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


DroAna_CAF1_left   A-TGTATAGATGTGTTGCCACAGATA-GTTGCGATTT-CCATTCATACTTATAAT-TGTTAT-CAAATTTA-TTCAAGAAAAA-GGAGCACCACTCAGAATTCGCTCTATTCGTG-TTAC
DroEre_CAF1_left   AAT-GATTTGAAATGATGAAAATATT-TTTCAGGAGA-GAATTCATGTCTCCACA-GAATTT-AAATTGAT-TAGCTAAAAAG-GGGGCACCACTCAGAATTCGCTCTATCCGTTTCTAC
DroGri_CAF1_left   TTC-GCTGGCA-CTACAACACAGTCG-AAAAACAATTCTAATTTTAGCTCTATGT-TCAAAT-TGATTATT-TAAAAAGGTTT-TGTACACCACTCAGAATTCGTTCTATTCGTG-TTAC
DroMel_CAF1_left   AAA-TCCGAAA-ACAATTTAAATACT-ATAAAGAACATAAGCACAATAATGAGAT-ATACTT-AAATTAAT-TCGCATAAAAG-GGGGCACCACTCAGAATTCGCTCTATCCGTTTCTAC
DroMoj_CAF1_left   CTA-TAACAACTACCGAGAACACGTT-CCGCTTACTC-TCTTTTC-TCTCCTCTT-CCATGAAAT-TTATTATTTAAAAAATT-TGAGAACCACTCAGAATTCGTTTTATTCGTG-TGAC
DroPer_CAF1_left   ATGT-AACAATTCCACTACTATTTCT-CCCTTGGCTG-GGCTGCGCTTATTACAA-GCTTTT-CAAATTTA-TTGTTAAAAAG-GGTACACCACTCAGAATTCGTTCTATCCGTT-TTAC
DroPse_CAF1_left   --GC-AACAATTCCACTACTATTTCT-CCCCTGGCTG-GGCTGCTTACTAGAAGT-TTTTCAAATGATTGG-GTGTAAAAAAGGGTTACACCACTCAGAATTCGTTCTATCCGTT-TTAC
DroSec_CAF1_left   AAT-ACTATTA-AGAACATAAGCATA-AAAAACCCTGCTAAGATTGGCTGATCAA-GTATTG-TAATTGAT-TTGCATAAAAG-GGGGCACCACTCAGAATTCGCTCTATCCGTTTCTAC
DroSim_CAF1_left   AAT-ACTATTA-AGAATATAAGCATA-AAAAACTCTGCTAAGGTTGGCTGTAAAA-GTATTG-TAATTGAT-TTGCATAAAAG-GGGGCACCACTCAGAATTCGCTCTATCCGTTTCTAC
DroVir_CAF1_left   TTT-AATTGCG-CTGCAATAAAACGGAACAAA--GTACTCACATAGTCAGTATTGTTTTACA-TTTATTCA-TTCAAAAATTT-GGTACACCACTCAGAATTCGTTCTATTCGTG-TTAC
DroYak_CAF1_left   ATA-AGTTTTAGAAGGAAATTTCCTT-CAAGAAACTA-ATCTTCCTACTTAAGCA-TTGTTT-ATATTGAT-TTGCATAAAAG-AGAGCACCACTCAGAATTCGCTCTATCCGTGGTTAC
DroWil_CAF1_left   TCA-AACCCCA-TAAACCAAATCTCT-TGCAATATTTGAAATATTTTCTACTAAT-TGAAAT-TGATTAAT-AAAAAAGTGTA-GATACACCACTCAGAATTCGTTCTACTCGTT-TTAC

DroAna_CAF1_left   CGAGCGATCATCGAAGCCCGACGACCCGGAGGATGCGGA-CACC-GAAGCGCCACACCACAAAGGCCGCTGGACAAATCCTCACGCTGCCGAATAGAACGATTCACCTCATCAACGCGGG
DroEre_CAF1_left   CGAGCGATCATCGAAGCCCTGCGTCCCGAAAGA-------TG-C-GAAGCA-----CCA-AAAGGACACTGGACAAATCCTCACGCTGCCGAATAGAACGATTCAACTCATCAACGCGGG
DroGri_CAF1_left   CGAGCGATCATCGAAGCGCCACGCCCACAACAC---GGATAA-CCGAAGTC--ATACCGCAAAGGGCATCACGCAAAACCTCACGCTGCCGAATAAAACGATTCACCTCATCAACGCGGG
