Subspecies Start bp Coordinates for the gene insertions End bp Genes Inserted
Glaberrima 14233 CCTTGTAAATAAGcttttttttttggaa(1)ctatttactcagcaaCATCAGTAGCTGC 27782 GLAgene05, 06
Rufipogon 19108 TCTTATAAATAAG------CATCAGTAGCTGC 20783
Glaberrima 16232 TATTCAGCAACATcatcggtagctgcat(2)ctatttactcagcaaCATCAGTAGCTGC 27782 ORGLA01G0009100
Rufipogon 20758 TATTCAGCAACAT------CATCAGTAGCTGC 20783
Glaberrima 31007 CAGCACACCCACAcaccacaaaaatgca(3)cacaggtttttatcaGCAGCTGGAATTT 34599 GLAgene10
Rufipogon 23458 CAGCACACACACAggggcggatccagga(.)gcagaagtttcagtgGCAGTTGGAATTC 26752
Glaberrima 36973 CTCCGATGTTAAGaaaatggcgagacgg(4)cagcccggagggagtAACAACCATTATT 48007 GLAgene12, 13, 14
Rufipogon 30979 CTCCGATGTTAAG------(.)------AACAACCATTATT 41145
Glaberrima 78755 AACAGCCATCCTAagctgtagagcatgc(5)attttctcagctgatAGCCATCCTGCGC 93288 GLAgene23, 24, 25
Rufipogon 85340 GATAGCCATCCTAtaatgtaagacttgc(.)------cAGCCATCCTACTC 93864
Glaberrima 11373 ATAGCTCTTCTTAcatatcaaaatggtc---aatgaatagcgtaccACAAGATCACATT 11502
Rufipogon 13603 ATAACTCTTCTTAacaaggaaatcagac(6)aatgaacaatatataACAAGATTACATT 16133 Gene4
Glaberrima 31008 CAGCACACCCACAcaccacaaaaatgca---aatgaacctgcaggaTACTGCATAAAAG 32575
Rufipogon 23458 CAGCACACACACAggggcggatccagga(7)cccgaacctgaatatTACTGCATAAAAG 24248 Gene8
Glaberrima44856 AGAGAAAAAAAAAtgttgcatcatcaac---accggatctttacctGCCGTCA---GCG 45069
Rufipogon 35133 AGAGAAAAAAAAAaacaaagcagagcta(8)attagacagatcggcGCCGTCAgcgGCG 39029 Gene10
Glaberrima 54791 TGTACTCATGTAAttctgat------cccttctctgttaatTCAGCTACATCAT 62452
Rufipogon 47659 TGTACTCATGTAAattgcaatactgtaa(9)tctctctttttttacTCAGCAACATCAT 54946 Gene12, 13
Glaberrima97501 TTCATGCATGTCAgcaatgtcagagatc---tcacacccagcacagTGTGAAGAACAGG 101076
Rufipogon 98496 CTCATGCATGTCAatagcactagatatc(10)ctgattgccgagacTGTGAAACACAGG 106243 Gene23, 24
Rufipogon 12686 TTGTTCCTAGTGT------(11)cggttccatgcttaaGGATTGAATAGTG 13991 Gene4, ORRUFI01G0008900, 9000,9200
Japonica 9618 TTTTTCCTAGTGTtcctcctctagattg---ggtcaatgccgcgatGGATTGAATAGTG 20765
Rufipogon 28656 ATCATATAGACTAgggttaatttgatct(12)aaccctatagactaTGACTCTATGAGC 29881 ORRUFI01G0009900
Japonica 124561 ATCATATAGACTA------TGACTCTATGAGC 124585
Rufipogon 42355 ttcTTCTCCATTAcagttggagttgcca(13)cattttcatcgcagCCTAGCTACTGGC 57332 Gene12, 13, ORRUFI01G0009400, 9500
Japonica 142017 ---TTCTCCATTA------atttcactgttaacaCCTAGCTACTGGC 142376
Rufipogon 78369 AGTATGCCTGACTtgagtttgctgcatt(14)gagtgaaggaacagTGAGTTTGCTGCA 87427 ORRUFI01G00010100, 10200
Japonica 215282 AGTATGCCTGACT------TGAGTTTGCTGCA 215308
Rufipogon 91374 TTTCCAATTTACAgccccacac------(15)------TAAACTTAGTACAC 93932 ORRUFI01G00010400
Japonica 218854 TTTTCAGTTTACAatccactcatatgaa---aatatgtgatacataTAAACTTAGTACAC 244585
Rufipogon 12686 TTGTTCCTAGTGT------TCCTCCACTAGAT 12711
Japonica 9618 TTTTTCCTAGTGTtcctcctctagattg(16)caaggttctcctgcTCCTGCTCTAGAT 19615 LOC_Os01g02320-2334
Rufipogon 14278 GGCTCGGCCCACAtaatacagtcaggct---gagtgaagttgttgtAACAGCACTCCTA 19248
Japonica 21184 GTCTCGGCCCACAcgtaatccggcgcgg(16)ggtaccattctcgcAACAGCCTTCCTG 24982 LOC_Os01g02350-2360
