T7_96197_2;blast_gaps=1;Target=LE_HBa0108M03_T7_96197 29 266 +;is_problematic=0;blast_percent_identity=99.58;blast_mismatches=0;blast_evalue=5e-126
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_start	9358	9596	458	-	0	ID=C12HBa0079F24.1-LE_HBa0220M08_T7_385160_2;blast_gaps=1;Target=LE_HBa0220M08_T7_385160 28 265 +;is_problematic=0;blast_percent_identity=99.58;blast_mismatches=0;blast_evalue=5e-126
C12HBa0079F24.1	BLAST_tomato_bac_ends	clone_end	12002	12434	811	-	0	ID=C12HBa0079F24.1-SL_EcoRI0091J18_SP6_356038_1;blast_gaps=0;Target=SL_EcoRI0091J18_SP6_356038 1 433 +;is_problematic=0;blast_percent_identity=100.00;blast_mismatches=0;blast_evalue=0.0
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	match	9551	13928	0.993	+	0	ID=SGN-E300172_alignment_2;Target=SGN-E300172 1 584 +
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	match_part	9551	9709	0.987	+	0	ID=GTH_SGN_E_tom_match_part_1;Target=SGN-E300172 1 157 +;Parent=SGN-E300172_alignment_2
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	match_part	9787	9943	0.994	+	0	ID=GTH_SGN_E_tom_match_part_2;Target=SGN-E300172 158 313 +;Parent=SGN-E300172_alignment_2
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	match_part	13658	13928	0.996	+	0	ID=GTH_SGN_E_tom_match_part_3;Target=SGN-E300172 314 584 +;Parent=SGN-E300172_alignment_2
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	gene	9551	13928	.	+	0	ID=GTH_SGN_E_tom_gene_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	mRNA	9551	13928	.	+	0	ID=GTH_SGN_E_tom_gene_1_AGS_1;Parent=GTH_SGN_E_tom_gene_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	exon	9551	9709	0.987	+	0	ID=GTH_SGN_E_tom_exon_1;Parent=GTH_SGN_E_tom_gene_1_AGS_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	exon	9787	9943	0.994	+	0	ID=GTH_SGN_E_tom_exon_2;Parent=GTH_SGN_E_tom_gene_1_AGS_1
C12HBa0079F24.1	GenomeThreader_SGN_E_tomato	exon	13658	13928	0.996	+	0	ID=GTH_SGN_E_tom_exon_3;Parent=GTH_SGN_E_tom_gene_1_AGS_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	gene	8667	8709	1	+	.	ID=g1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	transcript	8667	8709	.	+	.	ID=g1.t1_1;Parent=g1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	8667	8709	.	+	1	ID=g1.t1.cds_1;Parent=g1.t1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	stop_codon	8707	8709	.	+	0	Parent=g1.t1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	gene	9929	16282	1	+	.	ID=g2_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	transcript	9929	16282	.	+	.	ID=g2.t1_1;Parent=g2_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	start_codon	9929	9931	.	+	0	Parent=g2.t1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	9929	9943	.	+	0	ID=g2.t1.cds_1;Parent=g2.t1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	13658	13681	.	+	0	ID=g2.t1.cds_2;Parent=g2.t1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	CDS	16097	16282	.	+	0	ID=g2.t1.cds_3;Parent=g2.t1_1
C12HBa0079F24.1	AUGUSTUS_tom_cdna	stop_codon	16280	16282	.	+	0	Parent=g2.t1_1
C12HBa0079F24.1	AUGUSTUS_tom_ugs	gene	8667	8709	1	+	.	ID=g1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	transcript	8667	8709	.	+	.	ID=g1.t1_2;Parent=g1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	CDS	8667	8709	.	+	1	ID=g1.t1.cds_2;Parent=g1.t1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	stop_codon	8707	8709	.	+	0	Parent=g1.t1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	gene	9929	16282	1	+	.	ID=g2_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	transcript	9929	16282	.	+	.	ID=g2.t1_2;Parent=g2_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	start_codon	9929	9931	.	+	0	Parent=g2.t1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	CDS	9929	9943	.	+	0	ID=g2.t1.cds_4;Parent=g2.t1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	CDS	13658	13681	.	+	0	ID=g2.t1.cds_5;Parent=g2.t1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	CDS	16097	16282	.	+	0	ID=g2.t1.cds_6;Parent=g2.t1_2
C12HBa0079F24.1	AUGUSTUS_tom_ugs	stop_codon	16280	16282	.	+	0	Parent=g2.t1_2
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	match	9566	14259	0.989	+	0	ID=SGN-U568431_alignment_1;Target=SGN-U568431 1 896 +
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	match_part	9566	9709	0.986	+	0	ID=GTH_SGN_U_tom_match_part_1;Target=SGN-U568431 1 142 +;Parent=SGN-U568431_alignment_1
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	match_part	9787	9943	0.994	+	0	ID=GTH_SGN_U_tom_match_part_2;Target=SGN-U568431 143 298 +;Parent=SGN-U568431_alignment_1
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	match_part	13658	14259	0.988	+	0	ID=GTH_SGN_U_tom_match_part_3;Target=SGN-U568431 299 896 +;Parent=SGN-U568431_alignment_1
