##gff-version 3
#SOFTWARE INFO: GeMoMa 1.8; SIMPLE PARAMETERS: reads: 1; splice: true; coverage: UNSTRANDED; gap opening: 11; gap extension: 1; maximum intron length: 15000; static intron length: true; intron-loss-gain-penalty: 25; e-value: 100.0; contig threshold: 0.4; region threshold: 0.9; hit threshold: 0.9; predictions: 10; avoid stop: true; approx: true; protein alignment: true; prefix: ; tag: mRNA; verbose: false; timeout: 3600; sort: false; replace unknown: false; Score: ReAlign
PGA_scaffold_9	GeMoMa	mRNA	49750	54893	.	+	.	ID=AH000001.mRNA1_R0;ref-gene=AH000001;aa=365;raa=304;score=813;prediction=0;bestScore=813;ce=10;rce=10;tae=1;tde=1;tie=1;minSplitReads=10;tpc=0.9808;minCov=0;avgCov=12.5151;pAA=0.6396;iAA=0.5257;lpm=23;maxScore=1538.0;maxGap=38;nps=0;start=M;stop=*
PGA_scaffold_9	GeMoMa	CDS	49750	49824	.	+	0	Parent=AH000001.mRNA1_R0;de=true;pc=1;minCov=9
PGA_scaffold_9	GeMoMa	CDS	49904	49981	.	+	0	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=10
PGA_scaffold_9	GeMoMa	CDS	51902	51997	.	+	0	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=10
PGA_scaffold_9	GeMoMa	CDS	52089	52164	.	+	0	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=12
PGA_scaffold_9	GeMoMa	CDS	52256	52357	.	+	2	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=13
PGA_scaffold_9	GeMoMa	CDS	52458	52540	.	+	2	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=13
PGA_scaffold_9	GeMoMa	CDS	52644	52751	.	+	0	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=13
PGA_scaffold_9	GeMoMa	CDS	52881	53018	.	+	0	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=14
PGA_scaffold_9	GeMoMa	CDS	54107	54212	.	+	0	Parent=AH000001.mRNA1_R0;ae=true;de=true;pc=1;minCov=14
PGA_scaffold_9	GeMoMa	CDS	54661	54893	.	+	2	Parent=AH000001.mRNA1_R0;ae=true;pc=0.9099;minCov=0
PGA_scaffold_9	GeMoMa	mRNA	21389959	21393334	.	+	.	ID=AH000001.mRNA1_R1;ref-gene=AH000001;aa=331;raa=304;score=710;prediction=1;bestScore=813;ce=9;rce=10;tae=1;tde=1;tie=0.875;minSplitReads=0;tpc=0.9789;minCov=0;avgCov=20.9275;pAA=0.6328;iAA=0.5113;lpm=16;maxScore=1538.0;maxGap=38;nps=0;start=M;stop=*
PGA_scaffold_9	GeMoMa	CDS	21389959	21390033	.	+	0	Parent=AH000001.mRNA1_R1;de=true;pc=1;minCov=18
PGA_scaffold_9	GeMoMa	CDS	21390118	21390195	.	+	0	Parent=AH000001.mRNA1_R1;ae=true;de=true;pc=1;minCov=20
PGA_scaffold_9	GeMoMa	CDS	21390345	21390440	.	+	0	Parent=AH000001.mRNA1_R1;ae=true;de=true;pc=1;minCov=21
PGA_scaffold_9	GeMoMa	CDS	21390524	21390599	.	+	0	Parent=AH000001.mRNA1_R1;ae=true;de=true;pc=1;minCov=21
PGA_scaffold_9	GeMoMa	CDS	21390914	21390996	.	+	2	Parent=AH000001.mRNA1_R1;ae=true;de=true;pc=1;minCov=21