Rufipogon 23457 GCAGCACACACACaggggcggatccagg---agtcacagtaggctgCGACTGCGTCgtt 24159
Japonica 29967 GCAGCACACACACcacagaaatgcgccg(16)acgaagaaacttgtCGACTGCGTCaat 120204 LOC_Os01g02370-2540
Rufipogon 40361 AACATGCACAAGT------TTCACTCATCCTC 40387
Japonica 137313 AACATGCACAAGTttcactcatcctcct(17)aaaacatgcacaagTTCACTCGTCCTC 141426 LOC_Os01g02580-2590
Rufipogon 58455 CACAAACCTGCAT------AGCACTGAATACG 58481
Japonica 143495 CAGAAACCTGCATgttgctgtgtagaca(17)acacaaacctgcatAGCACTGAATACG 192384 LOC_Os01g02600-2670
Rufipogon 69579 ATTATTTTTGTCT------GCACTAACATCAG 69605
Japonica 199408 ATTATTTTTGTCTgtttgtccgtgcgaa\(18)cagaaagtttgtgGCACTAACATCAG 206519 LOC_Os01g02700-2710
Rufipogon 91428 TCCAGCAAAACACtggcaattatgcccg------TAAACTTAGTACA 93932
Japonica 218911 GCCAGCAAAACACacatgagcgtcacat(19)atatgtgatacataTAAACTTAGTACA 244585 LOC_Os01g02740-2770
Rufipogon 196782 GAAGACATACTAT------TGTGGAGATTAtg 106808
Japonica 257427 GAAGACATACTATcccactaatataacc(20,27)taatactgtctTGTGGAGATTAag 2741179 LOC_Os01g02800-2840
Indica 916373 CCCAGGTGAATGA------GGTGATTGTAGTG 916400
Japonica 727719 CCCAGGTGACTGAcgcaattttgatggt(21)ccccaggtgaatgaGGTGATTGTAGTG 737717 LOC_Os01g02320
Indica 940691 ataTTCATATTAAcatcatatagatgt-----taatgaatctagacATACATACATACA 940746
Japonica 752307 tacTTCATATTAAacagataagcttaca(22)atatatacatatatATACATATATATA 759424 LOC_Os01g02380
Indica 991708 AGCCGATTAGGTT------AAATACTAATATC 991735
Japonica 812657 AGCCGATTAGGTTtgacggagctcgtgg(23)tcaccgacaaggttAAATACTAATATC 828661 LOC_Os01g02510, 2520, 2530
Indica 992729 GGTAAGAATCCAC------TGTTAGTGTGAAC 992756
Japonica 829755 GGTAAGAATCCACtgttagtgtgaacgc(23)atcaagggggagaaTGTTAGTGTGAAC 836271 LOC_Os01g02540
Indica 1037169GGCGTCATGGCGG------CGGTATGGGCGAC 1037196
Japonica 866506 GGCGCCATGGCGGtacgggcgacggcga(24)cagatgcgccatggCGGTACGGGCGAC 901160 LOC_Os01g02610, 2629, 2650, 2660
Indica 1063867cttAAAATAAAAGtaagtccataaccta---gattggattgaccggTGGAGAAGTCggt 1064195
Japonica 932180 ataAAAATAAAAGcaacttataaggaca(24)gacgatgaagggctTGGAGAAGTCcgg 938754 LOC_Os01g02730, 2740 partial
Indica 1064223ctaTGGTGGTGGTggttcagttgcat------atatttatcatcatAAGGTTAAATAac 1064277
Japonica 956202 tacTGGTGGTGGTcgcaactcattgaac(24)ttttgatgggtgacAAGGTTAAATAga 951359 LOC_Os01g02750
Indica 1064261atAAGGTTAAATAacaactgttatatgg----nnnnnnnnnnnnnnATCCTATGATATC 1064525
Japonica 951343 acAAGGTTAAATAgatctgaggtgtgat(24)tcctttccttatgaATCCTATGATATC 956755 LOC_Os01g02760
Indica 1071647AGTTGGACTATGAtcagctaatgc------cctaatttttatTCTCTGCATAATC 1071677
Japonica 960813 AGTTGGGCTGTGAgccttctgtctagaa(25)cgctaatttcctccTCTCTGCATGTTC 976159 LOC_Os01g02780
Indica 1072748AAGACTTGCAGAA------CATGCTGGCATAA 1072775
Japonica 977231 AAGACTTGCAGAAgaaggtaccataatt(26)tgcaagactcaggaCATGCTGGCATAA 997795 LOC_Os01g02800, 2810, 2830, 2840
Indica 859763 CACGACGGCGCCGggagatacatgaaga(28)nnnnnnnnnnnnnnGGAGATACATGAA 905504
Japonica 726941 CACGACGGCGCCG------GGAGATACATGAA 726968 BGIOSIBCE000107, 108
Indica 905857 TTGTCCCTAGTGTtcctcctctggattg(28)caaggttctcctgcTCCTGCTCTAGAT 915727
Japonica 727048 TTTTTCCTAGTGT------TCCTCCTCTAGAT 727075 BGIOSIBCE000109, 110