Figure S6. Multiple sequence alignment of all the sequencedmiR1861-clusters individually shows the significant conservation in the cluster sequences among the Oryza species.The presence of distinct nucleotide substitutions and indelswere also evident with the Cluster-VII being the most diverged. Cluster-I O.sativa_indica_ ATTCAACCAAACCTAGCACACAACTACATCTCTTCTTCATAAACGTTCTGCTGGTTCCAA O.nivara TAACAACCAAACCTAGCACACAACTACATCTCTTCTTCATAAACGTTCTGCTGGTTCCAA O.rufipogon ATTCAACCAAACCTAGCACACAACTACATCTCTTCTTCATAAACGTTCTGCTGGTTCCAA O.glaberrima ATTCAACCAAACCTAGCACACAACTACATCTCCTCTTCATAAACGTTCTGCTGGTTCTAA ***************************** ************************ ** O.sativa_indica_ CTTCGTGTTGCATATTCTTAGGCTCGGTCTTGAGGCAGGAACTGAGTAGTTGGTGAACTC O.nivara CTTCGTGTTGCATATTCTTAGGCTCGGTCTTGAGGCAGGAACTGAGTAGTTGGTGAACTC O.rufipogon CTTTGTGTTGCATATTCTTAGGCCCGGTCTTGAGGCAGGAACTGAGTAGTTGGTGAACTC O.glaberrima CTTCGTCTTGCGTATTCTTAAGCCCGATCTAGAGGCAGGAACTGAGTAGTTGTTGAACTT *** ** **** ******** ** ** *** ********************* ****** O.sativa_indica_ GCTCTATTTTGTTCATTCACTCGCGACGCGGTTCCTGTCCTAAGACCGAGTCTGTGAATA O.nivara GCTCTATGTTGTTCGTTCACTCGCGACGCGGTTCCTGTCCTAAGACCGAGTCTGTGAATA O.rufipogon GCTCTATGTTGTTCGTTCACTCGCGACACGGTTCCTGTCCCAAGACCGAGTCTGTGAATA O.glaberrima GCTCTATGTTGTTCGTTCACCCACTATTCGATTCCTATCCCAAGATCGAGTCTATGAATA ******* ****** ***** * * * ** ***** *** **** ******* ****** O.sativa_indica_ TACAAATGTGATTTTTTT-AATACATTCTTACACCCACTCTTTTTTCCAAGTTCCACCAT O.nivara TACAAATGTGATTTTTTT-AATACATTCTTACACCTACTCTTTTTTCCAAGTTCCACCAT O.rufipogon TACAAATGTAATTTTTTT-ACTACATTCTTATACCCACTCTTTTTTCCAAGTTCCACCAT O.glaberrima TACAAATGTGATTTTTTTTACTACATTCTTACACCCACTATTTTTTCCAAGTTCCACCAT ********* ******** * ********** *** *** ******************** O.sativa_indica_ CCGTTTGTAAATATAACCTACT O.nivara CCGTTTGTAAATATAACCTACT O.rufipogon CCGTTTGTAAATATAACCTACT O.glaberrima CCGTTTGTAAATCGAACCTACT ************ ******** Cluster-II O.sativa_indica_ CTGCTGGTTCTAACTTCGTCTTGCATATTCTTAGGCCCAATCTTGACGCAGGAACTGAGT O.rufipogon CTGCTGGTTCTAACTTCGTCTTGCATATTCTTAGGCCCAATCTTGACGCAGGAACTGAGT O.nivara CTGCTGGTTCTAACTTCGTCTTGCATATTCTTAGGCCCAATCTTGACGCAGGAACTGAGT O.glaberrima CTGCTGGT-CTAACTTCGTCTTGCATATTCTTAGGCCCAATCTTGACGCAGGAACTGAGT ******** *************************************************** O.sativa_indica_ AGTTCGTGAACTCGCTCTATGTTGTTCGTTCACCCACTATTCGGTTCCTGTCCCAAGATC O.rufipogon AGTTCGTGAACTCGCTCTATGTTGTTCGTTCACCCACTATTCGGTTCCTGTCCCAAGATC O.nivara