1.
Annotated protein coding genes:
Group of genes                                  	Name of genes
Subunits of ATP synthase                        	atpA, atpB, atpE, atpF, atpH, atpI
Subunits of NADH-dehydrogenase            	ndhA, ndhB, ndhB_copy2, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK
Subunits of cytochrome b/f complex          	petA, petB, petD, petG, petL, petN
Subunits of photosystem I                       	psaA, psaB, psaC, psaI, psaJ
Subunits of photosystem II                      	psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, ycf3
Large subunit of ribosome                       	rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl23_copy2, rpl2_copy2, rpl32, rpl33, rpl36
Small subunit of ribosome                       	rps11, rps12, rps12_copy2, rps14, rps15, rps16, rps18, rps19, rps19_copy2, rps2, rps3, rps4, rps7, rps7_copy2, rps8
DNA dependent RNA polymerase              	rpoA, rpoB, rpoC1, rpoC2
Subunit of rubisco                              	rbcL
c-type cytochrom synthesis gene             	ccsA
Envelop membrane protein                        	cemA
Maturase                                              	matK
Protease                                              	clpP
Subunit of Acetyl-CoA-carboxylase           	accD
Translational initiation factor             	None
Conserved open reading frames             	ycf1, ycf2, ycf2_copy2, ycf4
Other genes                                           	None

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                      	None
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)     	[12912:13056](-)	[11787:12196](-)	
clpP               	(3/3)     	[74085:74470](-)	[73184:73475](-)	[72265:72528](-)	
ndhA               	(2/2)     	[125250:125805](-)	[123693:124231](-)	
ndhB               	(2/2)     	[99421:100197](-)	[97962:98720](-)	
ndhB_copy2    	(2/2)     	[145104:145880](+)	[146581:147339](+)	
petB               	(2/2)     	[77380:77385](+)	[78210:78851](+)	
petD               	(2/2)     	[79065:79072](+)	[79822:80317](+)	
rpl16               	(2/2)     	[85305:85313](-)	[83712:84143](-)	
rpl2               	(2/2)     	[88215:88605](-)	[87109:87542](-)	
rpl2_copy2    	(2/2)     	[156696:157086](+)	[157759:158192](+)	
rpoC1               	(2/2)     	[23442:23873](-)	[21102:22703](-)	
rps12               	(3/3)     	[71012:71125](-)	[101562:101793](-)	[101000:101025](-)	
rps12_copy2    	(3/3)     	[71012:71125](-)	[143508:143739](+)	[144276:144301](+)	
rps16               	(2/2)     	[6845:6884](-)	[5779:6041](-)	
ycf3               	(3/3)     	[45474:45597](-)	[44515:44744](-)	[43602:43754](-)	

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


4.
Genes with internal stop codon:
None

5.
Genes with nonstandard start codon:
Genes             	Start codon
rps14             	GTG
rps19             	GTG
rpl2              	ACG
ndhD              	ACG
rpl2_copy2        	ACG
rps19_copy2       	GTG

6.
Genes with nonstandard stop codon:
Genes             	Stop codon
None              	None

7. Conclusion
This genome has 131 genes (112 unique genes). Including:
85 protein-coding genes (78 are unique)
38 tRNA genes (30 are unique)
8 rRNA genes (4 are unique)

Details are as follows:

