Highly Conserved (but not perfect) Genes. n = 34

Genes with no mismatches and conserved orthologs in mojavensis and virilis n = 3 (showing only valid orthologous sequences)


Color Code:    mir sequence   mir* sequence   predicted mir*   mutation

miR-285   chr3L:11920019-11920158
Species Sequence
dm2 TCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAG--GAGAACCCACTC-A---------ATT-TAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAA
Sim1 TCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAG--GAAAACCCACTC-A---------ATT-CAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAA
Sec1 TCAAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAG--GAAAACCCACTC-A---------ATT-CAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAA
Yak2 TCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAA--GACAACCCACTC-A---------ATT-CAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAA
Ere2 TCGAGTCGAAGAACTGAGATCGATTGGTGCATAGATATCAA--GAAGCCCCACTC-A---------ATT-CAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAA
Ana3 TCGAATCAAAGAACTGAGATCGATTGGTGCATAGATATCAA--GGAGATCCGATC-A---------TTT-CAATTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAC
dp4 TCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAA--GAGGACTCGCTA-A---------TTTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAAC
Wil1 TCGAATTAAAGAACTGAGATCGATTGGTGCATAGATAATAT--GCGAATTCTATC-ATTTGATTTCATT-CAATTCTAGCACCATTCGAAATCAGTGCTTTTGATTAGAAC
Vir3 TCAAATTGAAGAACTGAGATCGATTGGTGCATAGATATCGCCCAAAAAGTAATTC-A---------TTT-CAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTCGAAC
Moj3 TCAAATTGAAGAACTGAGATCGATTGGTGCATAGATAACGCCCAAAAAGTCATTTTA---------TTT-CAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTGGAAC
Gri2 TCAAATTGAAGAACTGAGATCGATTGGTGCATAGATATCGTCCAAGAA-TAATTTAA---------TTT-CAATTCTAGCACCATTCGAAATCAGTGCTTTGTATTGGAAC

miR-79   chr2L:16694462-16694599
Species Sequence
dm2 TGACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAG
Sec1 TGACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTGTGCAG
Yak2 TGCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTATACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAG
Ere2 TGCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAG
Ana3 TGCTTAACCGATGCTTTGGCGCTTTAGCTGTATGATAGATTTAAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCCGCAG
dp4 TGCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGC-TCTGTGG
Per1 TGCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGC-TCTGTGG
Wil1 GGTCTTGCCTATGCTTTGGCGCTTTAGCTGTATGATAGATTTG-ACTACTTCATAAAGCTAGATTACCAAAGCATGGGCTCTGGCTG
Vir3 CGCACTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTGAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGC-TCTGTGG
Moj3 CCCATTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAA-TACTTCATAAAGCTAGATTACCAAAGCATTGGC-TCTGTGG
Gri2 CACATTGCCGTCGCTTTGGCGCTTTAGCTGTATGATAGATTTGAA-TACTTCATAAAGCTAGATTACCAAAGCATCGGCGCCTGTGG

miR-9c   chr2L:16693832-16693964
Species Sequence
dm2 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Sec1 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Yak2 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Ere2 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Ana3 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
dp4 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Per1 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Wil1 TTTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Vir3 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT---TACAGTTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Moj3 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT---CACATATTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG
Gri2 ATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTC---TATATCTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTG

Genes with 1 mismatch and conserved orthologs in mojavensis and virilis. n = 7


miR-1   chr2L:20475013-20475144
Species Sequence
dm2 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TA-TATTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG
Sim1 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TA-TACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG
Sec1 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TA-TACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG
Yak2 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATA-TACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG
Ere2 CCTGTGAGAGTTCCATGCTTCCTTGCATTCAATAGT-TA-TACTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG
Ana3 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATA-ATATCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCA
dp4 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATA-ACATAAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCA
Per1 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATA-ACATAAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCA
Wil1 CTCTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATATTAAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGTC
Vir3 CCTTTGAGAGTTCCATGCTTCCTTACATTCAATAGTATT-CAAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG
Moj3 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATT-TATATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG
Gri2 CCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTATA-TAAATAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCG

miR-14   chr2R:5065554-5065657
Species Sequence
dm2 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Sim1 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Sec1 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Yak2 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Ere2 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Ana3 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
dp4 TGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Per1 TGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Wil1 TGCAACCTATGTGGGAGCGAGACGAGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Vir3 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Moj3 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGATTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG
Gri2 TGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGG

miR-252   chr3R:9289920-9290053
Species Sequence
dm2 AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGT
Sim1 AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGT
Sec1 AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGT
Yak2 AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGT
Ere2 AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGT
Ana3 GAAGTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGT
dp4 CGGTTTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCG-GT
Per1 CGGTTTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCG-GT
Wil1 AGATTTGCTTTACTAAGTACTAGTGCCGCAGGAGTTTGGTTCGTGTCCGTAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGACGACT
Vir3 ====TTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATTAAAGCGACTAGT
Moj3 ====TTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGGTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATCAAAGCGACGAGT
Gri2 ----TTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATTAAGGCGACGAAT

miR-281-2-3p   chr2R:7686039-7686171
Species Sequence
dm2 AATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT--A-AGA----CCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAA
Sim1 AATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAG----A-AAG----CATTTAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGA-
Sec1 AATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT--A-AGA----CCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAA
Yak2 AATAGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT--A-ATA----CCAATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAA
Ere2 AATTGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT--A-ATA----CCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAA
Ana3 AATAGTGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTTAAA-ACA----CGGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAACATTCGAA
dp4 AATAGTGAAATAAAGAGAGCTATCCGTCGACAGTCAAGTT--A-AT-----CAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAA
Per1 AATAGTGAAATAAAGAGAGCTATCCGTCGACAGTCAAGTT--A-AT-----CAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAA
Wil1 AATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCCAGTTT-A-ATACATCCGAATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAA
Vir3 AATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGCT--ATA------CAGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAA
Moj3 AATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT--ATATA----CATATTTTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAA
Gri2 AATAGCGAAATGAAGAGAGCTATCCGTCGACAGTCAAGTT--ATATA----CCGATTGTAATACTGTCATGGAATTGCTCTCTTTGTATAATATTCGAA

miR-305   chr2L:7425951-7426064
Species Sequence
dm2 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGT-CTCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGAT
Sim1 TCT--CCCATGTCTATTGTACTTCATCA-GTGCTCTGGTGTGT-CTCGTAACCCGGCACATGCTGAAGTACACTCAATATGAGGCGAT
Sec1 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGT-CTCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGAT
Yak2 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGG-CCCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGAT
Ere2 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGG-TCCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGAT
Ana3 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCC-ACCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGAA
dp4 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGT-CCTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAA
Per1 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGT-CCTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAA
Wil1 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCCGTTTGTAACCCGGCACATGTTGAAGTACACTCAATATGTGGCGAT
Vir3 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGA-CTTGTAACCCGGCACATGTTGAAGTACACTCAATATGCGTTGAT
Moj3 TCTCCCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCA-GTGGAAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGAT
Gri2 TCT--CCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCA-CTCGTAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGAT

miR-308   chr2R:9730644-9730747
Species Sequence
dm2 GTCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTT-GCAATCCAAATCACAGGATTATACTGTGAGATGACCAGCG--------TG
Sim1 GTCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTT-GCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCG--------TG
Sec1 GTCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTT-GCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCG--------TG
Yak2 GTCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCCTTTT-GCAACTCAAATCACAGGATTATACTGTGAGATGACCAGCG--------TG
Ere2 GTCTCGACGCCTCGCAGTATATTTTTGTGTTTTGTTTCGTTTT-GCAAATCAAATCACAGGATTATACTGTGAGATGACCAGCG--------TG
Ana3 GTCTCGTCGCCTCGCAGTATATTTTTGTGTTTTGTTT-GGTTT-GAAACTCAAATCACAGGATTATACTGTGAGATGCCAAGCG--------TG
dp4 GTCTTGACGCCTCGCAGTATATTTTTGTGTTTTGTTGTG-TCT-GAAACGCAAATCACAGGATTATACTGTGAGATGCTGGGCG--------TG
Per1 GTCTTGACGCCTCGCAGTATATTTTTGTGTTTTGTTGTG-TCT-GAAACGCAAATCACAGGATTATACTGTGAGATGCTGGGCG--------TG
Wil1 ATTCTTGCGTCTCGCAGTATATTTTTGTGTTTTGTTCAATTTG-TCAACTCAAATCACAGGATTATACTGTGAGCTGCGAAATGGAAATCCACG
Vir3 --TTCGATGTCTCGCAGTATACTTTTGTGTTTTGTTT-ATTTT-GAAAATCAAATCACAGGATTATACTGTGAGTTATCGGCTG--------TA
Moj3 --TTCGATGTCTCGCAGTATATTTTTGTGTTTTGTTT-ATTAT-AAAAATCAAATCACAGGATTATACTGTGAGTTATCGGCTG--------AA
Gri2 --GTCGATGTCTCGCAGTATATTTTTGTGTTTTGTTT-ATTTTTGAAAATCAAATCACAGGATTATACTGTGAGTTATCGCCAG--------CA

miR-92a   chr3R:21472207-21472342
Species Sequence
dm2 TGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTA
Sim1 TGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTA
Sec1 TGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTA
Yak2 TGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTTGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTA
Ere2 TGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAAT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTA
Ana3 CAAATTTCCCGTAGGACGGGAAGGTGTCAAGGTTTTGAA-TTAAATT-AAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTC
dp4 GAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTAAATTTTGAAC-AAACATTGCACTTGTCCCGGCCTATGGGCGGCTTGTC
Per1 GAGATTGCCCGTAGGACGGGAAGGTGTCAACGTTTTACATTTTGAAC-AAACATTGCACTTGTCCCGGCCTATGGGCGGCTTGTC
Wil1 CAAATTTCTCGTAGGACGGGAAGGTGTCAACGTTTTGCCTTATGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTA
Vir3 CAAACTGCTTGCAGGACGGGAAGGTGTCAACGTTTTGCTTTATGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTG
Moj3 TAAATTGCTTGCAGGACGGGAAGGTGTCAACGTTTTACCTTTTGATTCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTATC
Gri2 TAAATTGCTTGCAGGACGGGAAGGTGTCAACGTTTTGCATTTTGAATCAAACATTGCACTTGTCCCGGCCTATGAGCGGTTTGTG