AGTTCGTGAACTCGCTCTATGTTGTTCGTTCACCCACTATTCGGTTCCTGTCCCAAGATC O.glaberrima AGTTCGTGAACTCGCTCTATGTTGTTCGTTCACCCACTATTCGGTTCCTGTCCCAAGATC ************************************************************ O.sativa_indica_ GAGTCTGTGAATATACAAATATGATTTTTTTT---ACTACATTCTTACACCCACTCTTTT O.rufipogon GAGTCTGTGAATATACAAATATGATTTTTTTTTTTACTACATTCTTACACCCACTCTTTT O.nivara GAGTCTGTGAATATACAAATATGATTTTTTT----ACTACATTCTTACACCCACTCTTTT O.glaberrima GAGTCTGTGAATATACAAATATGATTTTTTT----ACTACATTCTTACACCCACTCTTTT ******************************* ************************* O.sativa_indica_ TTTCAAGTTCTAGCATCCGTTTGTGAATATGACCTACTCCTGCAAATTCATAAACTCGGT O.rufipogon TTTCAAGTTCTAGCATCCGTTTGTGAATATGACCTACTCCTGCAAATTCATAAACTCGGT O.nivara TTTCAAGTTCTAGCATCCGTGTGTGAATATGACCTACTCCTGCAAATTCATAAACTCGGT O.glaberrima TTTCAAGTTCTAGCATCCGTGTGTGAATATGACCTACTCCTGCAAATTCATAAACTCGGT ******************** *************************************** O.sativa_indica_ GTTGCATATTCTTAGACCCGATCTTGTAGCAAGAACTGAGTAGTTCGTTAACTCGCTACG O.rufipogon GTTGCATATTCTTAGACCCGATCTTGTAGCAAGAACTGAGTAGTTCGTTAACTCGCTACG O.nivara GTTGCATATTCTTAGACCCGATCTTGTAGCAAGAACTGAGTAGTTCGTTAACTCGCTACG O.glaberrima GTTGCATATTCTTAGACCCGATCTTGTAGCAAGAACTGAGTAGTTCGTTAACTCGCTACG ************************************************************ O.sativa_indica_ CGGTTCTTGTCACAAGACCGAGCCTGTGAATATGCAAAGGTGG O.rufipogon CGGTTCTTGTCACAAGACCGAGCCTGTGAATATGCAAAGGTGG O.nivara CGGTTCTTGTCACAAGACAGAGCCTGTGAATATGCAAAGGTGG O.glaberrima CGGTTCTTGTCACAAGACAGAGCCTGTGAATATGCAAAGGTGG ****************** ************************ Cluster-III O.sativa_indica_ TTGCTGGTTCC--AACTTCGTGTTGGATATTTTTAGGCTCGGTCTTGAGGCAGGAACTGA O.rufipogon CTGCTGGTTCC--AACTTCGTGTTGCATATTCTTAGGCCTGGTCTTGAGGCAGGAACTGA O.nivara TTGCTGGTTCC--AACTTCGTGTTGGATATTCTTAGGCTCGGTCTTGAGGCAGGAACTGA O.glaberrima CTGCAAATTCATAAACTCGGTGTTGCATATTCTTAGGCCCGGTCTTGTGGCAAGAACTGA *** *** **** ****** ***** ****** ******* **** ******* O.sativa_indica_ GTAGTTGGTGAACTCGTTTTATTTTGTTCATTCACTCGGGACGCGGTTCCTGTCCTAAGA O.rufipogon GTAGTGGGGGAACTCGCTTAAGGTGGTTGGTCCACTCGGGACAGGGTCCTGGTCCCAAGC O.nivara GTAGTTGGTGAACTCGCTTTATGTTGTTCGTTCACTCGGGACGCGGTTCCTGTCCTAAGA O.glaberrima GTAGTTCGTTAACTCGCT----------------------ACGCGGTTCTTGTCACAAGA ***** * ****** * ** *** * *** *** O.sativa_indica_ CCGAGTCTGTGAATATACAAATGTGATTTTTTTAATACATTCTTACACCCCCTCTTTTTT O.rufipogon CGGAGTCGGGGAAAATACAAAGGTAATTTTTTTAATCCATTCTTCCCCCCATTCTTTTTT O.nivara CCGAGTCTGTGAATATACAAATGTGATTTTTTTAATACATTCTTACACCTACTCTTTTTT