85 protein-coding genes (78 are unique)
Genes             	Length  	Location
accD              	1530    	[59786:61315](+)	
atpA              	1524    	[10197:11720](-)	
atpB              	1497    	[55433:56929](-)	
atpE              	402     	[55035:55436](-)	
atpF              	555     	[12912:13056](-)	[11787:12196](-)	
atpH              	246     	[13558:13803](-)	
atpI              	744     	[14917:15660](-)	
ccsA              	966     	[118342:119307](+)	
cemA              	690     	[63194:63883](+)	
clpP              	942     	[74085:74470](-)	[73184:73475](-)	[72265:72528](-)	
matK              	1533    	[2151:3683](-)	
ndhA              	1095    	[125250:125805](-)	[123693:124231](-)	
ndhB              	1536    	[99421:100197](-)	[97962:98720](-)	
ndhB_copy2        	1536    	[145104:145880](+)	[146581:147339](+)	
ndhC              	363     	[51839:52201](-)	
ndhD              	1503    	[119510:121012](-)	
ndhE              	306     	[121634:121939](-)	
ndhF              	2226    	[114349:116574](-)	
ndhG              	531     	[122147:122677](-)	
ndhH              	1182    	[125807:126988](-)	
ndhI              	537     	[123053:123589](-)	
ndhJ              	477     	[50527:51003](-)	
ndhK              	672     	[51112:51783](-)	
petA              	969     	[64106:65074](+)	
petB              	648     	[77380:77385](+)	[78210:78851](+)	
petD              	504     	[79065:79072](+)	[79822:80317](+)	
petG              	114     	[67427:67540](+)	
petL              	96      	[67168:67263](+)	
petN              	90      	[28789:28878](+)	
psaA              	2253    	[40585:42837](-)	
psaB              	2205    	[38355:40559](-)	
psaC              	246     	[121148:121393](-)	
psaI              	111     	[62180:62290](+)	
psaJ              	135     	[68343:68477](+)	
psbA              	1062    	[577:1638](-)	
psbB              	1527    	[74902:76428](+)	
psbC              	1422    	[34734:36155](+)	
psbD              	1062    	[33725:34786](+)	
psbE              	252     	[66209:66460](-)	
psbF              	120     	[66080:66199](-)	
psbH              	228     	[77029:77256](+)	
psbI              	111     	[8222:8332](+)	
psbJ              	123     	[65698:65820](-)	
psbK              	186     	[7639:7824](+)	
psbL              	117     	[65936:66052](-)	
psbM              	105     	[29961:30065](-)	
psbN              	132     	[76795:76926](-)	
psbT              	108     	[76612:76719](+)	
psbZ              	189     	[36829:37017](+)	
rbcL              	1428    	[57644:59071](+)	
rpl14             	369     	[83258:83626](-)	
rpl16             	441     	[85305:85313](-)	[83712:84143](-)	
rpl2              	825     	[88215:88605](-)	[87109:87542](-)	
rpl20             	354     	[69869:70222](-)	
rpl22             	519     	[86160:86678](-)	
rpl23             	309     	[88607:88915](-)	
rpl23_copy2       	309     	[156386:156694](+)	
rpl2_copy2        	825     	[156696:157086](+)	[157759:158192](+)	
rpl32             	162     	[117258:117419](+)	
rpl33             	201     	[68916:69116](+)	
rpl36             	114     	[82128:82241](-)	
rpoA              	999     	[80528:81526](-)	
rpoB              	3216    	[23900:27115](-)	
rpoC1             	2034    	[23442:23873](-)	[21102:22703](-)	
rpoC2             	4137    	[16790:20926](-)	
rps11             	423     	[81592:82014](-)	
rps12             	372     	[71012:71125](-)	[101562:101793](-)	[101000:101025](-)	
rps12_copy2       	372     	[71012:71125](-)	[143508:143739](+)	[144276:144301](+)	
rps14             	303     	[37919:38221](-)	
rps15             	282     	[127036:127317](-)	
rps16             	303     	[6845:6884](-)	[5779:6041](-)	
rps18             	333     	[69288:69620](+)	
rps19             	279     	[86732:87010](-)	
rps19_copy2       	279     	[158291:158569](+)	
rps2              	711     	[15866:16576](-)	
rps3              	666     	[85510:86175](-)	
rps4              	624     	[46824:47447](-)	
rps7              	324     	[100618:100941](-)	
rps7_copy2        	324     	[144360:144683](+)	
rps8              	399     	[82672:83070](-)	
ycf1              	5727    	[127725:133451](-)	
ycf2              	7074    	[89325:96398](+)	
ycf2_copy2        	7074    	[148903:155976](-)	
ycf3              	507     	[45474:45597](-)	[44515:44744](-)	[43602:43754](-)	
ycf4              	555     	[62478:63032](+)	