Genes with 2 mismatch and conserved orthologs in mojavensis and virilis. n = 6


miR-133   chr2L:20604189-20604327
Species Sequence
dm2 AAC-ACTGTGTGTAGCTGGTTGACATCGGGTCAGATCTG-TT-TTTCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTG
Sim1 AAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTG-TT-TTTTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTG
Sec1 AAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTG-TT-TTTTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTG
Yak2 AAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-TTCCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTG
Ere2 AAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTG-TT-TTCCTAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTG
Ana3 AAC-GCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATCT-TTTCAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTG
dp4 AACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-TATCAAGTATTTGGTCCCCTTCAACCAGCTGTAT-CAGTGGTTG
Per1 AACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-TATCAAGTATTTGGTCCCCTTCAACCAGCTGTAT-CAGTGGTTG
Wil1 AAC-ACTGAATGTAGCTGGTTGACATCGGGTCAGATCTATTTATTTGAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTG
Vir3 AAC-GCTGTGTGTAGTTGGTTGACATCGGGTCAGATCTATTT-CTGAAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTG
Moj3 AAC-GCTGTGTGTAGTTGGTTGACATCGGGTCAGATCTGTTT-TT-CGAGAATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTG
Gri2 AAC-GCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-ATTCGAGTATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTG

miR-283   chrX:15341872-15342012
Species Sequence
dm2 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Sim1 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Sec1 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Yak2 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Ere2 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Ana3 ATTCTTAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTATGCCTGATTA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTCGAATTG
dp4 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCA-AGATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Per1 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCA-AGATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Wil1 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTATGCCTAGATATTTGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Vir3 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG
Moj3 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCCC-AATA--TGAAACACTCGGAATTTCAGTTGGTATATACTTTTTTGAATTG
Gri2 ATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCCA-AATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTG

miR-284   chr3R:8377216-8377356
Species Sequence
dm2 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGG-CAAGGCTTGAATAATGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGA
Sim1 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGG-CAAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGA
Sec1 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGG-CAAGGCTTGAATACTGCTCCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCGA
Yak2 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGG-CAAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAA
Ere2 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGG-CAAGGCTTGAGTACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAA
Ana3 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTGAGGG-CAAGGCTTGAGAACTGCTTCAGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAA
dp4 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGG-CAAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAA
Per1 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGGGAAGG-CAAGGCTTGAGCACTGCTTCTGAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAA
Wil1 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTTAGGGGAAAGGCTTGAGCATTGCATACTAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAA
Vir3 TGCGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAAGG-GAAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCCCAA
Moj3 TGCGTTGCAGTTCCTGGAATAAAGTTGACTGTGTCGCCTGTAAGGG-GAAGGCTTTTGCATTGCTTACAAAGTCAGCAACTTGATTCCAGCAACTGCGGCCCAA
Gri2 TGGGTTGCAGTTCCTGGAATTAAGTTGACTGTGTAGCCTGTAAGAG-GAAGGCTTGTGCACTGCTTACAAAGTCAGCAACTTGATTCCAGCAATTGCGGCTCAA

miR-304   chrX:15342875-15343003
Species Sequence
dm2 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TAAG-CCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGC
Sim1 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAG-CCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGC
Sec1 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAG-CCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGC
Yak2 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAG-CCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGC
Ere2 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAG-CCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGC
Ana3 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATT-TGAG-CCATTTGACGGACTCACTTTGCAACTGGAGATTGCTCGAGACTGCGGC
dp4 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATT-TGAG-GCATTTGACACACTCACTTTGCAACTGGAGATTGCTCGAAACTGCGGC
Wil1 TGTAACATTGATTAATCTCAATTTGTAAATGTGAGCGATT-TAAATCCATTCGATGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGC
Vir3 TGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTAAA-GTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGC
Moj3 TGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTTAA-CTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCAGC
Gri2 TGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATTATTAA-GAATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGC

miR-316   chr3L:21602534-21602663
Species Sequence
dm2 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCAATTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
Sim1 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
Sec1 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
Yak2 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCAACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
Ere2 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCAACAACGACAGGAAAGGGAAAAAGGCGTATTCACTATGAGT
Ana3 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTAATTCAAACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
dp4 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTCGATCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
Per1 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTCGATCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
Wil1 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTTAACTAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGT
Vir3 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATT-GAGCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAAT
Moj3 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGACGTTTTATT-GAACAACGGCAGGGAAGGGAAAAAGGCGTATTTACTATGAAT
Gri2 TTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATT-GAGCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAAT

miR-7   chr2R:16120909-16121037
Species Sequence
dm2 GTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTT
Sim1 GTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTT
Sec1 GTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTT
Yak2 GTGCATTTCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTT
Ere2 GTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTT
Ana3 GTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTTTATGGTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTC
dp4 GTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCT
Per1 GTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCT
Wil1 ATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTAATAAAATTAACAATAAATCCCTTGTCTTCTTATGGCGTGTATTT
Vir3 ATGCTTTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTATGGCGCGCAT-T
Moj3 GTGCTTGCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTAA---TAACAATAAATCCCTTGTCTTCTTATGGCTCGCAT-T
Gri2 ATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGTTAA---TAACAATAAATCCCTTGTCTCCTAACGGCGCGCAT-T