O.glaberrima CCGAGTCTGTGAATATGCAAAGGTGG------------AACCCTGCAACACGAGT----- * ***** * *** ** **** ** * * * * * * O.sativa_indica_ TCAAGTTCCAACATCCGTTTG-GGAATATGACCTACTCCTGCAAATTCCTAAACTCGGGG O.rufipogon TCAAGTTCCAGCATCCGTTTG-TGAATATGACCTACTCCTGCAAATTCATAAACTCGGTG O.nivara GCAAGTTCCAGCATCCGTTTG-TGAATATGACCTACTCCTGCAAATTCCTAAACTCCGTG O.glaberrima ---AGGTGTAATAATGGCTTGCTGGTTCCAACTTCGTGTTGCATATTCTTAGGCTCGGTC ** * * * * *** * * ** * * **** **** ** *** * O.sativa_indica_ TTGCATATTCTTAAGCCCGGGCTTGGGGCAAAAACTGAATAATTCGTTAACTCCCTACCC O.rufipogon TTGCATATTCTTAGGCCCGGGCTTGGGGCAAAAACTGAATAATTCGTTAACTCCCCACCC O.nivara TTGCATATTCTTAAGCCCGGTCTTGTGGCAAGAACTGAATAATTCGTTAACTCCCTACCC O.glaberrima TTGAGGCAGGAACTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTCGCGACGC *** * * * ** * ****** **** * ** * O.sativa_indica_ GGTTCTTGGCACAAAACCGAATCTGGGAATATGCAAAGGTGG------------------ O.rufipogon CGGTCCTGGCCCCAGACCCAATCCGGGAATAAGCCAAGGGGGGACACGACGCGGTTCTTG O.nivara GGTTCTTGTCCCAAGAACCAATCTGTGAATATGCCAAGGTGGTT---------------- O.glaberrima GGTTCCTGTCCTAAGACCGAGTCTGTGAATATACAAATGTGATT---------------- * ** ** * * * * * ** * ***** * ** * * Cluster-IV O.nivara TGCTGGTT-CTAACTTCGTCTTGCGTATTCTTAGGCCCGATCTTGAGGCAGGAACTGAGT O.rufipogon TGCTGGTT-CTAACTTCGTCTTGCGTATTTTTAGGCCCGATCTTGAGGCAGGAACTGAGT O.sativa_indica_ TGCTGGTTTCTAACTTCGTCTTGCGTATTCTTAGGCCCGATCTAGAGGCAGGAACTGAGT O.glaberrima TGCTGGTTTCTAACTTCGTCTTGCGTATTCTTAGGCCCGATCTAGAGGCAGGAACTGAGT ******** ******************** ************* **************** O.nivara AGTTGTTGAACTTGCTCTATGTTGTTCGTTCACCCACTATTCGGTTCCTGTCCCAAGATC O.rufipogon AGTTGGTGAACTTGCTCTATGTTGTTCGTTCACCCACTATTCGGTTCCTGTCCCAAGATC O.sativa_indica_ AGTTGGTGAACTCGCTCTATGTTGTTCGTTCACCCGCTATTCGGTTCCTGCCCCAAGACC O.glaberrima AGTTGGTGAACTCGCTTTATGTTGTTCGTTCCCCCGCAATACGGTTCCTGTCCCAAGACC ***** ****** *** ************** *** * ** ********* ******* * O.nivara GAGTCTATGAATATAC----------------AAATGTGATTTTTTTTACTACATTCTTA O.rufipogon GAGTTTATGAATATAC----------------AAATGTGATTTTTTTTACTACATTCTTA O.sativa_indica_ GAGTCTGTGAATATACGAGTCTGTGAATATACAAATGTGATTTTTTT-AATACATTCTTA O.glaberrima GAGTCTGTGAATATAC----------------AAATGTGATTTTTTT-AATACATTCTTA **** * ********* *************** * ********** O.nivara CCCCCACTATTTTTTTCAAGTTCCACCATCCGTTTGTGAATATGACCTACTCCTGCAAAT O.rufipogon CACCCACTATTTTTTTCAAGTTCCAACATCCATTTGTGAATATGACCTACTCCTGCAAAT O.sativa_indica_ CCCCCACTCTTTTTTTCAAGTTCCAACATCCGTTTGGGAATATGACCTACTCCTGCAAAT O.glaberrima