CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CTTGGGAAACT-GTTGG-AAAATCAAGGG-GACAGGT----T-TAAATT-TAGG----TTGAAGTCAAAATTATGTTT-A-TTCTGTAATAAAAAAAAA-CATAA--ATATAA-AAAAAA DroEre_CAF1_left ATGGGTCT--CCG-AAGTTGTAAGTTTAATATGCTGCCA--AGCCTGCA-GTAT----TGTATTTTACTGC--A--CT-A-CTTACCACAGAAAA-AAG-GAAAATTAAA--T-AAAAAA DroGri_CAF1_left GAATTTGG--G-AACTT-AATAACGGTTG-TTGGACC----G-TCGACA-GCGT----AATCATATTTTGGTTAGTAA-A-AAATATAAAATTATAAAA-CTGACAATAAACC-AAAAAA DroMel_CAF1_left GCAGTAAA--G-T-ATG-CTTTTGCCATT-AGTAGTTTATAATAATAAT-AATA----TAATAATAATAAT--AATAA-T-AATAACACAGAAAATTAA-AAGAATTATA--T-AAAAAA DroMoj_CAF1_left AGAAATGC--A-A-AAA-GAGATATGTAA-ATATAAA------ATATTT-TTTAACTCATTTTAATATTAAATAAAAA-A-ATATTAATTAAATAAATA-AAGCA--AAAAAA-AAAAAA DroPer_CAF1_left AAAACAGT--A-A-TAA-ATGGAATAATT-TAGAACTAA--TTTATAGCTTATA----TTAAAATATT--ACATACAA-AAAAATATACAAATTA--TTGAATAA-TAAAAGG-AAAAAT DroPse_CAF1_left AAAAAACA--G-T-AAT-AAATGGAATAA-TTTAGAACT--AATTTATA-GCTT----ATATTAAAATATT--AAATA-C-AAAAATATAAAAATTATT-GAATAATAACAGG-AAAAAT DroSec_CAF1_left AAATATAC--T-G-ATA-AGCAAGCAGTA-GCGTGTGCT--TTCCCCAT-AGTT----GTTTATAATAATG--GGTTT-A-TTTAACACAGAAAATTAA-GAGAATTAAAT-A-AAAAAA DroSim_CAF1_left AAATATGC--T-G-ATA-AGCAAGCAGCA-GCGTATGCT--TTTACCAT-AGTT----GTTATTAATAATG--GGTTT-G-TTTAACACAGAAAATTAA-GAGAATTATAT-AAAAAAAA DroVir_CAF1_left TTTATAAA--A-AGTAA-AACGAATATGC-CTACATA----TGAATAAA-CTTT----ATTTATATTGTTGCGGGTAC-G-CTCATATTTTTGGAATTA-GATAA-AAGTTGA-AAAGAA DroYak_CAF1_left AAATGTGC--T-G-ACA-TGCATGCATTT-GAATTTTAC--TGCAATAC-CTAT----AAGTACTTTATAC--CAGTACT-TTTACCACAAAAAA-AAA-GGGTTTTATATAA-AAAAAA DroWil_CAF1_left ATTTAAAT--T-A-GAA-ATTTAACAAAA-TTACGCTAT--TCTCTCGC-TATT----CACAAAATTTTATA-AAATT-A-AAATAAAAATATGTTTAA-TAAAA-ATTTAGA-AAAAAA DroAna_CAF1_left TTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCCCTTGAAT---CCATCCGGAGAATAACCCT-TCCCA-AG DroEre_CAF1_left ATTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCGCTTGGAG---GCACGGAGAAAATAAC-TA-AACTTAGG DroGri_CAF1_left TTGACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCACATGATA--ATCAAGTTGAA----TTTAC-TAAAT-TT DroMel_CAF1_left TTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCCCTTATAT---ATGCGAAGAAAGTAAC-TG-AACTTAGG DroMoj_CAF1_left TTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCGCTGGGGG--CA-CCCGATCAAAGTAC-AG-GATATGAA DroPer_CAF1_left ATGACGTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCGCTTGGAC---TCGAGCGGAAATATAC-CC-CATTCCAA