CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GGAGT--G-TTGGGCTCT-GTCC-A--GG---AGCAGATAAGG----ACTCCCAAG------TCAGAGAACAAATT-----AACAGA-AAGGTTTCCCTTCCTGTCATAAATGTTAGGTT DroEre_CAF1_left GGGCT--C-CGGACTTAA-AGTCCTTAAA---T-TACAAAT-T---ACGGGCTAGGA-----AGTCCGGTCATACA-CAAAATCTTTGCCTTCAGGTATAAGAGT-----GCA------- DroMel_CAF1_left CGCAGATAGCGCACCACA-GGAC-T--CC---G-GACTTAAAG---TACTTAAATT------ACAAATTACGGACA-A---GGAAGTCCGGTCATGACCGATATCC---TAGA------- DroPer_CAF1_left GTGTT--T-CGTGCTGTA-ACAAAACAGAAGGGGATGCGATGC----TCTCCGGCCA-----AAGGTTCACG--TA--------TTC-CATTCGGTTGTGGAACCT---TACG------- DroPse_CAF1_left CGTG---------CTGTA-ACAAAACAGAAGGGGATGCGATGC----TCTCCGGCCC-----AAGGTTCACG--TTGT---GGGTTCCCATTCGGTTGTGGAACCT---TACG------- DroSec_CAF1_left CAGAT--AGCGCACCACA-GGAC-GCACA---G-GACTTAAGG---TCCTTAAATT------ACAAATTACGGGCA-A---GGAAGTCCGGTCAGGACCGATATCC---TAGA------- DroSim_CAF1_left CAGAT--AGCGCACCACA-GGAC-GCACA---G-GACTTAAAG---TCCTTAAATT------ACAAATTACGGGCA-A---GGAAGTCCGGTCAGGACCGATATCC---TAGA------- DroVir_CAF1_left CCTGG--T-TTAATGGTT-ATCG-ATTCA---G-CTACAGCGCTACATCTTTCGCA------TATTTTTACC---------TGAGTTCAATTACAACTTGCCTGCT---TTAC------- DroWil_CAF1_left TCCCG--C-TGGGTGGGCGCTCG-TCTCT---G-TTCTGTCATCGGACATCAGAAG------TCTTTCGGTC---------TGAGGGGATGTTCTCTTTGCTCTCA---GAAG-T----- DroYak_CAF1_left GGACT--C-CGGACTTAA-AGTGCTTAAA---T-TACAAAT-T---ACGGGCATGGA-----AGTCCGGTCATACC-CAAAATCTTTGAATTCAGGTATTAGAGA-----GTA------- DroMoj_CAF1_left TTCCT--T-AGAGGCTCG-GCAGCAA-TC---C-CGCACTT-T---TCCACATAGGAAGTCTTCACAATTCTACCT------GAGTTGACCCATTCTTACAGCTC-----ACA------- DroAna_CAF1_left TCAGATA-CTG-CCTA--T-TTTTGGACC-TTTTGCATTG--AGC-TGCC-TCCTCTTGAAATTCCCAACTAGTTCTGGCAGTGACCTTAAGGAAACCCTCTACCTGAGCAGGAGAAAGC DroEre_CAF1_left -AGTAAG-CCG-TGTT--GCATACTTTCT-CGGTGAAATATCCTCGACAC-TCTGCCTGAAATTCCCAAGCAGTTCTGGCAGATCCCTCAAGGACATCCCAGAGTTGGGCGCTGGAAGGC DroMel_CAF1_left -ATTCCG-AAGTTGTT--GCATACCTTTT-TGGTGCACTATTGCCGACAC-TTCTCCTAAAATTCCCAAACAGTTCTGGCAGATCTCTCAAGGAGATCCCAGAATTGGGCGGAGAAAAGC DroPer_CAF1_left -CGTACC-ATA-TTTGTGTTGCATACTTT-AGGTGCAGACAGATT-TCCG-GGCA-CTACAATTCCCAACCGGTTCTAGCCACAGGGGCAAGGAAACCCTGCTGTCGAGCGGAGAAAAGC DroPse_CAF1_left -GGTACC-ATT-TTTGTGTTGCATACTTT-AGGTGCAGACAGATT-TCCG-GGCA-CTACAATTCCCAACCGGTTCTACCCGCAGGGGCAAGGAAACCCTGCAGTCGAGCGGAGGAAAGC DroSec_CAF1_left -ATTCTG-AAGTGGTT--GCATACATTTC-TGGTGCACTATCACCGACAC-TGCGCTAGAAATTCCCAAACAGTTCTGGCAGATCTCTTAAGGAGAGCCCAGAATTGGGCGGAGAAAAGC DroSim_CAF1_left -ATTCTG-AAGTTGTT--GCATACTTTTC-TGGTGCACTATTACCAACAC-TGCGCTAGAAATTCCCAAACAGTTCTGGCAGATCCCGCAAGGAGAGCCCAGAATTGGGCGGAGAAAAGC DroVir_CAF1_left --ATTAGATCAATTGT--GTTGCCTATTTAAGGGCGTCATAGTTTTACAGCATCATCTGTAATTCCCAAACGGTTTTAACAATGTGTACATGGAAACCTTAGCACAGAGCCGAAAAAAGC DroWil_CAF1_left -TTTAAAAATTGTGTT--GCATATCTTTC-AGGTAGAATTTACTTGCCACTTCCCTTTACAATTCCCAACAAGTTCTAGCAACTCAGGCATGGTAACCCCTATGCTGAGCAGAGAAAAGC DroYak_CAF1_left -AGTAAG-CAT-TGTT--GCATACTTCTT-TGGTGCAGCAACCCCGAAAC-GCTGCCTGAAATTCCCAAGTAGTTCTGGCAGATCCCTCAAGGAGATCCCAGAGTTGAGCGGCGAAAAGC DroMoj_CAF1_left -CAGTTA-AATCTGTA--GTATATCTAAG-GGA-GTTTAATTGCCAACAC----AAACGTAATTCCCAACCAGTTTTGACAATGTTAACATGGAAACCCCAGGCTAGAGATGAGTTAGGC DroAna_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGACCTGGCCATTGCAC-C-TCGGCTGGGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroEre_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGCCATTGCAC-C-TCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroMel_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGCCATTGCAC-C-TCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroPer_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACCAAGGCGTGTTCCTCCGGAGTGAGGCTTGGCCATTGCAC-T-GCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroPse_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACCAAGGCGTGTTCCTCCGGAGTGAGGCTTGGCCATTGCAC-T-GCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroSec_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGCCATTGCAC-C-TCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroSim_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGCCATTGCAC-T-ACGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroVir_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGCCATTGCACAT-TCGGTTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroWil_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGCCATTGCACAT-TCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroYak_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGCCATTGCAC-C-TCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroMoj_CAF1_left ATACTTACCTGGCGTAGAGGTTAACCGTGATCACGAAGGCG-GTTCCTCCGGAGTGAGGCTTGGTCATTGCAC-TTTCGGCTGAGTTGACCTCTGCGATTATTCCTAATGTGAATAACTC DroAna_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATAAATAAT-AAATATT-AAAAAAAGATAATAGTTGTCAGTTCCATC-CTGGCTCCT DroEre_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATTAAAAAT-AAATATT-AAAAATCTAACTCTTCAGTCGCTAACTAG-ATTGAAGAG DroMel_CAF1_left GTGCGCGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATTTAAAAT-AAATATT-GAAAAGAAAACGACTCAACTTTAGTTAATAATTAG-ATT DroPer_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATAAATAAT-AAATATC-GAACCATTGGCAATAGAGTAGAGTACTAT-CAAAATTGA DroPse_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATAAATAAT-AAATATC-AGAGCAGTACAAATAGAAATAGGAAATTA-AGTTAGTTG DroSec_CAF1_left GTGCGCGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATTTAAAAT-AAATATT-GAAAAGAAAACGCT-TAGTTTTAGTTAATAATTAGATTG DroSim_CAF1_left GTGCGCGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATTTAAAAT-AAATATT-GAAAAGAAAACGCT-TAGTTTTAGTTAATAATTAGATTG DroVir_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATTAATTAA-TACATTTGAC-AAAACTCTATATAAACAGTATGTTGG-CTTACAATG DroWil_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACCTTAATTAA-TAAATTTCAG-AAACTAATAGTGAAGAAAAATCGTCT-TGTCTAGTA DroYak_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATTTAAAAT-AAATCAA-AAAAAAAATAAACTTCATTGATTTGCTTT-ATTAGATTG DroMoj_CAF1_left GTGCGTGTAATTTTTGGTAGCCGGGAATGGCGTTCGCGCCGTCCCGACATATATGAATATATATA-ATTGTTGAAACTGT-TAATGATAGTACGA-TTATCATAG