CACCCACTATTTTTTTCAAGTTCCAGCATCCGTTTGTGAATATGACCTACTCCTGCAAAT * ****** **************** ***** **** *********************** O.nivara TCTTAAACTCGGGGTTGCATATTCTTAGGCCCAGTCTTGTGGCAAAAACTAATTAGTTCG O.rufipogon TCATAAACTCGGTGTTGCATATTCTTAGGCCCAGTCTTGTGGCAAAAACTGAGTAGTTCG O.sativa_indica_ TCATAAACTCGGGGTTGCATATTCTTAGGCCCGGTCTTGGGGCAAGAACTGGGTAATTCG O.glaberrima TCATAAACTCGGTGTTGCATATTCTTAGGCCCGGTCTTGTGGCAAGAACTGAGTAGTTCG ** ********* ******************* ****** ***** **** ** **** O.nivara TTAACTTGCTACGCGGTTCTTGTCACAAAACCAAGCCTGTGAATATGCAAAGTGGGTTTT O.rufipogon TTAACTCGCTACGTGGTTCTTGTCACAAAATCGAGCCTGTGAATATGCAAAGTTGGTTTT O.sativa_indica_ TTAACTTGCTACCCGGTTCTTGGCACAAGAACGAGCCTGTGAATATGCAAAGGTGGTTTT O.glaberrima TTAACTCGCTACGCGGTTCTTGTCACAAGACCGAACCTGTGAATATGCAAAGGTGGGTTT ****** ***** ******** ***** * * * ***************** ** *** O.nivara CTCTATGAATATGGCATATTCTAAATTCCTATTCTTTGTCAACTTTGTAAAAATTGTTCC O.rufipogon CTCTATGAATATGGCATATTCTAAATTCCTATTCTTTGTCAACTTTGTAAAAATTGTTCC O.sativa_indica_ CTCTATGAATATGGCATATTCTAAATTCCTATTCTTTGTCAACTTTGTAAAAATTGTTCC O.glaberrima CTCTATGAATATGGCATATTCTAAATTCCTATTCTTTGTCAACTTTGTAAAAATTGTTCC ************************************************************ O.nivara CAATTGATCCCTTCTACTTG O.rufipogon CAAATGATCTCT-CTACTTG O.sativa_indica_ CAAATGACCTCTC-TACTTG O.glaberrima CAAATGACCCCCCCTACTTG *** *** * * ****** Cluster-V O.sativa_indica_ TTCTTACGCCCGGTC-TTGAGGCAG--ACTGAGTAGTTGGTGAACTCGCTCTATGTTGTT O.glaberrima TTCTT-CGCCCGATCCTTGGGGCAG--ACTGAGTAGTTGGTGAACTCGCTCTATGTTGTT O.rufipogon TTCTT-TAGCCGGTTCTTGAGGCAGGAACTGAGTAGTTGGTGAACTCGCTCTATGTTGTT O.nivara GTCATCTAGCCGGTC-TTGAGGCAGG-ACTGAGTAGTTGGTGA-CTCGCTCT-TGTTGTT ** * *** * *** ***** **************** ******** ******* O.sativa_indica_ CGTTCACTCGCGACACGGTTCCTGTCCCAAGACCGAGTCTGTGAA O.glaberrima CGTTCACTCGCGACACGGTTCCTGTCCCAGGTCCGAGTCTGTGAA O.rufipogon CGTTCACTCGCGACACGGTTCCTGTCCCAAGACCGAGTCTGTGAA O.nivara CGTTCACTCGCGACACGGTTCCAGTCCCA-GACCGAGTCTGTGAA ********************** ****** * ************* Cluster-VI O.glaberrima -AACGTTCTGCTGGTTCCAACTGCGTGTTGTATATTCTTAGGCCCAATCTTATGGC-AGG O.rufipogon -AACGTTCTGCTGGTTCCAACTGCGTGTTGCATATTCTTAGGCCCGATCTTGAGGCCAGG O.nivara TCAC-TTCTGCTGGTTCCAACTGCGTGTTGCATATTCTTAGGCCCGATCTTGAGGC-AAG O.sativa_indica_ -AACGTTCTGCTGGTTCCAACTGCGTGTTGCATATTCTTAGGCCCGATCTTGAGGC-AAG ** ************************* ************** ***** *** * * O.glaberrima AACTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCATTCACTCGCTACACG-GTTCCTG- O.rufipogon AACTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTTGCTACACG-GTTCCTG- O.nivara AATTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTTGCTACACG-GTTCCTG- O.sativa_indica_ AATTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTTGCTACACGAGTTCCTGG ** ******************************** ****** ******** ******* O.glaberrima TCCCAAGATCGAGTCTATGAATATGCAAAT-GTGATTTTCTCTGGTGAATATGACA O.rufipogon TTCCAAGATCGAGTCCGTTAATATGCAAAGAGTGATTTTCTCTGGTGAATATGACA O.nivara TCCCAAGATCGAGTCCGTTAATATGCAAAG-GTGATTTTCTCTGGTGAATATGACA O.sativa_indica_ TCCCAAGATCGAGTCCGTTAATATGCAAAG-GTGATTTTCTCTGGTGAATATGACA * ************* * ********** ************************* Cluster-VII O.sativa_indica_ CCGTTCTGCTGGTTCC--AACTTCGTGTGGCATATTCTTAGGCCC--GGTCTTGA-GGCA O.rufipogon CCGTTCTGCTGGTTCC--AACTTCGTGTTGCATTTTCT---AGCC--GGTCT-GA-GGCA O.nivara --------------------------------TCTCTTAGGGGCCCGGGTCTTGAAGGCA O.glaberrima CCGTTCTGCAAATTCATAAACTCGGAGTTGCATATTCTTAGGCCC--GGTCTTGT-GGCA * * * ** ***** * **** O.sativa_indica_ GAAACTGAGTAGTTGGTGAACTCG-----CTCTATGTTGTTCGTTCACTCGCGACACGGT O.rufipogon GGA-CTGAGTAGTTGGTGAACTCG-----CTCTATGTTGTTCGTTCACTCGCGACACGGT O.nivara GGAACTGAGTAGTTGGTGAACTCAGCCTTCCTTATGTTGTTCGTTCACTCGCGACACGGT O.glaberrima AGAACTGAGTAGTT---------------------------CGTTAACTCGCTACGCGGT * ********** **** ****** ** **** O.sativa_indica_ TCCTGTCCCAA-GACCGAGTCTGTGAATATACAAATGTGATTTTTTT-AATACATTCTTA O.rufipogon TCCTGTCCCAA-GGCCGAGTCTGTGAATATACAAATGTGATTTTTTT-AATACATTCTTA O.nivara TCCTGTCCCAAAGACCGAGTCTGTGAATATACAAATGTGATTTTTTTTAATACTTTCTTA O.glaberrima TCTTGTCACAA-GACCGAGTCTGTGAATATGCAAAGAGAGTTTTCTCTAGGAATATGACA ** **** *** * **************** **** **** * * * * * O.sativa_indica_ CACCCACTCTTTTTTTCAAGTTCCAGCATCCGTTTGTGAATATGACCTACTCCTGCAAAT O.rufipogon CACCCACTCTTTTTTTCAAGTTCCACCATCCGTTTGTGAATATGACCTACTCCTGCAAAT O.nivara CCCCCACTCTTTTTTTCAAGTTCCAGCATCCGTTTGTGAATATGACCTACTCCTGCAAAT O.glaberrima TATTCTAAATTCCTATTCTTTGTCAAC-----TTTGTAAAAATTGCT--CCCGAATGATC * ** * * * ** * ***** ** ** * * * * O.sativa_indica_ TCATAAACTCGGAGTTGCATATTCTTAGGCCCGGTCTTGTGGCAAGAACTGAGTAATTCG O.rufipogon TCATAAACTCGGGGTTGCATATTCTTAGGCCCGGTCTTGGGGCAAAAACTGAATAATTCG O.nivara TCATAAACTCGGTGTTGCATATTCTTAGGCCCGGTCTTGTGGCAAGAACTGAGTAGTTCG O.glaberrima TCTCTACTACGAAACCCTTTATCACTTCCCCCAATGTTGGTCATACTCACCCTTTTTTTT ** * ** *** * *** * *** * * ** O.sativa_indica_ TTAACTCGCTACGCGGTTCTTGTCAC-AAGACCGAGTCTGTGAATATGCAAAGGTGGTT- O.rufipogon