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, 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, ycf15, ycf15_copy2, 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 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 None Other genes None 2. Multicopy genes with different lengths: Genes Length Location rpl2 864 join{[87447:87841](-), [86351:86821](-)} rpl2_copy2 861 join{[153848:154239](+), [154868:155338](+)} ycf1 1224 [110602:111826](+) ycf1_copy2 4785 [125489:130274](-) 3. Common intron-contained genes: Genes exons exon1 exon2 exon3 atpF (2/2) [13838:13982](-) [12652:13061](-) clpP (3/3) [73810:73878](-) [72708:73004](-) [71897:72124](-) ndhA (2/2) [122981:123536](-) [121286:121824](-) ndhB (2/2) [97708:98484](-) [96266:97021](-) ndhB_copy2 (2/2) [143206:143982](+) [144669:145424](+) petB (2/2) [76833:76838](+) [77569:78264](+) petD (1/2) [79137:79661](+) rpl16 (1/2) [83159:83518](-) rpl2 (2/2) [87448:87841](-) [86352:86821](-) rpl2_copy2 (2/2) [153849:154239](+) [154869:155338](+) rpoC1 (2/2) [24097:24549](-) [21705:23315](-) rps12 (3/3) [71615:71728](-) [99901:100131](-) [99334:99360](-) rps12_copy2 (3/3) [71615:71728](-) [141559:141789](+) [142330:142356](+) rps16 (2/2) [5995:6034](-) [4932:5146](-) ycf3 (3/3) [46574:46700](-) [45595:45824](-) [44696:44848](-) ### 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 psbC GTG psbT ATC rps19 GTG rpl32 ATC ycf1_copy2 ATA 6. Genes with nonstandard stop codon: Genes Stop codon None None 7. Conclusion This genome has 96 genes (84 unique genes). Including: 87 protein-coding genes (79 are unique) 1 tRNA genes (1 are unique) 8 rRNA genes (4 are unique) Details are as follows: Nonstandard gene annotation ('/gene' tags possibly be missing in your GenBank file) tRNA-His [9:84](-) tRNA-Lys join{[1581:1617](+), [4111:4149](+)} tRNA-Gln [7359:7431](-) tRNA-Ser [47312:47399](+) tRNA-Arg [132104:132179](-) tRNA-Cys [28896:28969](+) tRNA-Asp [32045:32121](-) tRNA-Tyr [32433:32517](-) tRNA-Glu [32575:32650](-) tRNA-Thr [48658:48733](+) tRNA-Gly [38575:38647](+) tRNA-Met [153313:153388](+) tRNA-Leu [146001:146084](+) tRNA-Phe [50318:50392](+) tRNA-Val [139824:139896](-) tRNA-Trp [68262:68336](-) tRNA-Pro [68496:68572](-) tRNA-Ile join{[137777:137810](-), [136923:136964](-)} tRNA-Ala join{[135976:136013](+), [136813:136851](+)} tRNA-Asn [131413:131487](+) 87 protein-coding genes (79 are unique) Genes Length Location accD 1476 [59311:60786](+) atpA 1524 [11067:12590](-) atpB 1497 [54896:56392](-) atpE 411 [54489:54899](-) atpF 555 [13838:13982](-) [12652:13061](-) atpH 246 [14308:14553](-) atpI 744 [15478:16221](-) ccsA 972 [115918:116889](+) cemA 690 [62819:63508](+) clpP 594 [73810:73878](-) [72708:73004](-) [71897:72124](-) matK 1518 [1882:3399](-) ndhA 1095 [122981:123536](-) [121286:121824](-) ndhB 1533 [97708:98484](-) [96266:97021](-) ndhB_copy2 1533 [143206:143982](+) [144669:145424](+) ndhC 363 [52411:52773](-) ndhD 1410 [117140:118549](-) ndhE 303 [119286:119588](-) ndhF 2247 [111795:114041](-) ndhG 531 [119816:120346](-) ndhH 1182 [123538:124719](-) ndhI 507 [120699:121205](-) ndhJ 477 [51092:51568](-) ndhK 