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	gene	9566	14259	.	+	0	ID=GTH_SGN_U_tom_gene_1
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	mRNA	9566	14259	.	+	0	ID=GTH_SGN_U_tom_gene_1_AGS_1;Parent=GTH_SGN_U_tom_gene_1
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	exon	9566	9709	0.986	+	0	ID=GTH_SGN_U_tom_exon_1;Parent=GTH_SGN_U_tom_gene_1_AGS_1
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	exon	9787	9943	0.994	+	0	ID=GTH_SGN_U_tom_exon_2;Parent=GTH_SGN_U_tom_gene_1_AGS_1
C12HBa0079F24.1	GenomeThreader_SGN_U_tomato	exon	13658	14259	0.988	+	0	ID=GTH_SGN_U_tom_exon_3;Parent=GTH_SGN_U_tom_gene_1_AGS_1
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	gene	8667	8709	1	+	.	ID=g1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	transcript	8667	8709	.	+	.	ID=g1.t1_3;Parent=g1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	CDS	8667	8709	.	+	1	ID=g1.t1.cds_3;Parent=g1.t1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	stop_codon	8707	8709	.	+	0	Parent=g1.t1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	gene	9929	16282	1	+	.	ID=g2_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	transcript	9929	16282	.	+	.	ID=g2.t1_3;Parent=g2_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	start_codon	9929	9931	.	+	0	Parent=g2.t1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	CDS	9929	9943	.	+	0	ID=g2.t1.cds_7;Parent=g2.t1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	CDS	13658	13681	.	+	0	ID=g2.t1.cds_8;Parent=g2.t1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	CDS	16097	16282	.	+	0	ID=g2.t1.cds_9;Parent=g2.t1_3
C12HBa0079F24.1	AUGUSTUS_tom_pot_cdna	stop_codon	16280	16282	.	+	0	Parent=g2.t1_3
C12HBa0079F24.1	BLAST_ath_pep	match	1241	1333	33.9	-	0	ID=AT1G55320.1_fwd_alignment_1;blast_gaps=0;Target=AT1G55320.1 687 717 +;blast_match_length=-92;blast_percent_identity=48.39;blast_mismatches=16;blast_evalue=4e-28
C12HBa0079F24.1	BLAST_ath_pep	match	1398	1598	73.6	-	0	ID=AT1G55320.1_fwd_alignment_2;blast_gaps=0;Target=AT1G55320.1 624 690 +;blast_match_length=-200;blast_percent_identity=53.73;blast_mismatches=31;blast_evalue=4e-28
C12HBa0079F24.1	BLAST_ath_pep	match	1712	1810	60.5	-	0	ID=AT1G55320.1_fwd_alignment_3;blast_gaps=0;Target=AT1G55320.1 587 619 +;blast_match_length=-98;blast_percent_identity=81.82;blast_mismatches=6;blast_evalue=4e-28
C12HBa0079F24.1	BLAST_ath_pep	match	1241	1333	33.9	-	0	ID=AT1G55320.2_fwd_alignment_1;blast_gaps=0;Target=AT1G55320.2 471 501 +;blast_match_length=-92;blast_percent_identity=48.39;blast_mismatches=16;blast_evalue=5e-28
C12HBa0079F24.1	BLAST_ath_pep	match	1398	1598	73.6	-	0	ID=AT1G55320.2_fwd_alignment_2;blast_gaps=0;Target=AT1G55320.2 408 474 +;blast_match_length=-200;blast_percent_identity=53.73;blast_mismatches=31;blast_evalue=5e-28
C12HBa0079F24.1	BLAST_ath_pep	match	1712	1810	60.5	-	0	ID=AT1G55320.2_fwd_alignment_3;blast_gaps=0;Target=AT1G55320.2 371 403 +;blast_match_length=-98;blast_percent_identity=81.82;blast_mismatches=6;blast_evalue=5e-28
C12HBa0079F24.1	BLAST_ath_pep	match	16551	16829	145	+	0	ID=AT1G55350.1_fwd_alignment_1;blast_gaps=1;Target=AT1G55350.1 30 123 +;blast_match_length=278;blast_percent_identity=68.09;blast_mismatches=29;blast_evalue=1e-33
C12HBa0079F24.1	BLAST_ath_pep	match	16551	16829	145	+	0	ID=AT1G55350.2_fwd_alignment_1;blast_gaps=1;Target=AT1G55350.2 30 123 +;blast_match_length=278;blast_percent_identity=68.09;blast_mismatches=29;blast_evalue=1e-33
C12HBa0079F24.1	BLAST_ath_pep	match	16551	16829	145	+	0	ID=AT1G55350.3_fwd_alignment_1;blast_gaps=1;Target=AT1G55350.3 30 123 +;blast_match_length=278;blast_percent_identity=68.09;blast_mismatches=29;blast_evalue=1e-33
C12HBa0079F24.1	BLAST_ath_pep	match	16551	16829	145	+	0	ID=AT1G55350.4_fwd_alignment_1;blast_gaps=1;Target=AT1G55350.4 30 123 +;blast_match_length=278;blast_percent_identity=68.09;blast_mismatches=29;blast_evalue=1e-33
C12HBa0079F24.1	BLAST_ath_pep	match	1235	1333	28.5	-	0	ID=AT5G23050.1_fwd_alignment_1;blast_gaps=0;Target=AT5G23050.1 683 715 +;blast_match_length=-98;blast_percent_identity=36.36;blast_mismatches=21;blast_evalue=7e-22
C12HBa0079F24.1	BLAST_ath_pep	match	1398	1598	64.7	-	0	ID=AT5G23050.1_fwd_alignment_2;blast_gaps=2;Target=AT5G23050.1 619 686 +;blast_match_length=-200;blast_percent_identity=50.72;blast_mismatches=32;blast_evalue=7e-22
C12HBa0079F24.1	BLAST_ath_pep	match	1709	1813	53.5	-	0	ID=AT5G23050.1_fwd_alignment_3;blast_gaps=0;Target=AT5G23050.1 581 615 +;blast_match_length=-104;blast_percent_identity=71.43;blast_mismatches=10;blast_evalue=7e-22