DroPse_CAF1_left ATTACGTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCGCTTGGAG---TCGAACGGAAATATAC-CCCATTCCAAG DroSec_CAF1_left ATTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCGCTTGAAT---GTACGGAGAAAATAAC-TG-AACTTAGG DroSim_CAF1_left TTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCAACTTGAAT---GCATGGAGAAAATAAC-CG-AACTTAGG DroVir_CAF1_left ATTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCACTTGTGAAATACGACCAA---GTTAC-AG-AATAT-CA DroYak_CAF1_left TTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCGCTTGAAC---GTAGGGAGAAAATAAC-TC-AAGTTAGG DroWil_CAF1_left TTTGGTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCTTGGAAGGCAACTATGCTGACCATTACACCACCGACGCCCCTTGATT---AACACTAG-AATTTC---T--A------ DroAna_CAF1_left CTAAGTCAGATAAGAAAGTGCG--A-GCAATGAGTGTGAGTGAT---AA-CGAAAGCTA-AAGAGG--GGACGAGCAACTA-AGCTTTATCTCT-T--CTAAGCAA-TTCAATT-TAA DroEre_CAF1_left CAAAGAGTGATAAGAAAAAGAA--A-GAGAGTGAGAG-AGGGAC-TGAG--CTTAA--G-CT-TAACCTACA-CAAATTAAAATTTG-AGATCTAA--ATATAGAACGCCTAAT-CAA DroGri_CAF1_left GAAGCACAAGTTCTTAAGCCAT--A-TTATTTCTAAA-AGCATA---TT-TTAAAGAGA-AGTAAA--AGC-GCTTTTAAC-TTGATTATAATA-T--TGAATGAA-CT-TTCT-ATT DroMel_CAF1_left CGTAGGCAAGAGAGAGAGAGAGAGA-GAGAGAGAGAG-C--GAG---GC-ACTCAC--T-GAGATAGAGAGAGAACTAGAA-AAGTCGGCTGAATA--TCAGCTTA-GCCTACA-AAA DroMoj_CAF1_left ATATCTGAAACTTTCTA-AGTC--AGGAAATATTTTA-GGCATA---CCTAAA--TATG--AATTG--GTTTTTAATTTGA-ATTTAATAACTT-G--TG-TTCAG-CTCA--T-ATG DroPer_CAF1_left GAAGCTGATATCAGAACGAGAA--C-GATGCAGAGAA-AGAAGG-AGAG-GGAGAG--A-G--AGAGGGAGAG-G-TACAG-AGTGGAAGTGGTAAGGGATAGGGT-CTATCAT-AGG DroPse_CAF1_left -AAGCTGATATCAGAACTA-CT--C-GAGAACGCTGC-AGAGAA-AGAG-AGAGAGGTA-CAGAGT--GAAAGTGGTAAGG-GATAGGGTCAAT-C--ATAGGAAT-CATTTTG-TGT DroSec_CAF1_left CGAAGGGAGATAAGCAAGA--AATA-GAAACACCCAC-TAAGAT-AGAG-AGAGAA--T-AATCA---GCTTAGCCTACAC-AAACTAAATTTTAA--AATCTAAA-TATAGAACACC DroSim_CAF1_left CGAAGGGAGATAAGAAAGAGAGACA-GAGACACCCAC-TGAGAT-AGAG-AGGGAA--T-TAGAAA--ATACGGTTGAATA-TCAGCTTAGC-C-T--ACACAAAC-TAAATTT-TAA DroVir_CAF1_left AAATCGCAT-ATTTTGAGCCTA--A-CTAGAACAACT-TTATTC-C-CA-GTTCATTTTTAAATAT--TTT-GTTTATTGC-TCTTATCA--CT-T--CCCTTTTC-GACAA---ATC DroYak_CAF1_left CGAAGTGAGAAAAGAAA-AGAA--A-GAAAGAGAGAG-AGGGACCCTCT--GAGAT----AG-AGAGAGTTA-TAAAATAA-GTCGGAATTTCAGCTTAACCAACA-CAAACTA-AAA DroWil_CAF1_left ----CTAAATATAAATGTG-GG--T--TAAAACTATA-TA-CAT-A-TATAATGAA--A-AA---------CCCATAAATC-ATAAATGTGC-C-T--TATCGAAA-CAATTAA-CTT