PGA_scaffold_9	GeMoMa	CDS	21391100	21391207	.	+	0	Parent=AH000001.mRNA1_R1;ae=true;de=true;pc=1;minCov=21
PGA_scaffold_9	GeMoMa	CDS	21391338	21391475	.	+	0	Parent=AH000001.mRNA1_R1;ae=true;de=true;pc=1;minCov=22
PGA_scaffold_9	GeMoMa	CDS	21392536	21392641	.	+	0	Parent=AH000001.mRNA1_R1;ae=true;de=true;pc=1;minCov=22
PGA_scaffold_9	GeMoMa	CDS	21393102	21393334	.	+	2	Parent=AH000001.mRNA1_R1;ae=true;pc=0.9099;minCov=0
PGA_scaffold_16	GeMoMa	mRNA	1682441	1683717	.	+	.	ID=AH000035.mRNA1_R0;ref-gene=AH000035;aa=197;raa=238;score=230;prediction=0;bestScore=230;ce=2;rce=2;tae=0;tde=0;tie=0;minSplitReads=0;tpc=0;minCov=0;avgCov=0;pAA=0.5317;iAA=0.3532;lpm=13;maxScore=1157.0;maxGap=34;nps=0;start=M;stop=*
PGA_scaffold_16	GeMoMa	CDS	1682441	1682455	.	+	0	Parent=AH000035.mRNA1_R0;de=false;pc=0;minCov=0
PGA_scaffold_16	GeMoMa	CDS	1683142	1683717	.	+	0	Parent=AH000035.mRNA1_R0;ae=false;pc=0;minCov=0
PGA_scaffold_9	GeMoMa	mRNA	19429791	19430903	.	-	.	ID=AH000035.mRNA1_R1;ref-gene=AH000035;aa=206;raa=238;score=226;prediction=1;bestScore=230;ce=2;rce=2;tae=0;tde=0;tie=0;minSplitReads=0;tpc=0;minCov=0;avgCov=0;pAA=0.5556;iAA=0.3532;lpm=11;maxScore=1157.0;maxGap=18;nps=0;start=M;stop=*
PGA_scaffold_9	GeMoMa	CDS	19430889	19430903	.	-	0	Parent=AH000035.mRNA1_R1;de=false;pc=0;minCov=0
PGA_scaffold_9	GeMoMa	CDS	19429791	19430393	.	-	0	Parent=AH000035.mRNA1_R1;ae=false;pc=0;minCov=0
PGA_scaffold_11	GeMoMa	mRNA	16411086	16411820	.	+	.	ID=AH000035.mRNA1_R2;ref-gene=AH000035;aa=245;raa=238;score=84;prediction=2;bestScore=230;ce=1;rce=2;tae=NA;tde=NA;tie=NA;minSplitReads=NA;tpc=0;minCov=0;avgCov=0;pAA=0.6545;iAA=0.1951;lpm=12;maxScore=1157.0;maxGap=4;nps=0;start=A;stop=*
PGA_scaffold_11	GeMoMa	CDS	16411086	16411820	.	+	0	Parent=AH000035.mRNA1_R2;pc=0;minCov=0
PGA_scaffold_5	GeMoMa	mRNA	33470018	33470686	.	-	.	ID=AH000035.mRNA1_R3;ref-gene=AH000035;aa=223;raa=238;score=67;prediction=3;bestScore=230;ce=1;rce=2;tae=NA;tde=NA;tie=NA;minSplitReads=NA;tpc=0;minCov=0;avgCov=0;pAA=0.6387;iAA=0.1639;lpm=10;maxScore=1157.0;maxGap=14;nps=0;start=K;stop=*
PGA_scaffold_5	GeMoMa	CDS	33470018	33470686	.	-	0	Parent=AH000035.mRNA1_R3;pc=0;minCov=0
PGA_scaffold_16	GeMoMa	mRNA	11180963	11181655	.	-	.	ID=AH000035.mRNA1_R4;ref-gene=AH000035;aa=231;raa=238;score=22;prediction=4;bestScore=230;ce=1;rce=2;tae=NA;tde=NA;tie=NA;minSplitReads=NA;tpc=0;minCov=0;avgCov=0;pAA=0.5967;iAA=0.1893;lpm=9;maxScore=1157.0;maxGap=7;nps=0;start=E;stop=*
PGA_scaffold_16	GeMoMa	CDS	11180963	11181655	.	-	0	Parent=AH000035.mRNA1_R4;pc=0;minCov=0