TTAACTCCCTACCCGGTTCTTGTCCC-AAAACCGAGTCTGTGAATATGCAAAGGGGGTT- O.nivara TTAACTCGCTACGCGGTTCTTGTCACTAAGACCGAGTCTGTGAATATGCAAAGGTGGTT- O.glaberrima TTCATTTTTTTTTTTTTACCCCTTGTTTTGTTTTTTTTTATAAGAACCCAAACAAACCCC ** * * * * * * * * * * * **** O.sativa_indica_ --TTCTCTGTGAATATGACATATTCTAAATTCCTATTCTTTGTCAACTTTGTAAAAATTG O.rufipogon --TTCCCTATGAATAAGAAATATTCCAAATTCCTATTTTTTGTCCAATTTTAAAAAATTG O.nivara --TTCTCTGTGAATATGACATATTCTAAAT-CCTAT--CTTGTCAACTGAAG-------- O.glaberrima CATTTCTTATTCATTATTTGCTCCCTCAACCCTGGTCGCCTGACAGCCTTTATATG---- ** * * ** * ** * * ** * O.sativa_indica_ CTCCCGAATGA--TCTCTCTACTCCTTTATATG O.rufipogon CCCCCGAAAGAACTCTCTCTACTCCTTTATATG O.nivara --------------------------------- O.glaberrima --------------------------------- Cluster-VIII O.sativa_indica_ --ATAAACGTTCCGCGGGTTCCAACTTTGTGTTGCATATTT-TTAGGCCCGGTCTTGAGG O.glaberrima TCATAAACGTTCCGCTGGTTCCAACTTCGTGTTGCCAATTTCTTAGGCTCGGTCTTGAGG O.rufipogon TCATAAACGTTCCGCTGGTTCCAACTTCGTGTTGCATATTC-TTAGGCCCGGTCTTGAGG O.nivara TCATAAACGTTCCGCTGGTTCCAACTTCGTGTTGC--ATTTCTTACGCTCGGTCTTGAGG ************* *********** ******* *** *** ** *********** O.sativa_indica_ CAGAAAATGAGTAGTTGGTGAACTCGCTTTATGTTGTTCGTTCACTCGCGACACGGTTCC O.glaberrima CAGGAACTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTCGCGACACGGTTCC O.rufipogon CAGGAACTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTCGCGACACGGTTCC O.nivara CAGGAACTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTCGCGACACGGTTCC *** ** ********************* ******************************* O.sativa_indica_ TGTCCCAAGACGGAGTCTGTGAATATACAAATGTGATTTTTTTAATA-CATTTTTACACC O.glaberrima TGTCCCAAGGCCGAGTTTGTGAATATACAAATGTGATTTTTTTAATA-CATTTTTACACC O.rufipogon TGTCCCAAGATCGAGTCTGTGAATATACAAATGTGATTTTTTTAATA-ATTTCTTACCCC O.nivara TGTCCCAAGACCGAGTCTGTGAATATACAAATGTGATTTTTTTTATAACTTTCTTACCCC ********* **** ************************** *** ** **** ** O.sativa_indica_ CACTCTTTTTTTCAAGTTCCAGCATCTGTTTGTGAATATGACCTATTCCTGCAAATTCAT O.glaberrima CACTCTTTTTTTCAAGTTCCAGCATCCGTTTGTGAATATGACCTACTCCTGCAAATTCAT O.rufipogon CCCCTTTTTTTTCAATTTCCACCATCCGTTTGTGAATATGACCTACTCCTGCAAATTCAT O.nivara CCTCTTTTTTTCCAGTTTCCACCTCCGTTTTGTGATAATGACCTACTCCTGCAAATTCTA * ****** ** ***** * * ******* ******** ************ O.sativa_indica_ AAACTCGGTGTTGCATATTTTTAGGCCCGGTCTTGTGGCAAGAACTGAGTAGTTTGTTAA O.glaberrima AAACTCGGTGTTGCATATTTTTAGGCCCGGTCTTGTGGCAAGAACTGAGTAGTTCGTTAA O.rufipogon AAACTCGGGGTTGCATATTCTTAGGCCCGGTCTTGGGGCAAAAACTGAGTATTTCTTTAA