CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left -CTA-ATTTT--AGGTCGGAGAAAATAGGAA-ACCCAACGA--GCACGCAAGAGGGTTGAT-AGGCGAACGAATG--TTCTCTGCTTGTGCTA--GAACTTTGTCGCTGGGCACAGCATG DroEre_CAF1_left -GCA-ATGCG--CTAATTTTGTCTCTGAGAA-CGTCAACAA--CAAGCGGTGAGAGCGCAG-AGGGATGGACGCT--CTCCCACCTTGTGACT--GAACTCTGGCCGCTCACACTGCATG DroGri_CAF1_left -TTT-TCATGTGACAAACAAAGAGGC---AA-ATAC---TG--AAAGAGAACATTGAGCGTACTAGT-GCGCTCTCACGTTTGCTGATTATATTGCGACTTTGTGCACACTGCTTGCATG DroMel_CAF1_left -GCT-CAATGCGCTAATTTTAGCTCCGAGAA-TGGC---TA--CAAGCGCTGAGAGCAAAAGAGGGATGGACGCT--CTCTCACCTTGTCACT--GAACTCTGGCCACACACAAGACATG DroPer_CAF1_left -GCC-CATAG-GCTATTTTTAGCTCTGCAGA-GAAC-AAAA--CAAGCGAAGAGAGCGGCTGTCTGTTTG-TGCT--CTCTCAGCATATGATA--GAACTTTGGCGTAATTGTTCGCATG DroPse_CAF1_left -GCC-CATAG-GCTATTTTTAGCTCTGCAGA-GAAC-AGAA--CAAGCGAAGAGAGCGGCTGTCTGTTTG-TGCT--CTCTCAGCATATGATA--GAACTTTGGCGTAAATGTTCGCATG DroSec_CAF1_left -GCG-CAATGCGCTAATTTTAGCTCCGTGAA-TGTC---TA--CAAGCGCTGAGAGCGCAAGAGGGATGGACGCT--CTCTCACCTTGTGACT--GAACTCTGGCCACACACGAGACATG DroSim_CAF1_left CGCG-CAATGCGCTAATTTTAGCTCCGAGAA-TGTC---TA--CAAGCGCA-AGAGCGTAAGAGGGATGGACGCT--CTCTCACCTTGTGACT--GAACTCTGGCCACACACGGGACATG DroVir_CAF1_left -GAGTGAGAGA-GAAAGACATCGAGAGCGTC-TATT---CA--CAACACAAAACGAGCAAACTTGTGGTTCGCTC--ATTGCTGCTTGTGATG--GAACTTTGTGCGCAGTGCTTCCAAG DroYak_CAF1_left -CGCGCAGTGAGCTAATTTTAGCTCTGAGAA-CGTC---AA--CAAGCTGTGAGAGCGCAG-AGGGATGGACGCT--CTCTCACCTTGTTACT--GAACTCTGGACACTGAAGTCACATG DroMoj_CAF1_left -AAC-AACAA-CAACAATAGCTGCGTGAGAACGAGC-ATGTCCATTCAATGTACGCAA-GAGCAAAGTTCTTTGT--GCTGCTTGTATTGATT--GTTCGTTA---GCACTGCTTGCATG DroAna_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTATGTTTCGATTGATG-AAGCATTTACTTTTTTAT-TTTAT-TTTT DroEre_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTA-GCTTCT-----GG-AAGCATTTATGTTTTTTG-TTTTA--TAT DroGri_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTACGCACAA-A--AAG-GTGCGAAAATAGATTTT--TTGTA-TATT DroMel_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTATGCTTCT-G----A-AAGCATTTACTTTTTTCT-ATATT-ATAT DroPer_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTATGTCCGA-TTGAAA-GGGCATTGTATTCTTTTT-TATAT---AT DroPse_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTATGTCCGA-TTAAGA-GGGCATTGTATTCTTTTT-TTCTTCGTTT DroSec_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTATGCTTCT-G----G-AAGCATTTACTTTTTTTT-CTGTACTATT DroSim_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTATGCTTCT-G----G-AAGCATTTAATTTTTTTT-CTATACTATT DroVir_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTAGCGATAC-GAAAGTAGTCGC-----GCAGAATAGCTATTTTATT DroYak_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTAGCTATCT-GGAAGCATTTAT-----ATTTTTCT-TTATTGAACT DroMoj_CAF1_left TGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTAGCATACT-G--AAG-TGTGCGGTAAATTTTTTT-TTTTA-ATTT DroAna_CAF1_left -ATT-TATTTA-----TCTATTTTTTT---TAGTATATAATAATTAGATTTCCCAAATATACTATCTGCACTT-GTATTAAGAACAC-AC---AAT- DroEre_CAF1_left -TTT-TTTGCT-----TTGCTTTATTC---TGAGTAGTATTTTAGTATAATTACATTTATTGGTACATCTAGCATGGAAAATTTTAT-TA---TGT- DroGri_CAF1_left -TTT-A-CACTT----TCTACTTCATA-TTTG-CAT--TAAATTAACATTTTAATGGCTTA-TTATGGTTAAG-G---AAAATTATT-TT---GTT- DroMel_CAF1_left TTTT-G-CTTT-----GCTAAATGAAT-TTCTTTTG--GTTCAGAAAAGGTGCCATAGTTA-ATGTGTGAAAA-TCTTTGTATTTAT-TA---CAAA DroPer_CAF1_left TTAT-A-TATTTTTTATCGTAGAAATAGTATTTTAT--GGTT-------TATTTAGTATTT-GCAATAAAGTT-TCCTATGAAAATGATCATGAAA- DroPse_CAF1_left TCTT-A-TATTATTTATCGTAGAAATAGTATTTTAT--GGTT-------TATTTAGTATTT-GCAATAAAGTT-TCCTATGAAAATGATC---ATG- DroSec_CAF1_left TTTT-G-CTCT-----GCTATATGAAA-TTCGCTTG--GTTCAGAAAAGGTGCCGTAAGTA-TTGTGTGAAAA-TCTTTGTATTTAT-AA---CAA- DroSim_CAF1_left TTTT-G-CTCT-----GCTATATGAAA-TTCGCTTG--GTTCAGAAAAGGTGCCGTGGTTA-TTGTGTGATAA-TCTTTGTATTTAT-TA---CAA- DroVir_CAF1_left -TTT-T-TAAA-----TCATAATGTTT-TTAAAATT--AAAAAGTACATTTTTTTAGAAAG-GATTTTTTAGA-AATTTTAAATTAT-AT---ATA- DroYak_CAF1_left -ATA-T-ATAT-----TTTTTATGCTT---TGTATTTTCTGTGATGTATGTTGGTATAATTATATCTGCTAGA-AATATGTCCGTAG-GT---TAT- DroMoj_CAF1_left -TTATT-AATA-----CATATAAATTA-TATTTTTA--TTT-TTAATATTTGTTAAACAAA-AA---GTATGC-ATATAATTTAAAA-AA---TCA-