38 tRNA genes (30 are unique)
Genes          	Location
trnH-GUG       	[62:136](-)	
trnK-UUU       	[4433:4469](-)	[1860:1894](-)	
trnQ-UUG       	[7025:7096](-)	
trnQ-UUG_copy2 	[7198:7270](-)	
trnS-GCU       	[8495:8582](-)	
trnG-UCC       	[9029:9051](+)	[9750:9797](+)	
trnR-UCU       	[9982:10053](+)	
trnC-GCA       	[28264:28334](+)	
trnD-GUC       	[31220:31293](-)	
trnY-GUA       	[31594:31677](-)	
trnE-UUC       	[31737:31809](-)	
trnT-GGU       	[32491:32562](+)	
trnS-UGA       	[36384:36471](-)	
trnG-GCC       	[37459:37529](+)	
trnfM-CAU      	[37694:37767](-)	
trnS-GGA       	[46460:46546](+)	
trnT-UGU       	[47815:47887](-)	
trnL-UAA       	[48739:48773](+)	[49199:49248](+)	
trnF-GAA       	[49604:49676](+)	
trnV-UAC       	[54508:54546](-)	[53890:53924](-)	
trnM-CAU       	[54732:54804](+)	
trnW-CCA       	[67672:67746](-)	
trnP-UGG       	[67907:67980](-)	
trnI-CAU       	[89089:89162](-)	
trnL-CAA       	[97330:97410](-)	
trnV-GAC       	[103127:103198](+)	
trnI-GAU       	[105219:105255](+)	[106209:106243](+)	
trnA-UGC       	[106308:106345](+)	[107146:107180](+)	
trnR-ACG       	[110957:111030](+)	
trnN-GUU       	[111631:111702](-)	
trnL-UAG       	[118184:118263](+)	
trnN-GUU_copy2 	[133599:133670](+)	
trnR-ACG_copy2 	[134271:134344](-)	
trnA-UGC_copy2 	[138956:138993](-)	[138121:138155](-)	
trnI-GAU_copy2 	[140046:140082](-)	[139058:139092](-)	
trnV-GAC_copy2 	[142103:142174](-)	
trnL-CAA_copy2 	[147891:147971](+)	
trnI-CAU_copy2 	[156139:156212](+)	

8 rRNA genes (4 are unique)
Genes          	Location
rrn16             	[103430:104920](+)	
rrn23             	[107339:110143](+)	
rrn4.5            	[110242:110344](+)	
rrn5              	[110570:110690](+)	
rrn5_copy2     	[134611:134731](-)	
rrn4.5_copy2   	[134957:135059](-)	
rrn23_copy2    	[135158:137962](-)	
rrn16_copy2    	[140381:141871](-)	

This genome has 23 genes with intron(s).
Details are as follows:

19 gene(s) have 1 intron(s)
Genes	Exons
rps16	[6845:6884](-)	[5779:6041](-)	
atpF	[12912:13056](-)	[11787:12196](-)	
rpoC1	[23442:23873](-)	[21102:22703](-)	
petB	[77380:77385](+)	[78210:78851](+)	
petD	[79065:79072](+)	[79822:80317](+)	
rpl16	[85305:85313](-)	[83712:84143](-)	
rpl2	[88215:88605](-)	[87109:87542](-)	
ndhB	[99421:100197](-)	[97962:98720](-)	
ndhA	[125250:125805](-)	[123693:124231](-)	
ndhB_copy2	[145104:145880](+)	[146581:147339](+)	
rpl2_copy2	[156696:157086](+)	[157759:158192](+)	
trnK-UUU	[4433:4469](-)	[1860:1894](-)	
trnG-UCC	[9029:9051](+)	[9750:9797](+)	
trnL-UAA	[48739:48773](+)	[49199:49248](+)	
trnV-UAC	[54508:54546](-)	[53890:53924](-)	
trnI-GAU	[105219:105255](+)	[106209:106243](+)	
trnA-UGC	[106308:106345](+)	[107146:107180](+)	
trnA-UGC_copy2	[138956:138993](-)	[138121:138155](-)	
trnI-GAU_copy2	[140046:140082](-)	[139058:139092](-)	

4 gene(s) have 2 intron(s)
Genes	Exons
rps12	[71012:71125](-)	[101562:101793](-)	[101000:101025](-)	
ycf3	[45474:45597](-)	[44515:44744](-)	[43602:43754](-)	
rps12_copy2	[71012:71125](-)	[143508:143739](+)	[144276:144301](+)	
clpP	[74085:74470](-)	[73184:73475](-)	[72265:72528](-)