1.
Annotated protein coding genes:
Group of genes                                  	Name of genes
Subunits of ATP synthase                        	ORF113, ORF113_copy2, atpA, atpB, atpE, atpF, atpH, atpI
Subunits of NADH-dehydrogenase            	ORF113, ORF113_copy2, ndhA, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Subunits of cytochrome b/f complex          	ORF113, ORF113_copy2, petA, petB, petD, petG, petL, petN
Subunits of photosystem I                       	ORF113, ORF113_copy2, psaA, psaB, psaC, psaI, psaJ
Subunits of photosystem II                      	ORF113, ORF113_copy2, psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbM, psbN, psbT, psbZ, ycf3
Large subunit of ribosome                       	ORF113, ORF113_copy2, rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36
Small subunit of ribosome                       	ORF113, ORF113_copy2, rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps7_copy2, rps8
DNA dependent RNA polymerase              	ORF113, ORF113_copy2, rpoA, rpoB, rpoC1, rpoC2
Subunit of rubisco                              	ORF113, ORF113_copy2, rbcL
c-type cytochrom synthesis gene             	ORF113, ORF113_copy2, ccsA
Envelop membrane protein                        	ORF113, ORF113_copy2, cemA
Maturase                                              	ORF113, ORF113_copy2, matK
Protease                                              	ORF113, ORF113_copy2, clpP
Subunit of Acetyl-CoA-carboxylase           	ORF113, ORF113_copy2, accD
Translational initiation factor             	ORF113, ORF113_copy2
Conserved open reading frames             	ORF113, ORF113_copy2, ycf1, ycf2, ycf2_copy2, ycf4
Other genes                                           	ORF113, ORF113_copy2

Possible missing protein coding genes:
Group of genes                                  	Name of genes
Subunits of ATP synthase                        	None
Subunits of NADH-dehydrogenase            	None
Subunits of cytochrome b/f complex          	None
Subunits of photosystem I                       	None
Subunits of photosystem II                      	psbL
Large subunit of ribosome                       	None
Small subunit of ribosome                       	None
DNA dependent RNA polymerase              	None
Subunit of rubisco                              	None
c-type cytochrom synthesis gene             	None
Envelop membrane protein                        	None
Maturase                                              	None
Protease                                              	None
Subunit of Acetyl-CoA-carboxylase           	None
Translational initiation factor             	infA
Conserved open reading frames             	ycf15
Other genes                                           	None

2.
Multicopy genes with different lengths:
Genes             	Length  	Location
None              	None    	None

3.
Common intron-contained genes:
Genes           	exons 	exon1 	exon2 	exon3
atpF               	(2/2)     	[14046:14190](-)	[12877:13286](-)	
clpP               	(3/3)     	[76732:76802](-)	[75559:75850](-)	[74710:74937](-)	
ndhA               	(2/2)     	[126826:127377](-)	[125220:125759](-)	
ndhB               	(2/2)     	[101087:101863](-)	[99648:100403](-)	
ndhB_copy2    	(2/2)     	[147436:148212](+)	[148896:149651](+)	
petB               	(2/2)     	[79616:79621](+)	[80394:81035](+)	
petD               	(2/2)     	[81228:81235](+)	[82006:82480](+)	
rpl16               	(2/2)     	[87379:87387](-)	[85986:86384](-)	
rpl2               	(2/2)     	[90166:90556](-)	[89068:89501](-)	
rpl2_copy2    	(2/2)     	[158743:159132](+)	[159797:160231](+)	
rpoC1               	(2/2)     	[24687:25139](-)	[22333:23949](-)	
rps12               	(3/3)     	[74430:74543](+)	[145786:146016](+)	[146563:146589](+)	
rps12_copy2    	(3/3)     	[74430:74543](+)	[103283:103513](-)	[102710:102736](-)	
rps16               	(2/2)     	[6201:6240](-)	[5132:5325](-)	
ycf3               	(3/3)     	[48023:48146](-)	[47034:47263](-)	[46147:46299](-)	

### The exon column shows the number of (actual exons/expected exons). ###