PGA_scaffold_10	GeMoMa	mRNA	9562390	9562827	.	+	.	ID=AH000035.mRNA1_R5;ref-gene=AH000035;aa=146;raa=238;score=7;prediction=5;bestScore=230;ce=1;rce=2;tae=NA;tde=NA;tie=NA;minSplitReads=NA;tpc=0.9589;minCov=0;avgCov=27.4817;pAA=0.3697;iAA=0.1639;lpm=7;maxScore=1157.0;maxGap=43;nps=0;start=E;stop=*
PGA_scaffold_10	GeMoMa	CDS	9562390	9562827	.	+	0	Parent=AH000035.mRNA1_R5;pc=0.9589;minCov=0
PGA_scaffold_5	GeMoMa	mRNA	7997823	7998482	.	+	.	ID=AH000035.mRNA1_R6;ref-gene=AH000035;aa=220;raa=238;score=0;prediction=6;bestScore=230;ce=1;rce=2;tae=NA;tde=NA;tie=NA;minSplitReads=NA;tpc=0;minCov=0;avgCov=0;pAA=0.5934;iAA=0.1494;lpm=10;maxScore=1157.0;maxGap=12;nps=0;start=E;stop=*
PGA_scaffold_5	GeMoMa	CDS	7997823	7998482	.	+	0	Parent=AH000035.mRNA1_R6;pc=0;minCov=0
PGA_scaffold_21	GeMoMa	mRNA	9776570	9777276	.	-	.	ID=AH000035.mRNA1_R7;ref-gene=AH000035;aa=131;raa=238;score=-8;prediction=7;bestScore=230;ce=2;rce=2;tae=0;tde=0;tie=0;minSplitReads=0;tpc=0;minCov=0;avgCov=0;pAA=0.3682;iAA=0.1799;lpm=8;maxScore=1157.0;maxGap=39;nps=0;start=M;stop=*
PGA_scaffold_21	GeMoMa	CDS	9777242	9777276	.	-	0	Parent=AH000035.mRNA1_R7;de=false;pc=0;minCov=0
PGA_scaffold_21	GeMoMa	CDS	9776570	9776927	.	-	1	Parent=AH000035.mRNA1_R7;ae=false;pc=0;minCov=0
PGA_scaffold_1	GeMoMa	mRNA	22077323	22077670	.	-	.	ID=AH000035.mRNA1_R8;ref-gene=AH000035;aa=116;raa=238;score=-22;prediction=8;bestScore=230;ce=1;rce=2;tae=NA;tde=NA;tie=NA;minSplitReads=NA;tpc=0;minCov=0;avgCov=0;pAA=0.3109;iAA=0.1597;lpm=10;maxScore=1157.0;maxGap=44;nps=0;start=K;stop=*
PGA_scaffold_1	GeMoMa	CDS	22077323	22077670	.	-	0	Parent=AH000035.mRNA1_R8;pc=0;minCov=0
PGA_scaffold_5	GeMoMa	mRNA	25881799	25882685	.	+	.	ID=AH000035.mRNA1_R9;ref-gene=AH000035;aa=141;raa=238;score=-33;prediction=9;bestScore=230;ce=2;rce=2;tae=1;tde=0;tie=0;minSplitReads=0;tpc=0.7163;minCov=0;avgCov=0.7163;pAA=0.3644;iAA=0.1822;lpm=14;maxScore=1157.0;maxGap=70;nps=0;start=M;stop=*
PGA_scaffold_5	GeMoMa	CDS	25881799	25881837	.	+	0	Parent=AH000035.mRNA1_R9;de=false;pc=0;minCov=0
PGA_scaffold_5	GeMoMa	CDS	25882302	25882685	.	+	0	Parent=AH000035.mRNA1_R9;ae=true;pc=0.7891;minCov=0
PGA_scaffold_9	GeMoMa	mRNA	20151006	20158161	.	+	.	ID=AH000072.mRNA1_R0;ref-gene=AH000072;aa=468;raa=493;score=2052;prediction=0;bestScore=2052;ce=17;rce=18;tae=0.9375;tde=0.9375;tie=0.875;minSplitReads=0;tpc=0.9765;minCov=0;avgCov=6.4601;pAA=0.8848;iAA=0.8424;lpm=91;maxScore=2604.0;maxGap=25;nps=0;start=M;stop=*
PGA_scaffold_9	GeMoMa	CDS	20151006	20151038	.	+	0	Parent=AH000072.mRNA1_R0;de=true;pc=1;minCov=7
PGA_scaffold_9	GeMoMa	CDS	20151145	20151178	.	+	0	Parent=AH000072.mRNA1_R0;ae=true;de=true;pc=1;minCov=7