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 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, rpl23, rpl23_copy2, rpl2_copy2, rpl33, rpl36 Small subunit of ribosome rps11, rps14, rps15, rps16, rps18, rps19, 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, ycf1_copy2, 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 petN Subunits of photosystem I None Subunits of photosystem II None Large subunit of ribosome rpl22, rpl32 Small subunit of ribosome rps12 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 rpl2 828 join{[85670:86063](-), [84553:84988](-)} rpl2_copy2 831 join{[152231:152633](+), [153312:153741](+)} ycf1 5355 [109745:115100](+) ycf1_copy2 543 [128006:128549](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [49027:49170](+) [49912:50322](+) clpP (3/3) [71630:71700](-) [70634:70925](-) [69655:69882](-) ndhA (2/2) [117054:117617](+) [118895:119350](+) ndhB (2/2) [96597:97319](-) [95139:95894](-) ndhB_copy2 (2/2) [140976:141698](+) [142401:143156](+) petB (2/2) [74610:74615](+) [75452:76093](+) petD (2/2) [76296:76303](+) [77043:77517](+) rpl16 (2/2) [82897:82905](-) [81332:81742](-) rpl2 (2/2) [85671:86063](-) [84554:84988](-) rpl2_copy2 (2/2) [152232:152633](+) [153313:153741](+) rpoC1 (2/2) [38258:38719](+) [39514:41154](+) rps16 (2/2) [55963:56002](+) [56884:57113](+) ycf3 (3/3) [17023:17148](+) [17841:18068](+) [18861:19013](+) ### 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 rbcL GTG atpE ATT ndhK ATT psbC GTG rpoC1 ATT accD ATA ycf4 ATT psbL TTG psbB ATA rpoA ATT rps3 ATT rps19 GTG ndhI ATA ndhD ATT 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 117 genes (102 unique genes). Including: 80 protein-coding genes (74 are unique) 37 tRNA genes (28 are unique) 0 rRNA genes (0 are unique) Details are as follows: Nonstandard gene annotation ('/gene' tags possibly be missing in your GenBank file) 16S ribosomal RNA [135714:137205](-) 23S ribosomal RNA [130487:133300](-) 4.5S ribosomal RNA [130282:130386](-) 5S ribosomal RNA [129928:130049](-) 80 protein-coding genes (74 are unique) Genes Length Location accD 1353 [57595:58947](+) atpA 1533 [50413:51945](+) atpB 1497 [7749:9245](+) atpE 411 [9233:9643](+) atpF 555 [49027:49170](+) [49912:50322](+) atpH 246 [48388:48633](+) atpI 744 [46725:47468](+) ccsA 978 [123672:124649](-) cemA 690 [60714:61403](+) clpP 591 [71630:71700](-) [70634:70925](-) [69655:69882](-) matK 1518 [2145:3662](-) ndhA 1020 [117054:117617](+) [118895:119350](+) ndhB 1479 [96597:97319](-) [95139:95894](-) ndhB_copy2 1479 [140976:141698](+) [142401:143156](+) ndhC 363 [10938:11300](+) ndhD 1506 [121935:123440](+) ndhE 306 [120963:121268](+) ndhF 2325 [125768:128092](+) ndhG 531 [120216:120746](+) ndhH 1182 [115871:117052](+) ndhI 507 [119404:119910](+) ndhJ 477 [12162:12638](+) ndhK 771 [11201:11971](+) petA 963 [61582:62544](+) petB 648 [74610:74615](+) [75452:76093](+) petD 483 [76296:76303](+) [77043:77517](+) petG 114 [65651:65764](+) petL 96 [65398:65493](+) psaA 2253 [19829:22081](+) psaB 2205 [22107:24311](+) psaC 246 [121575:121820](+) psaI 105 [59360:59464](+) psaJ 135 [66513:66647](+) psbA 1062 [420:1481](-) psbB 1542 [72129:73670](+) psbC 1452 [26706:28157](-) psbD 1062 [28075:29136](-) psbE 252 [63904:64155](-) psbF 120 [63775:63894](-) psbH 222 [74252:74473](+) psbI 111 [54166:54276](-) psbJ 123 [63357:63479](-) psbK 186 [54771:54956](-) psbL 132 [63636:63767](-) psbM 105 [32286:32390](+) psbN 132 [74007:74138](-) psbT 102 [73840:73941](+) psbZ 189 [25862:26050](-) rbcL 1449 [5476:6924](-) rpl14 369 [80840:81208](-) rpl16 420 [82897:82905](-) [81332:81742](-) rpl2 828 [85671:86063](-) [84554:84988](-) rpl20 393 [68155:68547](-) rpl23 282 [86082:86363](-) rpl23_copy2 282 [151932:152213](+) rpl2_copy2 831 [152232:152633](+) [153313:153741](+) rpl33 135 [67158:67292](+) rpl36 114 [79627:79740](-) rpoA 984 [77754:78737](-) rpoB 3213 [35046:38258](+) rpoC1 2103 [38258:38719](+) [39514:41154](+) rpoC2 4158 [41354:45511](+) rps11 417 [78828:79244](-) rps14 303 [24419:24721](+) rps15 273 [115501:115773](+) rps16 270 [55963:56002](+) [56884:57113](+) rps18 312 [67612:67923](+) rps19 279 [84221:84499](-) rps2 711 [45765:46475](+) rps3 660 [83044:83703](-) rps4 606 [15822:16427](+) rps7 468 [97676:98143](-) rps7_copy2 468 [140152:140619](+) rps8 405 [80188:80592](-) ycf1 5355 [109746:115100](+) ycf1_copy2 543 [128007:128549](-) ycf2 6909 [86970:93878](+) ycf2_copy2 6909 [144417:151325](-) ycf3 507 [17023:17148](+) [17841:18068](+) [18861:19013](+) ycf4 588 [59636:60223](+) 37 tRNA genes (28 are unique) Genes Location trnH(gtg) [17:91](+) trnK-UUU [4388:4424](-) [1763:1797](-) trnM(cat) [9785:9857](-) trnV-UAC [10046:10084](+) [10680:10714](+) trnF(gaa) [13407:13480](-) trnL-UAA [14315:14319](-) [13909:13958](-) trnT(tgt) [15436:15510](+) trnS(gga) [16672:16759](-) trnM(cat)_copy2 [24884:24959](+) trnG(gcc) [25048:25116](-) trnS(tga) [26410:26502](+) trnT(ggt) [30297:30370](-) trnE(ttc) [31131:31205](+) trnY(gta) [31270:31355](+) trnD(gtc) [31781:31856](+) trnC(gca) [34109:34179](-) trnR(tct) [52178:52249](-) trnG-UCC [53256:53278](-) [52523:52572](-) trnS(gct) [53918:54004](+) trnQ(ttg) [55400:55471](+) trnW(cca) [65916:65989](-) trnP(tgg) [66182:66255](-) trnM(cat)_copy3 [86807:86881](-) trnL(caa) [94464:94546](-) trnV(gac) [100797:100868](+) trnI-GAU [102864:102905](+) [103856:103890](+) trnA-UGC [103955:103992](+) [104803:104837](+) trnR(acg) [108616:108690](+) trnN(gtt) [109317:109390](-) trnL(tag) [124741:124820](-) trnN(gtt)_copy2 [128905:128978](+) trnR(acg)_copy2 [129605:129679](-) trnA-UGC_copy2 [134306:134340](-) [133458:133492](-) trnI-GAU_copy2 [135390:135431](-) [134405:134439](-) trnV(gac)_copy2 [137427:137498](-) trnL(caa)_copy2 [143749:143831](+) trnM(cat)_copy4 [151414:151488](+) 0 rRNA genes (0 are unique) Genes Location This genome has 21 genes with intron(s). Details are as follows: 19 gene(s) have 1 intron(s) Genes Exons rpoC1 [38258:38719](+) [39514:41154](+) atpF [49027:49170](+) [49912:50322](+) rps16 [55963:56002](+) [56884:57113](+) petB [74610:74615](+) [75452:76093](+) petD [76296:76303](+) [77043:77517](+) rpl16 [82897:82905](-) [81332:81742](-) rpl2 [85671:86063](-) [84554:84988](-) ndhB [96597:97319](-) [95139:95894](-) ndhA [117054:117617](+) [118895:119350](+) ndhB_copy2 [140976:141698](+) [142401:143156](+) rpl2_copy2 [152232:152633](+) [153313:153741](+) trnK-UUU [4388:4424](-) [1763:1797](-) trnV-UAC [10046:10084](+) [10680:10714](+) trnL-UAA [14315:14319](-) [13909:13958](-) trnG-UCC [53256:53278](-) [52523:52572](-) trnI-GAU [102864:102905](+) [103856:103890](+) trnA-UGC [103955:103992](+) [104803:104837](+) trnA-UGC_copy2 [134306:134340](-) [133458:133492](-) trnI-GAU_copy2 [135390:135431](-) [134405:134439](-) 2 gene(s) have 2 intron(s) Genes Exons ycf3 [17023:17148](+) [17841:18068](+) [18861:19013](+) clpP [71630:71700](-) [70634:70925](-) [69655:69882](-)