CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroAna_CAF1_left   TTGGGATATTTAT-GTATTTATTTCCATATTTTTAATTGTTTTAAGTGCT-TTATTGCCAGGC-TTGCAGTTTTG----TT-TTGTAAAAA-GAACA---A--AAAATCGTTCTGGAGAT
DroEre_CAF1_left   AATTTATGTATTTATTTTGAGGATTTTAATTGTTTTAAGTGTTTGACTGC-CAAGAGTTTGT--AGTTGC--TTT----TT-GAGATATAC-CAAAA---ATAAAACGTAGTTTGGAGAT
DroGri_CAF1_left   TGTTTTGTTTGCGTTTCA-TTCATTACTATTTTTCCACTACTTTTGCAACCAAA-AATATTA--GGAAAA--AAC----TCGTGAATAAAA-AAGTT---GGTTTTATCCTTTTGGAGAT
DroMel_CAF1_left   AATTTATGTATTTATTTTCAGGATTTTAATTGTTTTATGTGTTTGACTGC-CAAGAGTTTGT--ATTTGG--TTT----TT-TAAATATAC-AAAAA---AGAAAACGTAGTTTGGAGAT
DroPer_CAF1_left   GTATTTATTTCCAGATTTTTAATTGT-TTTAAGTGTTTTGTTTTGCAAAG-TTGCTGTTTGC--AT--GT--TTC----GC-AAAAAAGTT-AGTGGACAAATACACCACTATTGGAGAT
DroPse_CAF1_left   GTATTTATTTCTAGATTTTTAATTGT-TTTAAGTGTTTTGTTTTGCAAAG-TTGCTGTTTGC--AT--GT--TTC----GC-AAAAAAGTT-AGTGGACAAATACACCACTATTGGAGAT
DroSec_CAF1_left   TTTAT--GTATTTATTTTCAGGATTTTAATTGTTTTAAGTGTTTGACTGT-CAAGAGTTTGTTTAGTTGG--TTT----TT-GAAATATAC-AAAAA---AGAAAAAGTAGGTTGGAGAT
DroSim_CAF1_left   AATTTATGTATTTATGTTCAGGATTTTAATTGTTTTAAGTGTTTGACTGC-CAAGAGTTTGT--AGTTGG--TTT----TT-GAAATGTAC-AAAAA---AGAAAACGTAGGTTGGAGAT
DroVir_CAF1_left   TGTTTTAAGTGTTTTGTTATGTTGTGGATGTTTTCTTTTTATT-ATTATT-TTTCAATACTG--ACAGAA--AGA----AG-AAATAAAAAAAAAAC---AGAAGTTTATCCTTGGAGAT
DroWil_CAF1_left   AACTATCTGACTGAAAAATGTATGTAAAATGAATCTTAGGAATGCGTAGG-AAAAAAAATTA--AGGAGA--AGG----GG-TTCCTTTAA-ACCCT---CTTCCTCTTTATTTGGAGAT
DroYak_CAF1_left   AATTTATGTATGTATTTTCAGGATTTTAATTGTTTTAAGTGTTTTACTGC-CAAGAGTTTGT--AGTTAG--TTT----TT-GAAATATAC-CAAAA---ATAAAACGTAGTTTGGAGAT
DroMoj_CAF1_left   TTGTTATTTTACTTTGTTTTTCAATAGTGGCTGACAAC-AACAAAAATAT-CAAACACAATA--AGTTGA--GTGAGCGCA--GCAAAAAG-TTGGT---A--GGAATATCCTTGGAGAT

DroAna_CAF1_left   GCGGGGTATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCTTCTTGGATTTCATTG-AATAACG----TTGAAATATC--AGTAGCTTGT-TTC
DroEre_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTGT-TGTGGATTACTGAAA--AA----AGGTTCAATATTCACTGCT-TTACCC
DroGri_CAF1_left   GCGGGGCATTGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTGT-GCTTCTCACCCATAT--AA----CGGTATTT---------TT-GTGCCC
DroMel_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTGT-TGTGGATTCCTGAAA--AG----AGGTTCAATATTCACTGCT-TTGCCC
DroPer_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCATCT-TGTGGATTGTCCACC--AA----AGGCACCAAT-GTATTGCC-TTTCTT
DroPse_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCATCT-TGTGGATTGTCCACC--AA----AGGCACCAAT-GTATTGCC-TTTCTA