681 [51688:52368](-) petA 963 [63701:64663](+) petB 702 [76833:76838](+) [77569:78264](+) petD 525 [79137:79661](+) petG 114 [68033:68146](+) petL 96 [67745:67840](+) petN 90 [29852:29941](+) psaA 2253 [41718:43970](-) psaB 2205 [39488:41692](-) psaC 246 [118792:119037](-) psaI 114 [61310:61423](+) psaJ 135 [68969:69103](+) psbA 1062 [240:1301](-) psbB 1521 [74348:75868](+) psbC 1386 [35853:37238](+) psbD 1062 [34808:35869](+) psbE 252 [66203:66454](-) psbF 120 [66074:66193](-) psbH 222 [76478:76699](+) psbI 111 [8374:8484](+) psbJ 144 [65682:65825](-) psbK 186 [7807:7992](+) psbL 117 [65935:66051](-) psbM 105 [30843:30947](-) psbN 132 [76234:76365](-) psbT 123 [76051:76173](+) psbZ 189 [37902:38090](+) rbcL 1428 [57149:58576](+) rpl14 369 [82645:83013](-) rpl16 360 [83159:83518](-) rpl2 864 [87448:87841](-) [86352:86821](-) rpl20 408 [70418:70825](-) rpl22 492 [85446:85937](-) rpl23 282 [87860:88141](-) rpl23_copy2 282 [153549:153830](+) rpl2_copy2 861 [153849:154239](+) [154869:155338](+) rpl32 183 [114664:114846](-) rpl33 201 [69516:69716](+) rpl36 114 [81482:81595](-) rpoA 1002 [79868:80869](-) rpoB 3213 [24555:27767](-) rpoC1 2064 [24097:24549](-) [21705:23315](-) rpoC2 4179 [17345:21523](-) rps11 417 [80937:81353](-) rps12 372 [71615:71728](-) [99901:100131](-) [99334:99360](-) rps12_copy2 372 [71615:71728](-) [141559:141789](+) [142330:142356](+) rps14 303 [39063:39365](-) rps15 273 [124823:125095](-) rps16 255 [5995:6034](-) [4932:5146](-) rps18 306 [69888:70193](+) rps19 279 [86011:86289](-) rps2 711 [16433:17143](-) rps3 657 [84805:85461](-) rps4 606 [47685:48290](-) rps7 468 [98813:99280](-) rps7_copy2 468 [142410:142877](+) rps8 405 [82088:82492](-) ycf1 1224 [110603:111826](+) ycf15 192 [100910:101101](-) ycf15_copy2 192 [140589:140780](+) ycf1_copy2 4785 [125490:130274](-) ycf2 6834 [88460:95293](+) ycf2_copy2 6834 [146397:153230](-) ycf3 510 [46574:46700](-) [45595:45824](-) [44696:44848](-) ycf4 555 [61841:62395](+) 1 tRNA genes (1 are unique) Genes Location trnG-TCC [9464:9485](+) [10175:10225](+) 8 rRNA genes (4 are unique) Genes Location rrn16 [102093:103583](+) rrn23 [105866:108674](+) rrn4.5 [108774:109042](-) rrn5 [109247:109510](+) rrn5_copy2 [132424:132554](-) rrn4.5_copy2 [132648:132916](+) rrn23_copy2 [133016:135824](-) rrn16_copy2 [138107:139597](-) This genome has 14 genes with intron(s). Details are as follows: 10 gene(s) have 1 intron(s) Genes Exons rps16 [5995:6034](-) [4932:5146](-) atpF [13838:13982](-) [12652:13061](-) rpoC1 [24097:24549](-) [21705:23315](-) petB [76833:76838](+) [77569:78264](+) rpl2 [87448:87841](-) [86352:86821](-) ndhB [97708:98484](-) [96266:97021](-) ndhA [122981:123536](-) [121286:121824](-) ndhB_copy2 [143206:143982](+) [144669:145424](+) rpl2_copy2 [153849:154239](+) [154869:155338](+) trnG-TCC [9464:9485](+) [10175:10225](+) 4 gene(s) have 2 intron(s) Genes Exons rps12 [71615:71728](-) [99901:100131](-) [99334:99360](-) ycf3 [46574:46700](-) [45595:45824](-) [44696:44848](-) rps12_copy2 [71615:71728](-) [141559:141789](+) [142330:142356](+) clpP [73810:73878](-) [72708:73004](-) [71897:72124](-)