CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CTTG---CTACAAAGGTTC-AAGTTCTG-----TGATGT---TGTCGGTTTAA--ATGTGGTAGAGAGAGAAGAAAGG--GGGAAAGA-----ACACGCTGACAC-GCTGCC---GCTGC DroEre_CAF1_left GTTG---GAATTTTTGTAAGCTGGTATG---TGAGCTGT---TGTTCGCCTCT--TTTACGGTTT------GAGCTCGAGTTTTGTGA-----AAAAGAAAA-AG-GTAAAC-GCGCTGG DroMel_CAF1_left GTTG---GAATTTTTGTAAGCTGGTATG---TGAGCTGT---TGTTCGCCTCT--TTTACGGTTT------GAGCTCGAGTTTTGTGA-----AAAAGAAAA-AG-GGAAAC-GCGCTGC DroMoj_CAF1_left TCCC---CCAGGTCCGAAAATAAAGAAG---GAAAAAGT---GGATTTCGAAG--GTTTTAT------GTGGAAGAGGAAATGCTGCA-----AGAAGCAGC-A--GAAGAG-A-GGAAT DroPer_CAF1_left TCTTTTTTTTGCTGTTTCTGCCGCGTTT---CAAGTTTT---TTTTTGCGCGCCGTCCCTTTTG----GGGGGGGCGGCAAGGGCGGA-----GCACGGCGA-ACGGAGGAG-A-AGATG DroPse_CAF1_left TTTT---TTTGCTGTTTCTGCCGCGTTT---CAAGTTTT---TTTTTGCGCGCCGTCCCTTTTGG-GCGGGGGGGCGGCAAGGGCGGA-----GCACGGCGA-ACGGAGGAG-A-AGATG DroSec_CAF1_left GGAA---TT---TTTGTAAGCTGGTATG---TGAGCTGTTGTTGTTCGCCTCT--TTTACGGTTT------GAGCTCGAGTTTTGTGA-----AAAAGAAAA-AG-GGAAAC-GCGCTGC DroSim_CAF1_left GGAA---TT---TTTGTAAGCTGGTATG---TGAGCTGTTGTTTTTCGCCTCT--TTTACGGTTT------GAGCTCGAGTTTTGTGA-----AAAAGAAAA-AG-GGAAAC-GCGCTGC DroVir_CAF1_left AAAA---AAGAAAACATAAGACAAAAAA---AAAATGTT---GGATTTTTTGA-------GCTGT-TCTGTGTGTCGGGAAAGAGGAA------ATTGCTGC-AA-GAAGAG-A-AGAAT DroWil_CAF1_left AAAA---TTGTTTTTTTTTTTTTTTTGGTTGGTTAGATG---GTTGGATGGTT------GGTTGT-TTGGTTGGTTCCCAAAAGTGTT------A-----TT-C--GTAAAAAGGAAATG DroYak_CAF1_left T-----------TTTGTAAGCTGGTATG---TGAGCTGTTGTTGTTCGCCTCT--TTTACGGTTT------GAGCTCGAGTTTTGTGAACAAAAAAAGAAAA-AG-GGAAAC-GCGCTGG DroGri_CAF1_left AGAA---GAAAAAACGCAACAAAAAAAA---GTTG-GAT---TTTTTTACGCT--GTTATTTGAT------TTGATGGAAAAAAGAGG-----AAATGTTGC-TC-AAAAAG-AAGAATT DroAna_CAF1_left CAAGATATTTCTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTAACATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCTAAAATCAACGAAAACATA- DroEre_CAF1_left CAAGATATT-TTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACCAAGT-GAA- DroMel_CAF1_left CAAGATATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACCAAGT-GAA- DroMoj_CAF1_left TCCAAAGTATGCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCAATTTAAATACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAACACAACTCAAACAAA- DroPer_CAF1_left TGTGTATTTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAGACAACGAAAA-ACA- DroPse_CAF1_left TGTGTATTTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAGACAACGAAAA-ACA- DroSec_CAF1_left CAAGATATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACCAAGT-GAA- DroSim_CAF1_left CAAGATATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACCAAGT-GAA- DroVir_CAF1_left TTGAAAATATGCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCAATTTATATACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACGAAGT-GAA- DroWil_CAF1_left CTGAAAATATGCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATTTAATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACGTTAC-GAA- DroYak_CAF1_left CAAGATATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACCAAGT-GAA- DroGri_CAF1_left CA-AAAATATGCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTAAATTTAAATACTCATAGGAACTTCATACCGTGCTCTTGGAAGACCAAAACACAACAAAGA-AACC DroAna_CAF1_left -AAGCGGAGTTGGTTTC-CCCTTCAACCAAAAAATCAAAAAAGAAAAAAAACTAA-AGACAGT-GATTT---AAAA-AT-GCAACGAAATT-C-GAAACAGAAA--A DroEre_CAF1_left -TGCAAAAATCCC--AAAAAGTATGGCGAAAACAAA--CAAA-AAGTGCGTTTTA-AAACGAT-GAGAAAACGCTG--G-ACAAACGAAAAGG-AAGTTGCAAATGA DroMel_CAF1_left -TGCAAAAATCCC--AAAAAGTATGGCGAAAACAAA--CAAA-AAGTGCGTTTTA-AAACGAT-GAGAAAACGCTG--G-ACAAACGAAAAGG-AAGTTGCAAATGA DroMoj_CAF1_left -AACGAAAACGAG-CGCAAAGCAAAGCGCAGTGCGAGGCAGC-CACAAAAAATAT-GGCGATTTAAAAC---GCAC-GC-ATAACGCTAGC-G-ACTTTTGCGA--A DroPer_CAF1_left -TACAAAAGGCGTTTTAAAACGCCTGCAAACGCTGCACCAAA-AAAATTGATAAA-AGTGAAC-GAGAA---ATAT-CC-ATGTATAAATCCTAAA-TGACTAA--A DroPse_CAF1_left -AACAAAAGGCGTTTTAAAACGCCTGCAAACGCTGC-ACACA-AAAATTGATAAA-AGTGAAC-GAGAA---ATAT-CC-ATGTATAAATCCTAAATGACTAAA--T DroSec_CAF1_left -TGCAAAAATCCCA-AAAAAGTATGGCGAAAACAAA--CAAA-AAGTGCGTTTTA-AAACGAT-GAGAAAACGCCT-GG-ACAAACGAAAAGG-AAGTTGCAAA--T DroSim_CAF1_left -TGCAAAAATCCCA-AAAAAGTATGGCGAAAACAAA--CAAA-AAGTGCGTTTTA-AAACGAT-GAGAAAACGCCT-GG-ACAAACGAAAAGG-AAGTTGCAAA--T DroVir_CAF1_left -ACGCGCAGCA-CACGGAACGAAGAGTGCGATTAAAAACGCA-CACATAACGCCAGCGACTTT-TGCAT---GCAG-AA-AACCGCCTACGTG-CGCTGTACAA--A DroWil_CAF1_left -AACAGCAACAAGAAAAAACAAAAAGCTAAAACCAAAACCCA-AAACGAAGGCTT-CTCCAAA-TATGG---CTGG-GC-AGGCAGAGAGAAA-TAGAAAGGAA--G DroYak_CAF1_left -TGCAAAAATCCC--AAAAAGTATGGCGAAAACAAA--CAAA-AAGTGCGTTTTA-AAACGAT-GAGAAAACGCTG-GACACAAACGAAAAGG-AAGTTGCAAA--T DroGri_CAF1_left CAACCTTAAGCGG--AATGCGATCAACAAATACGCA--CTTG-AAACACCAGCGA-C-TCTTT-TGCATTCAGAAAACT-ACGAAAAATAC-G-TGAGATGTGC--A