DroSec_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTGT-TGTGGATTCCTGAAA--AG----AGGTTCAATATTCACTGCT-TTGCCC
DroSim_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTGT-TGTGGATTCCTGAAA--AG----AGGTTCAATATTCACTGCT-TTGCCC
DroVir_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCTTGT-TGTACTGACTCATAA--AA----AGGCTCAATAACTATCG---CAGTTT
DroWil_CAF1_left   GCGGGGCATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCATAT-GAATATTGTCCACAT--AACGGTTCAATATCTAGTCTAATTT-GGCTCT
DroYak_CAF1_left   GCGGGGTATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCGTGT-TATGGATACCTGAAA--AA----AGGTTCATTATTCACTGCT-TTACCC
DroMoj_CAF1_left   GCGGGGTATCGATCCCCGTACCTCTCACATGCTAAGCGAGCGCTCTACCATCTGAGCTACATCCCCATGA-AGTACTCCCATACAC--AA----CGGTTTTATAACAACTGCA-GTTTTT

DroAna_CAF1_left   A-CTTACC-TCTG-GACAATTACCTGTAGTT-TATATAAATTGGTATGCAAGTCATTT-AGTGACCTGG-TTACAG-TTTCGTGGGCC-AGGTC-----------TGAACT--GG
DroEre_CAF1_left   A-CT-AAA-GCTG-AACAATTACCCGCAGTT-AAATTCAATTGGCATGCAAGTCGACC-AGCGACCTGG-TTACAG-TTTCATAGGCC-AAGTA-----------TGAACT-GGT
DroGri_CAF1_left   A-CT-TCA-ATA---AAATTGTCTCTTAGCC-AAAAACCAATTACA--CTTCCGATAA-ATTCAATTGA-AATGCA-TGCCATGAACT-GACCC-----------A-GTTT-GGC
DroMel_CAF1_left   A-CT-AAA-GCTG-GACAATTACCTGCAGCT-TAAATCAATTGGCATGCATGTCGACA-ATTGACCTGG-TTACAG-TTTCATAGGCC-AAGTA-----------TGAACT-GGT
DroPer_CAF1_left   GGTT-GGA-CAAT-TAGCAATACCTCTCTTT-ACCTTCAATTGGTATGCAAGTGGTGC-GACAAAGGTG-ACCCGG-ATACCGTTTCA-CAGTA-----------CAGGCC--TG
DroPse_CAF1_left   A-CA-ATA-CCTCTCTTTACCTTCAATTGGT-ATGCAAGTGGTGCGACAA--------------AGGTG-ACCTGG-ATACCGTTTCA-CAGTACAGGCCTGTTCCGAACTGGTT
DroSec_CAF1_left   A-CT-AAA-GCTG-GACAATTACCCGCAGCT-TAAATCAATTGGCATGCAAGTCGACA-ATCGACCTGG-TTACAG-TTTCATAGGCC-AAGTA-----------TGAACT-GGT
DroSim_CAF1_left   A-CT-AAA-GCTG-GACAATTACCCGCAGCT-TAAATCAATTGGCATGCAAGTCGACA-ATCGACCTGG-TTACAG-TTTCATAGGCC-AAGTA-----------TGAACT-GGT
DroVir_CAF1_left   T-TA-TGC-CCAC-TCCACCCATTTGTCGCT-AACCGAAATCGAATTACAATTACTGT-AGATTCAATT-GAAATTCAAGCTACGACGGAATGT-----------GGCCCA-AAT
DroWil_CAF1_left   T-GG-CCG-AAAA-GC-AATTACCTGGCAATTGAAATGC---ATAAGCCGTTACCACT-TACCTGACTTCAGTCTA-TCTCTTTTGTG-TGAAG-----------CCAAGT-CTG
DroYak_CAF1_left   A-CT-AAA-GCTG-GACAATTACCCGCAGTT-TAGTTCAATTGGCATGCAAGTCGACA-ACCGACCTGG-TTACAG-CTTCATAGGCC-AAGTA-----------TGAACT-GGT
DroMoj_CAF1_left   G-TA-CCCACTCG-AACAATTAATGTTGA-C-TCAATTGAAATTCAAGCGGTGTAATTGGCCTAGATTT-GTTTAT-AAGCTGGGTCT-GAA-C-----------TGGTTT-TCG