O.nivara AACCTCGTGTTTGCAAATTCTAAGGCCCGGTCTTGTGCCA-GAACTGAGTA-TTCGTTA- ** **** ***** *** * ************* * ** ********* ** *** O.sativa_indica_ CTCGCTACGCGGTTCTTGTCACAAGACCGAGTCTGTGAATATGCAAAGGTGGTTTTCTCT O.glaberrima CTCGCTACGCGGTTCTTGTCACAAGACCGAGTCTGTGAATATGCAAAGGTGGTTTTCTCT O.rufipogon CTCCCTACCCGGTTTTTGCCACAAAACCGAGCCTGTAAATATGCAAAGGTGGTTTTCTCT O.nivara CTCGCTACCCGGTTCTTGTCACAA-ACCGA-TCTGTGAATATGCAAAG-TGGTTT-CTCT *** **** ***** *** ***** ***** **** *********** ****** **** O.sativa_indica_ GTGAATATGACATATTCTAAATTCCTAT-------------TCTTTGTCAACTTTGTAAA O.glaberrima GTGAATATGACATATTCTAAATTCCTAT-------------TCTTTGTCAACTTTGTAAA O.rufipogon GTGAATATGACATATTCTAAATTCCTATCTGTCAACCTAATTCTTTGTCAACTTTGTAAA O.nivara GTGAATATGACATATTC-AAATTCCTAT-------------TCTTTGTCAACTTTG-AAA ***************** ********** *************** *** O.sativa_indica_ AATTGCTCCCGAATGATCTCTCTACTCCTTTATAT O.glaberrima AATTGCTCCCGAATGATCTCTCTACTCCTTTATAT O.rufipogon AATTGCTCCCGAATGATCTCTCTACTCCTTTATAT O.nivara AATTGCTCCCAAATGATCTCCT--CTCCTTTATAT ********** ********* *********** Cluster-IX O.glaberrima TAAACGTTCTGCTGGTTCCAACTGCGTGTTGTATATTCTTAGGGCCGGCCTTGAGGCAG- O.rufipogon TAAACGTTTTGCTGGTTCCAACTGCGTGTTGCATATTTTTAGGCCCGATCTTGAGGCAGG O.sativa_indica_ TAAA-GTTTTGGTGGTTCCAAATGGGTGTTGCATATTTTTAGGCCCGGTTTTGAGGCAGG O.nivara TAAACGTTTTGTTGGTTCCAATTGGGTGTTGAATATTTTTAGGCCCGTTTTTGGGGCAGG **** *** ** ********* ** ****** ***** ***** *** *** ***** O.glaberrima -ACTGAGTAGTTGGTGAACTCGCTCTATGTTGTTCGTTCACTCGCGACGCG-TTCCTGTC O.rufipogon AACTGAGTAGTTGGTGAACTCGCTTTATGTTGTTCGTTCACTCGTTACACGGTTCCTG-T O.sativa_indica_ AACTGAGTAGTTGGTGAACTCGCTTTATGTTGTTCATTCACTCGCGACACGGTTCCTGTC O.nivara AATTGAGTAGTTGGTGAACTCGTTTTATGTTGTTCGTTCACTCGGAACCGGGTTCCTGTC * ******************* * ********** ******** ** * ****** O.glaberrima CCAAGAACCGAGTCTGTGAATATACAAATGTGATTTTTTT-AATACATTCTTACACCCAC O.rufipogon CCCAAGATCGAGTCTGTGAATATACAAATGTGATTTTTTT-AATTCATTCCTACCCCCAC O.sativa_indica_ CCAAG-ACCGAGTCTGTGAATATACAAATGTGATTTTTTT-AATACATTCTTACACCCAC O.nivara CCAAG-ACCGAGTCTGTGAATATACAAATGTGATTTTTTTTAATACTTTCTTACACCCAC ** * * ******************************** *** * *** *** ***** O.glaberrima TCTTTTTTTCAAGTTCCAGCATCCGTTTGTGAATATGACTAACTACTA O.rufipogon TCCTTTTTTCAAGTTCCAACATCCGTTTGTGAATATGACCTACTACTG O.sativa_indica_ TCTTTTTTT-AAGTTCCAACATCCGTTTGTGAATATGACCTACTACTG O.nivara TCTTTTTTT-AAGTTCCAACATCCGTTTGTGAATATGACCTACTACTG ** ****** ******** ******************** ******