Genes with 3 mismatch and conserved orthologs in mojavensis and virilis. n = 2


miR-275   chr2L:7425774-7425912
Species Sequence
dm2 TCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTTTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGC-AGA
Sim1 TCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTTTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGC-AGA
Sec1 TCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTTGTTTTTTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGC-AGA
Yak2 TCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTTTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGCC-AGA
Ere2 TCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTTTATAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGCC-AGA
Ana3 TCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTT--GCA---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGC-AGA
dp4 TCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTTTTCACT---GCAGTCAGGTACCTGAAGTAGCGCGCGTGGTGCT-AGA
Per1 TCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTTTTCACT---GCAGTCAGGTACCTGAAGTAGCGCGCGTGGTGCT-AGA
Wil1 TCTCTTACCTTGCGCGCTAATCAGTGACCAGGGCTGATTTATTCAAT---ACAGTCAGGTACCTGAAGTAGCGCGCGTGGTTTT-AGA
Vir3 TCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTTGGTTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGA
Moj3 TCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTCGATTATCTCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCTAGA
Gri2 TCGTTTACCGCGCGCGCTAATCAGTGACCGGGGCTGGTTTTGATTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGA

miR-317   chr3R:5916827-5916959
Species Sequence
dm2 TGCAACTGCCATTGGGATA-CACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCG--TTTG
Sim1 TGCAACTGCCATTGGGATA-CACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCG--TTTG
Sec1 TGCAACTGCCATTGGGATA-CACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCG--TTTG
Yak2 TGCAACTGCCATTGGGATA-CACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCG--TTTG
Ere2 TGCAACTGCCATTGGGATA-CACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCG--TTTG
Ana3 TGCATCGGCTGCTGGGATA-CACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCG--TTTT
dp4 TGCAACTGCCGTTGGGATA-CACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCG--TTCT
Per1 TGCAACTGCCGTTGGGATA-CACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCG--TTCT
Wil1 TGCAACTGCCACTGGGATA-CACCCTGTGCTCGCTTTGAATATTGTGCAAACAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTTTT
Vir3 TGCAATTGCCGCTGGGATA-CACCCTGTGCTCGCTTTGA--ATTGTGCAAGCAAGTGAACACAGCTGGTggtatccagtggccg--ttgg
Moj3 TGCAATTGCCGCTGGGATA-CACCCTGTGCTCGCTTTGA--GTTTATGTTGCAAGTGAACACAGCTGGTGGTATCCAGAGGCCG--TTGA
Gri2 TGCAATTGCCACTGGGATATTGCCCTGTGCTCGCTTTGAATATTGTGTAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCG--TTTG


Genes with 4 mismatch and conserved orthologs in mojavensis and virilis. n = 5


miR-12   chrX:15343389-15343503
Species Sequence
dm2 CGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATC
Sim1 CGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATC
Sec1 CGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATC
Ere2 CGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAAACCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATC
Ana3 CGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACCGATC
dp4 CGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATC
Per1 CGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATC
Wil1 CGCCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATC
Vir3 cGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGC
Moj3 CGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCAATTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGC
Gri2 CGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACCAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGC

miR-124   chr2L:17562278-17562418
Species Sequence
dm2 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCA
Sim1 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCA
Sec1 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCA
Yak2 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCA
Ere2 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCA
Ana3 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAA
dp4 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAA
Per1 CGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAA
Wil1 CGTTTTTCTCCTGGTATCCACTGCAGGCCTATATGTTATTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAA
Vir3 CGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAA
Moj3 CGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAA
Gri2 CGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGTTTTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAA

miR-278   chr2R:11171908-11172046
Species Sequence
dm2 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCATTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Sim1 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Sec1 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Yak2 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Ere2 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Ana3 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTCGAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
dp4 GGTACGGTGCGACCGGACGATGGTTCACAACGACCGTG---TCTCTTAAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Per1 GGTACGGTGCGACCGGACGATGGTTCACAACGACCGTG---TCTCTTAAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Wil1 GGTACGGTGCGACCGGATGACGGTTCACAACGACCGTG---TCAATTTTACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Vir3 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTGCA-TACTTTTAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Moj3 GGTACGGTGCGACCGGATGATGGTTCACAACGACCGTACAGTTTTTTCAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT
Gri2 GGTACGGTGCGACCGGATGACGGTTCACAACGACCGTGCT-TATTTTTAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTT

miR-282   chr3L:3234533-3234670
Species Sequence
dm2 TCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAA--AG-CCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCG
Sim1 TCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAA--AG-CCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCG
Sec1 TCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAA--AG-CCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTG
Yak2 TCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATACGAA--AG-CCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTG
Ere2 TCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCAAA--AG-CCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCG
Ana3 TCCTTATAGATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAA--AG-TCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCG
dp4 GCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTGAA--AACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAA
Per1 GCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTGAA--AACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAA
Wil1 TCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTGGA--TT------CAGACATAGCCTATGAGAGGTTAGGTGTACCAAGGAG
Vir3 TCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCGAT--AT-ACGGTCAGACATAGCCTATGAGAGGTTAGGTGTACCAAGGGG
Moj3 TCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTGAT--AT-AAGATCAGACATAGCCTATGAGAGGTTAGGTGTAGCAAGGGG
Gri2 TCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCACTTTTTCAAT-TCAATCAGACATAGCCTATGAGAGGTTAGGTGTACAAATGGA

miR-957   chr3L:22452016-22452152
Species Sequence
dm2 TCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAG---TT-CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGC
Sim1 TCCACAATAGACCTTAATTTTCGACGTGTTTTGGTGTGCTGGGGAG---TT-CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGC
Sec1 TCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAG---TT-CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGC
Yak2 TCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAG---TT-ATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGC
Ere2 TCCACAATAGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAG---TT-CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGC
Ana3 CCTACAATGGCCCTTAGTTTTCGACGTGTTTTGGTGTGCAGGGGAG---TT-CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GAGGC
dp4 TCCACAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAG---TTGATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GCGGC
Per1 TCCACAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTGGGGAG---TTGATATTCCGATTGAAACCGTCCAAAACTGAGGCCAACTGT-GCGGC
Wil1 TCCGCAATGGACCTTAGTTTTCGACGTGTTTTGGTGTGCTTAGGAAGTTTT-CTATTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGTTGTGAT
Vir3 CCCACAATGGTTCTTAGTTTTAGACGTGTTTTGGTGTGCTTGA-AG---TT-TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCGATTGT-GAGGT
Moj3 CCCACAATGGATCTTAGTTTTAGACGTGTTTTGGTGTGCTTGGGAG---TT-TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGT-GAGGC
Gri2 CCCACAATGGATCTTAGTTTTAGACGTGTTTTGGTGTGCTTGGGAG---TT-TTGTTCCGATTGAAACCGTCCAAAACTGAGGCCAATTGT-GTGGT


Genes with mismatches in 1 or 2 positions and conserved orthologs in mojavensis and virilis. n = 11


miR-965   chr2L:243014-243161
Species Sequence
dm2 TCA----ACA-TTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCTGT-GATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGC
Sim1 TCA----ACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTGT-GAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGC
Sec1 TCA----ACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTGT-GAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGC
Yak2 TCA----ACA-TTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTTTGT-AAA-TTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGC
Ere2 TCA----ACA-TTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCTGT-AAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGC
Ana3 TCA----ACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCTTA-GAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGC
dp4 TCA----AAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATTC-GAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGC
Per1 TCA----AAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATTC-GAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGC
Wil1 ACA----ACA--TTTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGT
Vir3 ACACACAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAATG-AT-GAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGT
Moj3 TCA----AAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGTAAACA-AT-GAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGT
Gri2 TCA----AAT-GTTTAGGGGGTCAAACTGTACGTTATATGTGTAAATG-AA-GAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGT

miR-927   chrX:15799863-15799995
Species Sequence
dm2 TTGCTG-TAGAGTTTTAGAATTCCTACGCTTTACCGTGGCATA-CGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTACCGATCCA
Sim1 ATGCTG-TAGAGTTTTAGAATTCCTACGCTTTACCGTGGCATA-CGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATCGATCCA
Sec1 ATGCTG-TAGAGTTTTAGAATTCCTACGCTTTACCGTCGCATA-CGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATCGATCCA
Yak2 GCGCTG-TAGAGTTTTAGAATTCCTACGCTTTACCGTCGCATA-CGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTACCGATCCA
Ere2 GTGCTG-CAGAGTTTTAGAATTCCTACGCTTTACCGTGGCATA-CGAAATTCGGCAAAGCGTTTGGATTCTGAAACTCTACCGATCCA
Ana3 GTATTG-TGGAGTTTTAGAATTCCTACGCTTTACCGTTGCATA-TGAAATTAGGCAAAGCGTTTGGATTCTGGAACCCTATGTATTCA
dp4 ATATTG-TAGTGTTTTAGAATTCCTACGCTTTACCGTTGCAAAACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATGAGTCTG
Per1 ATATTG-TAGTGTTTTAGAATTCCTACGCTTTACCGTTGCAAAACGAAATTCGGCAAAGCGTTTGGATTCTGAAACCCTATGAGTCTG
Wil1 ACATTGGTAGCGTTTTAGAATTCCTACGCTTTACCGTCGCCTA-CGAAACTCGGCAAAGCGTTTGGATTCTGAAAC============
Vir3 CCATCG-TATCGTTTTAGAATTCCTACGCTTTACCGTCGTGTC-CGAAATTTGGCAAAGCGTTTGGATTCTGAAACGATAT-------
Gri2 CTATTG-TATTGTTTTAGAATTCCTACGCTTTACCGTCGTATA-CGAAATTTGGCAAAGCGTTTGGATTCTGAAACGGTAT-------