DroMel_CAF1_left   CGAGCGATCATCGAAGCCCTGCGTCCCGAACGA-------TG-C-GAGGCA-----CCACAAAGAACACTGGGCAAATCCTCACGCTGCCGAATAGAACGATTCAACTCATCAACGCGGG
DroMoj_CAF1_left   CGAGCGATCATCGAAGCGCTACACCCATC---ATACGTG-CAAC-AAG---TCACAACGTAAAGGGCATAACGCAAATCCTCACGCTACCGAATAAACCGATTCATCTCATCAGCGTGGG
DroPer_CAF1_left   CGAGCGATCATCGAAGCTCTGCGCCCCGAACGACACGGA-CACC-GAAGTGCCGCACCAGAAAGGGCGCTGGGCAAAACCTCACGCTGCCGAATAGGACGATTTAACTCATCAACGCGGG
DroPse_CAF1_left   CGAGCGATCATCGAAGCTCTGCGCCCCGAACGACACGGA-CACC-GAAGTGCCGCACCAGAAAGGGCGCTGGGCAAAACCTCACGCTGCCGAATAGGACGATTTAACTCATCAACGCGGG
DroSec_CAF1_left   CGAGCGATCATCGAAGCCCTGCGTCCCGAACGA-------TG-C-GAGGCA-----CCAACAAGGACACTGGGCAAATCCTCACGCTGCCGAATAGAACGATTCAACTCATCAACGCGGG
DroSim_CAF1_left   CGAGCGATCATCGAAGCCCTGCGTCCCGAACGA-------TG-C-GAGGCA-----CCAAAAAGGACACTGGGCAAATCCTCACGCTGCCGAATAGAACGATTCAACTCATCAACGCGGG
DroVir_CAF1_left   CGAGCGATCATCGAAGCGCCACGCCCACAAAAC---GAGTGA-T-AAAATC--ACATCGCAAAGAGCATCACGCAAATCCTCACGCTGCCGAATAAAACGATTCATCTCATCAACGCGGG
DroYak_CAF1_left   CGAGCGATCATCGAAGCCCTGCGTTCCGAACAG-------TG-C-GAAGCA-----CCACAAAGGACACTGGACAAATCCTCACGCTGCCGAATAGAACGATTCAACTCATCAACGCGGG
DroWil_CAF1_left   CGAGCGATCATCGAAACGCTGCGCCCCCAA------------------------------AGAGGGCACTGCGAAATACCTCACGCTGCCGAATAGAACGATCCAACTCATCAACGCGGG

DroAna_CAF1_left   TGTGCTTAGCTTTCATCTAATGTGAAAGTATGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAAAGATACAATCCATCGCCCGACGATGTTCCTGAGCTGCGGGCCAGA
DroEre_CAF1_left   TGCACTCAGCTTTCATCTAGTGTGAAAGTATGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTACCTTTTCGTTGCCCAACCTGTGGATCTTGGTGCGCCGCAGGCCAGA
DroGri_CAF1_left   TGTGAAGTGCTTTCAGATAGTGTGAAAGTAAGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAATTTTACAACGCCCATCAATGGGCTCTACTCGCCTCACCAGCAAGA
DroMel_CAF1_left   TGCACTTGGCTTTCAGCTAGTGTGAAAGTATGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAAGTTTTTGCTGCCCAACCTGTGGATCTTGGTGCGCTGCGGGCCAGA
DroMoj_CAF1_left   TATGGTGTGCTTTCATTTTGTGTGAAAGTAAGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAAATTTTCAACGCTCACCGAAGCGCTCTATACGCTGCGCTTCCAAGA
DroPer_CAF1_left   TGTGTTTGGCTTTCAATTTGTGCGAAAGTAAGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAACTTTTACAGCCACGACCTGTGGATCTTCACCCGCCGCGAGCTAGA
