CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ACATTTATTTTATAAAACAAAGA-G-------CGTTTATGG-TATGCCAAAGTATTACATCCATA----TTAACAAAGTCACACA----GCGTG---TTATGTTTTAAAATT-TTATTCA DroEre_CAF1_left CGAAAAAAACGAAAGCAA-GACTGA-------TAAGGGTAA-AAACAC---AGCTTAAATA-AAA----ATGTCAA-CGTATCTTT-TTCA-G----AAAT-CTCTA-TGGC-TTAAAAA DroGri_CAF1_left TGAATTAAAAATACGCGAGTTATCA-------GACAAAAGT-TGTGCTT--ATCATGTTCT-TACATACATACATGTATGGGAAGA-AATA-A----T--C-TTGGTATACA-TATAAAA DroMel_CAF1_left ATACATAACATACAATTATGTTCAC-------TGTATATTC-ACTGCT---TGAATATAAT-TTCGAAGGTATCTTTTTCAGAAATCCCTA-TA---T----GGCTTAAAAA-TAAGCAA DroPer_CAF1_left CAA-CAATTG-GAACTATATT---A-------GTGAGCGTG-ATTTAT---TTTGATA-TG-A-CTTTATGTAACT-GTGTCTATA-AATA-G----AAAG-TGATA-AAAT-AAAAAAT DroPse_CAF1_left CAA-CAATTT-GAACTATATT---A-------GTGAGCGTG-ATTTAT---TGTGATA-TG-A-CTTTATGTAACT-GTGTCTATA-AATA-G----AAAG-TGATA-AAAT-AAAAAAT DroSec_CAF1_left AAATGAAACATTCGTAAAA-AAAAA-------AAAAGAAAG-ACTGAA---GGGTAAGAAC-ACAGATTTCATACAATTTGTAAGACATCT-CT---AT---GGCTTAAAAA-AAAGCAA DroSim_CAF1_left ATAAATAAAACATTCGTAAAAAAAA-------GAAAGAAAG-ACTGAA---GGGTGAGAAC-ACAGATTTGATACAATTTGTAAGGCATCT-CT---AT---GGCTT-CAAA-AAAGCAA DroVir_CAF1_left CAAAGCGTGATTTATTATAAGTACAAACACACGAGTGT-TCATATA-A---AGTTTAT-TC-C-AATT----AACA-TATAATATA-CATA-TATATGATT-GAAAT-AAATGTT-TATG DroWil_CAF1_left AATAAGATTAAGAAACGTCAA---C-------GA---------ACGAA---GCCCTAT-CT-A-ATCAAATGAACA-GGGTCAATG-CACA-A----TA-G-TTTCA-TGTA-ATTCGTA DroYak_CAF1_left ATAACCAAGGCTAATCAACAAAATT-------TGTATAACA-AC---T---TGCTATTTAG-CACTTTATTAGGTAAAAACCCTAA-AATA-CG---AAACGAATTAAAAAA-AAAGTTT DroMoj_CAF1_left ATAGACATGGATAAACTATATA--C-------ACC-ATAT-TATTTAA---AAAACATTAA--TTATTATTATTTTAATA--AAAT-AATT--T---ACAT-AC-ATATAC--TATGCAT DroAna_CAF1_left -CGTTA---ATTAAT--AAATT-T-AAAAA-TAAATAAAATAAAAAAGGA-AA-C--CTTGTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroEre_CAF1_left -AGATT---TCCAAT--G--------ATAC-AAAAA------AAGAACAA-AA-A--ACTGTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroGri_CAF1_left -A--TG---AAAAT---AGTTTATTTAAAA-AAAAAAA----GAGTGCAAAAA-A--CCTTTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroMel_CAF1_left -CCATA---GATTAT--TTTCTA---ATGA-TAAAAAG----AAGAGCAA-AA-AAAACTGTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroPer_CAF1_left -TGAAT---TCAAAA--AAGAA----GAAA-AAGAA------ATTACCAC-TC-A--GATGTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroPse_CAF1_left -GGAAT---TCAAAA--AAGAA----GAAA-AAGAA------ATAACCAC-TC-A--GATATGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroSec_CAF1_left -CCTTA---TCATTCTTTTGTTT---ATGTTAAAAA------AAAAACAA-AA-A--AATGTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroSim_CAF1_left -CCTTA---CCATTT--TTGGTA---AGGT-TAAAA------AAAAACAA-AA-A--AATGTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroVir_CAF1_left TGA-AT---GTTAAA--AGTAT----AAAA-ATTAA------ATAAAAAA-AA-C--ACATTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroWil_CAF1_left -GTGGA---GA----AAAAGAAAA-CAAA--ACAAA------AAAAACTT-TT-A--CACTTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroYak_CAF1_left -CTGCA---GA----TTTGTTCTT-AATAA-TAAAA------A-AGAACA-AAAA--ACTGTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroMoj_CAF1_left ACATGTGATGAATAT--ATTC-------TA-AACAT------AAAAATAA-AA-A--AATCTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTT DroAna_CAF1_left AGACCGCTCGGCCACGCTGCCTTGGTGCTCATCGTGTCAAATGCGCACC-TTGAACTAAGCCCCATAGAAA----GCATA-GCGCAGGGTCG---TTGTTGGCATAGTTTTGGGGATGAT DroEre_CAF1_left AGACCGCTCGGCCACGCTGCCTATACCCACACGCTGTCAAATGCGCAAT-TTCAACATAGCAAGCCATGAA----GTCGA-GTGTTCTTCCT---TTGTTGGCATAATTTTGGGGTTGAT DroGri_CAF1_left AGACCGCTCGGCCACGCTGCCTTTTTCCATTTCGTGTCAAATGTGCTAT-TTGAATTCACAGCAAGCAACA----TGTAT-TTGGAATGAAA---GTGCTGGTATAGTTTTGGGGATGAT DroMel_CAF1_left AGACCGCTCGGCCACGCTGCCTGTACCCACACGTTGTCAAATGCGCAAT-TTCAACATAGCGAGCCTTGAA----GTTGA-GCGTAGTGGCA---TTATTGGCATAATTTTAGGGTGGAT DroPer_CAF1_left AGACCGCTCGGCCACGCTGCCTCTGACCGTTGAGTGCCAAAAGCACTAG-TTAAGCGCACGGCAGAGC--------CCAT-ACGGAATATGA---ATTCTGGCATAGTTTTGGGGATGAT DroPse_CAF1_left AGACCGCTCGGCCACGCTGCCTCTGACCGTTGAGTGCCAAAAGCACTAC-TTAAGCGCACGGCAGAGC--------CCAT-ACGGAATATGA---ATTCTGGCATAGTTTTGGGGATGAT DroSec_CAF1_left AGACCGCTCGGCCACGCTGCCTGTACTCTCACGTTGTCAAATGCGCACT-TTCAACATAGCGAGCCTTGAA----GTTGA-GCGCACTAGCA---TTATTGGCATAATTTTAGGGTGGAT DroSim_CAF1_left AGACCGCTCGGCCACGCTGCCTGTACTCACACGCTGTCAAATGCGCAAT-TTCAACATAGCGAGCCTTGAA----GTTGA-GCGCACTAGCA---GTATTGGCATAATTTTAGGGTGGAT DroVir_CAF1_left AGACCGCTCGGCCACGCTGCCTTGTTCAACCACGTGCCAAATGTGCAAC-TTGAAGGCACAGCACAGTACC----GTCCT-ACAGTTTAAAA---ATACTGGTCTAGTTTTGGGGATGAT DroWil_CAF1_left AGACCGCTCGGCCACGCTGCCGTTGGTGGTTGGGTGTCCAATGTTCA-A-TATAACACTTCGGTGCTTATG----TTCCGTTTGTAGTGCAT---ATTCTGGCATATTTTTGGGGATGAT DroYak_CAF1_left AGACCGCTCGGCCACGCTGCCTGTACTCATACGGTGTCAAATGCGCACT-TTCAACATAGCGAGCCTTGAA----GTCGA-GCACACTACCA---TTGTTGGCATAATTTTGGGGTGGAT DroMoj_CAF1_left AGACCGCTCGGCCACGCTGCCTCACACATGTTCGTGTCAAATATGCTACTTGAATCCGCAC-CACAATTCAGTTGTCTGT-CGTCTGCTACTAAAATGTTGGTATAGTTTCGGGGATGGT DroAna_CAF1_left TT-CTGAGCAGTGTTGCCGAGGCAG-T--CTCAAA-A-AGGTAGTAT-----A-AATCGTAT-TAACGCA DroEre_CAF1_left TT-TCCAGCAGTGTTGCCGACACTCGT--CGCAAA-AAAAGTAGTTG-----G-GAAAGTAG-T--GGCA DroGri_CAF1_left TT--CCACGAGTGTTGCCGAAGCGCAT--TTCAAAAAAAAGGAGCAGTCG--G-CTAAAAAGTA--GTGG DroMel_CAF1_left TT-TCCAGCAGTGTTGCCGACACTCGT--CTCAAA-AAAGGTAGTTG-----A-AAAAGTAG-T--GGTT DroPer_CAF1_left TTATGCAGCAGTGTTGCCAATGCTCTCA-CAGAAA-AGTAGTAGAAAGTAGTA-GGAGGCAT-G--CGCA DroPse_CAF1_left TTATGCAGCAGTGTTGCCAATGCTCTCA-CAGAAA-AGTAGTAGAAAGTAGTA-GGAGGCAT-G--CGCA DroSec_CAF1_left TT-TCCAGCAGTGTTGCCGACACTCAT--CTCAAA-AAAGGTAGTTG-----G-AATAGTAG-T--GGTT DroSim_CAF1_left TT-TCCAGCAGTGTTGCCGCCACTCGT--CTCAAA-AATAGTAGTTG-----G-AATAGTAG-T--GGTT DroVir_CAF1_left TT--TCACGAGTGTTGCCGAAGTACATGTGAAAAA-AGTAGTAGACAACAACG-AAAAGTAG-T--AGCA DroWil_CAF1_left TT-TCATTGTACAGTGTTGCCACCGTA--CTTAAG-TGAAAGAGTAG-----T-AACAA-TT-T--ACTA DroYak_CAF1_left TT-TCATGCAGTGTTGCCGACACTCGT--CTCAAA-AAAGGTAGTTG-----G-AAAAGTAG-T--TACA DroMoj_CAF1_left TT--TCACGAGTGTTGCCGAAGTACAT--TTTTAA-A-AGGTAGTAG-----ACAACAAAAC-A--AAAA