miR-988   chr2R:7674758-7674897
Species Sequence
dm2 GGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGATCT
Sim1 GGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGATCT
Sec1 GGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGATGATCT
Yak2 GGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGGTGACCT
Ere2 GGCATTTTGGGTGTGTGATTTGTAGCAAAGTGATATGTATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--GAAGGTGACCT
Ana3 GACATTTTGGGTGTGTGATTTGTGGCAAAGTGATAGGTATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--CAAGGTGCTTT
dp4 GACATTTTGGGTGTGTGATTTGTGGCAAAGTGATATGCATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGTTGA-AT
Per1 GACATTTTGGGTGTGTGATTTGTGGCAAAGTGATATGCATTTGAT--CATCCCCTTGTTGCAAACCTCACGCC--AAAGTTGA-AT
Wil1 GGCATTTCGGGCGTGTGATTTGTAGCAAAGTGATATGTACTTGAT--AATCCCCTTGTTGCAAACCTCACGCCGGAAAGATGT-CT
Vir3 CGCATTTTGGGCGTGTGATTTGTGGCAAAGTGATGAGC-TTGGATTCCATCCCCTTGTTGCAAACCTCACGCC--AAAGGTGGCGC
Moj3 CGCATTTTGGTCGTGTGATTTGTGGCAAAGTGATGAGC-TATGATTCCATCCCCTTGTTGCAAACCTCACGCT--GAAGGTGACGC
Gri2 TGCATTTTGGGCGTGTGATTTGTGGCAAAGTGATGAGC-T-TGATTCCATCCCCTTGTTGCAAACCTCACGCC--GAAGGTGGCGC

miR-989   chr2R:9661237-9661451
Species Sequence
dm2 ATTTTGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACACAGGTGACACTGAT--CC-----GGATTTGGTAGT-TGACAA-----ATCCTCCATGCC-GAGATTAGTTTCATTTTGCGTCTTTTGAATTCGA------ATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATT
Sim1 ATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACACTGGTGACACTGAT--CC-----GGATTTGGTAGT-TGACAA-----ATCCTCCATGCC-GAGATAAGTTTCATTTTGCGTCTTTTGAATTCGA------ATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATT
Sec1 ATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACACTGGTGACACTGAT--CC-----GGATTTGGTAGT-TGACAA-----ATCCTCCTTGCC-GAGATTAGTTTCATTTTGCGTCTTTTGAATTCGA------ATAGTTCATGTGATGTGACGTAGTGGAACATACCCGAAATT
Yak2 ATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACACAGGTGACACTGAT--CC-----GGATTTGGTGGT-GGACCC-----ATTCTC-ATTCC-GAGATTAGTTTTATTTTGCGTCTTTTGAATTCGA------ATAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTT
Ere2 ATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACCCAGGTGACACTGAT--CC-----GGATTTGGTAGTCGTACAA-----ATCCTCCATTCC-GAGTTAAGTTTCATTCTGCGTCTTTTGAATTCGA------ACAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTT
Ana3 GTTTCGGGAAGTGGCCACTACCTCGCAGTCACGTGATGCCAAAATGCAACTGACACTGAT--CC-----GGA---GATGGT--------------CCTCCATCCTTGGGATTAGTGTTAATTTGTGTTTTTTTTATTTGA------ATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTT
dp4 GTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGAT---------------------AT--CG-----GAATGCAATGAT----------------------CT-ACGTTAAAT-------TGTGTTTCTT---TTTGA------ATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTT
Per1 GTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGAT---------------------AT--CG-----GAATGCAATGAT----------------------CT-ACGTTAAAT-------TGTGTTTCTT---TTTGA------ATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTT
Wil1 GTTTTGGGAATTGGCCACTACCTCGCAGTCACGTGATGAGAGA-----------------------------------GAT----------------------GC-AAGAGGACT----TTGTATGCCATTTGCATTTAATATTTCATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGAGCTT
Vir3 GATTCGGGAATTGGCCACTACCTCGCAGTCACGTGATCCACAAACGCAGCCGGCTCTGGTGCTTGGGAAAAATACAATTTT-CTTTT------GTTTTC----CT-GGGCG----------CCGCAACGTTTTGCGTTCA--TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTT
Moj3 GATTCGGGAATTGGCCACTACCTCGCACTCACGTGATGCACTCAAAACGCCGACGAGGACGTCC-----AAATTCCATTTT-CTC--------GTTTTC----CT-CTGT-----------------CGTTTTGCGTTGA--TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTT
Gri2 GTTCCGGGAATTGGCCACTACCTCGCAGTCACGTGATGC---CACAAGGCGGGCACG-----CCGTGCAACATCCTCTCTT-CGTTTACACATCTCCTC----TT-GAGAGGA--------TTGCGTCGTTCCGCCTTGA-ATTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTT

miR-999   chr3R:17623928-17624073
Species Sequence
dm2 TCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCA
Sim1 TCAATTACCCCGACATAGTCGTACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCA
Sec1 TCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCA
Yak2 TCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCA
Ere2 TCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCA
Ana3 TCAATTACCCCGACATAGTCGTACGGTGAATGTTGTGTATTGGAAAGCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTgcca
dp4 =============CATAGTCGTACGGTGAATGTTGTGTATTGGA--CCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTCA
Per1 TCAATTACCATGACATAGTCGTACGGTGAATGTTGTGTATTGGA--CCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTCA
Wil1 TCAATTACCATGACATAGTCGTACGGTGAATGTTGTTTAT-GGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCA
Vir3 TCAATTACCGTGACATAGTCGTACGGTGAATGTTGTGTAT-GGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTTA
Moj3 TCAATTACCGTGACATAGTCGTACGGTGAATGTTGTTTAT-GGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGC-A
Gri2 TCAATTACCATGACATAGTCGTACGGTGAATGTTGTGTTT-GGAGTCCAATGTTAACTGTAAGACTGTGTCTTGGTGGTTGCCA

miR-1000   chr3R:21414560-21414700
Species Sequence
dm2 CGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATTATA--GTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTC
Sim1 CGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTTACACTATATTATA--GTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTC
Sec1 CGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATTATA--GTTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTC
Yak2 CGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATTATA--GCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTC
Ere2 CGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAACACTATATTATA--GCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTC
Ana3 CGCTTGCCGATGATATTGTCCTGTCACAGCAGTATTGTAATTCTATACTATATAGCTTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGTC
dp4 CGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAA--CTTAATTATA--GCCTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGCC
Per1 CGCTTGCCATTGATATTGTCCTGTCACAGCAGTATTGTAA--CTTAATTATA--GCCTACTGCTGGGTCGGGGCATTAACATTGTTGAGCGCC
Wil1 -GCTTGCCAGTGATATTGTCCTGTCACAGCAGTATAGTAA--CATATTCATT--TCGTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTC
Vir3 CGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTAC-GTTAAGCAATT--G-GTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTC
Moj3 CGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTAA-ATTAAGCAATT--G-GTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTC
Gri2 CGCTTGCCAGTGATATTGTCCTGTCACAGCAGTATTGTTA-ATTAAGCAATT--G-GTACTGCTGAGCCGGGGCATTAACATTGTTGAGCGTT

miR-184   chr2R:8845288-8845428
Species Sequence
dm2 GTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCACTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Sim1 GTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Sec1 GTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Yak2 GTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATT-GAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Ere2 GTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCATTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Ana3 GTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATAATGAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
dp4 GTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATTAAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Per1 GTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATTAAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Wil1 GTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Vir3 GTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Moj3 GTGCATTCGTACCCTTATCATTCTCGCGCCCCGTGTGCATATCTATACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA
Gri2 GTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGGATAACTATACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAA

miR-263b   chr3L:15808644-15808774
Species Sequence
dm2 CTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTT-AT----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCGGC
Sim1 CTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTG-AT----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCGGC
Sec1 CTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTG-AT----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCGGC
Yak2 CTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTT-AT----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACGGC
Ere2 --GACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGATTTT-AT----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACAGC
Ana3 CTGTCTTTGAATCTTGGCACTGGGAGAATTCACAGTTGATTTT-AT----TATTCTGTGGTTCTGCGGGTGCC-AAAATTGAAATAATGGC
dp4 CTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTCCAT---ATATTCTGTGGTTCTGCGGGTGCC-AAAATCGAATGTTCGGC
Per1 CTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTTCAT---ATATTCTGTGGTTCTGCGGGTGCCCAAAATCGAATGTTCGGC
Wil1 CTCACAATGCATCTTGGCACTGGGAGAATTCACAGTTGATTCTTATTCGATATTCTGTGGTTCTGCGGGTGCC-AAAATCTAATGTTTGAG
Vir3 CTGCCATTTCATCTTGGCACTGGGAGAATTCACAGTCGATTAC-AT--AATATTCTGTGGTTCTGCGGGTGCC-AAAATGTAATGTG----
Gri2 CTGCCATTACATCTTGGCACTGGGAGAATTCACAGTTGGTTAT-AT--AATATTCTGTGGTTCTGCGGGTGCC-AAACTGTAATGTG----

miR-274   chr3L:11630844-11630984
Species Sequence
dm2 TTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGCCG------------C-CAGGA----------------T--TACTCGTTTTTGCGATCACAAATTATGAAATTGCAGC
Sec1 TTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGATCA------------C-CAGGA----------------T--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGC
Yak2 TTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGTCG------------C-CAGGA----------------T--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGC
Ere2 TTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGCCG------------C-CAGGA----------------T--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGC
Ana3 TTGCAGTTTCGTTTTGTGACCGACACTAACGGGTATTTTACAGGACA------------TACAGGA----------------T--TACTCGTTTTTGCGATCACAAATCCTGAAATTGCAGC
dp4 CTGCAGTTTCATTTTGTGACCGACACTAACGGGTAA-TGGCTGGCCG--------------CAGGA----------------C--TACTCGTTTTTGCGATCAC-AATACTGAAATTGCAGC
Per1 CTGCAGTTTCATTTTGTGACCGACACTAACGGGTAA-TGGCTGGCCG--------------CAGGA----------------C--TACTCGTTTTTGCGATCAC-AATACTGAAATTGCAGC
Wil1 TTGCAGTTTCATTTTGTGACCGACACTAACGGGTAG-TAACGGGTTA------------A-CAAAGTCGTTTTTCTGGCCTTT--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAGC
Vir3 TTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTT---GGGGCA-CCTCGAATAC-G-CTGTT----------------T--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAAC
Moj3 TTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTT---GAGGCA-TCTCGTATTC-G-CTGTT----------------TTATACTCGTTTTTGCGATCACAAATTCTGAAATTGCAAC
Gri2 TTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTAA-AGGGCATCCTCGCATTCTG-CTGGC----------------T--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAAC

miR-33   chr3L:19731783-19731922
Species Sequence
dm2 GATGACACGAAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCCAA---TTG-C--TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCA
Sim1 GATGACACGAAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCCAA---TTG-C--TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCA
Sec1 GATGACACGAAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCCAA---TTG-C--TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCA
Yak2 GATGTCACGAAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCCAA---TTG-C--TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCA
Ere2 GATGACACGAAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCCAA---TTG-C--TTCAGGCAATACAACTTCAGTGCAAGCTCTGTGCATTTCA
Ana3 GATGTCACGCAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCCAC---TTG-C--TCCAGGCAATACAACTGCAGTGCAAGCTCTGTGCATTTCA
dp4 GATGACACGCAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCATC---TTGAT--TTCAGGCAATACAACTGCAATGCAAGCTCTGTGCATTTCA
Per1 GATGACACGCAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCATC---TTGAT--TTCAGGCAATACAACTGCAGTGCAAGCTCTGTGCATTTCA
Wil1 AGTTACACGAAGGTGCATTGTAGTCGCATTGTCTGTGCTCCAAAAAAAAAAAACCCCCAG---TTT-CTATTCAGGCAATACAACTGCAGTGCAAGCTTCGTGTGACTTA
Vir3 GCTGTTACGGAGGTGCATTGTAGTCGCATTGTCTGT-------------------CTCAAAT-TTG-C--CCGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCA
Moj3 GCTGTGACGGAGGTGCATTGTAGTCGCATTGTCTGT-------------------ATCCTTTATTC-T--CTGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCA
Gri2 GCTGTCACGAAGGTGCATTGTAGTCGCATTGTCTGT-------------------CCAAAAA-TTG-C--ATGCGGCAATACAACTGCAGTGCAAGCTCCGTGCAGTTCA

miR-956   chr3L:11747677-11747825
Species Sequence
dm2 CTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCACTGGCCC---------------------AAATGCAGTTTGCC---------------CGGAGACGCCGGT--------------------TAACCCAGC--------------ACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCA
Sim1 CTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCACTGGCCC---------------------AAATGCAGTTTGCC---------------CGGAGACGCCGGT--------------------TGCCCAAGC--------------ACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCC
Sec1 CTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCACTGGCCC---------------------AAATGCAGTTTGCC---------------CGGAGACGCCGGT--------------------TGCCCAAGC--------------ACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCC
Yak2 CTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCACTGGCCC---------------------AAATGCAGTTTGCC---------------CGGAGGAGCCGGT--------------------TTACCCAGC--------------ACTCAAGTGTGTAGTTTCGAGACCACTCTAATCCATTGCACCATTTTCC
Ere2 CTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCTAGTGCTCG-GCTCACCGGCCC---------------------AAATGCAGTTTGCC---------------CGGAGATGCCGGT--------------------TTCCTCAGC--------------ACTCAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCC
Ana3 TAGATCGTTATCGCGTTTGGAATGGTCTCGTTAGCTAACGAATGGACTA-----------------------------------------AAATGCAATTTGCA---------------ATTCGGCGCCAAT--------------------TATCCAGGC--------------GCCAAAAAGTTTAGTTTCGAGACCACTCTAATCCATTGCATGATCTTCA
dp4 CTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAACTGCTTGCGCGCATTGGCC----------------------AAATGCATTTCGCA---------------CCGGGATGGATGTGGATGTGGCTGGATGTGGTGTCCCCAAGC--------------ACAGCCAGGTGTAGTTTCGAGACCACTCTAATCCATTGCACCGCCCACC
Per1 CTGATCGT========================================================================================================================================================================================================================
Wil1 CTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAACAAGTGCTTGGGGCAATTGAGCCAAAAACAAAACAGAAAAAAGAAAATGCACTTTGCCATCAAAACGAATGTGCGAATATGCAATT--------------------TGGCCAGGCTCCTCGAACATAACACTAAGAGGTGTAGTTTCGAGACCACTCTAATCCATTGCCACATTTTTC
Vir3 ACGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAAC--------------ATTGACCA---------------------AAGCGCACCTTACA--------------------------GC---------------------------GT--------------A-------GTGTAGTTTCGAGACCACTCTAATCCATTGCATCGTTTCTG
Moj3 ACGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAAC--------------ATTAACCA---------------------AAGCGCACCTTACG--------------------------GC---------------------------GT--------------A-------GTGTAGTTTCGAGACCACTCTAATCCATTGCACCGTTTCTT
Gri2 GCGATCGTTATCGCGTTTGGAATGGTCTCGTTAGCTAAC----------------------------CA---------------------AAGCGCTCGTTACA--------------------------GC---------------------------GT--------------A-------GTGTAGTTTCGAGACCACTCTAATCCATTCCATCGCTTTTC