DroPse_CAF1_left   TGTGTTTGGCTTTCAATTTGTGCGAAAGTAAGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAACTTTTACAGCCACGACCTGTGGATCTTCACCCGCCGCGTGCTAGA
DroSec_CAF1_left   TGCACTTGGCTTTCAGCTAGTGTGAAAGTATGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAACTGTTCGCCGCCCAACCTGTGGATCTTGGTGCGCTGTCGGCCAGA
DroSim_CAF1_left   TGCACTTGGCTTTCAGCTAGTGTGAAAGTATGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAACTGTTCGCTGCCCAACCTGTGGATCTTGGTGCGCTGTAGGCCAGA
DroVir_CAF1_left   TGTGACTTGCTTTCAGAAAGTGTGAAAGTAAGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAACTTTTCAATGCCCACCAAAATGCTCTATACTCCACTCGACCAAGA
DroYak_CAF1_left   TGCGCTTGGCTTTCAGCTAGTGTGAAAGTATGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAACTACTCGCTGTCCAACCTGTGGATCTTGGTGCGCAGCACGCCAGA
DroWil_CAF1_left   TGTATGTGGCTTTCTTTCAATGTGAAAGTAAGTGAAGACTGACTACAGAAATGATCCTGTGAAGTATAGTCTTAAATTTTCAACGCCCGTCAATGGCCCCTTGGTGCTGATCGAGCTAGA

DroAna_CAF1_left   ACCACTTGCGAATCATAAACACGTAAAAAGAGGAAAAAAAACCACGCAACAT-GTTGCCC-GTA-AGTAT-G-CAGTGTAT-CT-TTCGC
DroEre_CAF1_left   ACAAGTTGGGAATTATAAGAGCGTGCG-CAC-GAACAAATTGAACAGCACGC-GCGGCGA-TAAGTGAG--C-GATGTATCTGCTTGTGG
DroGri_CAF1_left   ACCCATTGGGAATTATAACGCAGCTCA-CAT-GAAAAGAAACAAACAAAGTG-GTTGGTT-GCTATGCC--G-TCATCCACTGCTACTTG
DroMel_CAF1_left   ACTAGTTGAGAATCACAAGAGTGTGCG-CAT-GAACAAAATGAACAGCACGT-GGGGGGA-CAGGCGAA--A-GATGTATTAGTGCGTTG
DroMoj_CAF1_left   ACCCGTTGAGAATTCTAAGCGCTCACA-AAG--AGAAAAGAAACGCACATGG-TGGTTGCTGGTGCGTCGTCATCGCTAGC-TG--CCCT
DroPer_CAF1_left   ACCAGTTGGGAATTACAACAGCGTAAT-CAA-CGAAAAAGCAACTGATACGT-GGGGATT-ACTGCGCA--T-ATGGGAATATGGTTGCT
DroPse_CAF1_left   ACCAGTTGGGAATTACAACAGCGCGAA-CGA-CCAAAAAGCCACCGACACGT-GGGGATT-GTTCTGCC--T-ATGGAAATATGGTTGCT
DroSec_CAF1_left   ACTAGTTGGGAATCACAAGAGTGTGCG-CAT-GAACAAAAAGAACAGCACGT-AGGCAAG-CGATGAAT--C-AGGGCGTTGATATTATA
DroSim_CAF1_left   ACTAGTTGGGAATCACAAGAGTGTGCG-CAT-GAACAAAACGAACAGCACGT-GGGGCGA-TAGGCGAA--C-GCTGTATCAGTGCGTTG
DroVir_CAF1_left   ACCAATTGGGAATTCTAAGAAAGCGAA-AGA-AAAATAAACAAATCGTACAG-GGGTGTT-GTTGTGCG--C-TCACGTTCTATTACGTC
DroYak_CAF1_left   ACAAGTTGGGAATCACAAGAGTGTGCG-CAT-GAACAAAACGAACAGCACGC-GTTGCGA-TAAGTGAG--C-GCTGTATCAGCGTGCTG
DroWil_CAF1_left   ACCATTTGGGAATTCTAACAGGCACAT-TGA-GAAAAAACATATCAGTTGTGCGGTGACA-C-ATACAT--A-TACAACACGTTTTTGTG