CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left C-TACAA--GAA---AATGA-AAAAAATAT-CT--AAGGCTA---AAAATAGACAAAGATCGTTGT--TGGTTCTCGTCCGC--CTTTTTTCTTTT-CTTGGCT-AAATTGACGCTCTTT DroEre_CAF1_left G-CAAGT--CCA---GCAAT-AAGAAACTA-AA--AATAGTA-TCAAGTTACGCCCACACATTTAA--TTCTGGGGGCTGTT--GTTTTGAC--TT-CTTCGGT-AAATTCTTGTTCTTT DroMel_CAF1_left GGCTAGA--CCC---GTAAG-AAGAAACTA-AA--AATAATA-TGAAGTTACGCCCACACATCAAT--ATCTG-GGGCTGTT--GTTTTGAC--TT-GTTCGGT-AAATTCTCGTTTTTT DroMoj_CAF1_left G-AGACT--TCG---CAGAG-AAGACTCCC-AC--ACATTTA-AAGACTGAATACTATT-ATTATT--TTTTTTTTTAACTTT-TG-TAGCT--GTTCTTGGGT-AAATTGTCGATCCTT DroPer_CAF1_left A-AGACAGAGTG---GAAGG-CAGA-TATGACGCCCACATAAGGAGAACGAATTGTGGCTCGATGC--CGAGC-GAATGTTG--GCTCTT-------GTTCTGT-AAATTCTCCCATTTT DroPse_CAF1_left A-AGACAGAGTG---GAAGG-CAGA-TATGACGCCCACATAAGGAGAACGAATTGTGGCTCGATGC--CGAGC-GAATGTTG--GTTCTT-------ATTCTGT-ACATTCTCCCATTTT DroSec_CAF1_left G-CTAGA--CCC---GTAAG-AAGAAACTA-AA--AGTAGTG-TAAAGTTACGCCCACACATTAAG--ATATGGGGGCTGTT--GTTTTGAC--TT-GTTCGGT-AAATTGCCATTCTTT DroSim_CAF1_left G-CTAGA--CCC---GTAAG-AAGAAACTA-AA--AATAGTA-TAAAGTTACGCCCACACATCAAG--ATATGGGGGCTGTT--GTTTTGAC--TT-GTTCGGT-AAATTCCCGTTCTTT DroVir_CAF1_left A-GCGGC--TTAGAGACCCAGTTTGAGGAG-GA--AACTCC--CA------CACATATAAACCGAATGCTGTGTTAAAGTTTTAGTAGCTG---TT-CTTGGCT-AAATTGGCGCTTCTT DroYak_CAF1_left G-CAAGA--CCA---GCATG-GAGAAACTA-AA--AATAGTA-TCTAGTTACGCCCACACATCAAT--ATCTGGGGGCTGTT--GTTTTGAC--TT-CTTCGGT-TAATTCTAAAACTTT DroGri_CAF1_left T-CTTCG--AGT---TTTGG-AGTGGCGTC-GA--CAGAC-A-CCCACACAAGCAGAGACTGCAAA--CTGTGCAAAGATTT--GAGTCGCT--GT-TCTTTAGTGATTTCTGGCTCCTT DroAna_CAF1_left ATATAAGAGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAATT-TTTTTTCT-CCAACTACATA--CTC----TTTTAC DroEre_CAF1_left ATATAAGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTTTTTGTTTT-GTTTCGCCTTT--TCT----CCTTAC DroMel_CAF1_left ATATAAGAGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTTTTTGCGTTTTTTTCTTTATA--CCC----AATTAC DroMoj_CAF1_left ATATAAGAGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGGT-AAAGCTTT-TTTGCTTA-CT--TTT----ATTT-- DroPer_CAF1_left TTCCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTTGG-TAC-CTTT-T-TGCCGCCCT--CCC----CCGGAG DroPse_CAF1_left TTCCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTTGG-TAC-CTTT-T-TGCCGCCCT--CCC----CCGGAG DroSec_CAF1_left ATATAAGAGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGCT-TTTGCCTT-TTTTCTTTATA--CCC---------- DroSim_CAF1_left ATATAAGAGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTT-TTTGCTTT-TTTTCTTTATA--CCTTCTTTATTAC DroVir_CAF1_left ACATAAGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGGT-AAACCTTT-TTGTTTG--TA--CTT----AA---- DroYak_CAF1_left ATATAAGAGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTTTTTGCCTT-CTTTCTCTTTTTGCCC----AATTAC DroGri_CAF1_left ATATAAGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTGAAA-TTATCTTT-TTTTTTTCTGT--TTA----AGAATC DroAna_CAF1_left AAATCATTTATTTTTTTCAAGAAATTTCTTTTACTTACTCTGTGCACTGTCGGTGGAAGGTGAGAGCAAGACAATCAGCAGGCATATCACAAATGCGATTCGAAACAACC---------- DroEre_CAF1_left TTGTTCATGTTTAATTTCTTTTTACATTTTTTACTTACTCTGTGCACTGTCTGTGGAGGGCGAGAGCAAGACAATCAGCAGGCATATCACAAATGCGATTCGCAGCAATCGCGGTGG--- DroMel_CAF1_left TTGTTCATGTTTAATTTCTTTTTACATTTTTTACTTACTCTGTGCACTGTCTGCGGAGGGCGAGAGCAAGACAATCAGCAGGCATATCACAAATGCGATTCGCAGCAACCGCGGTGG--- DroMoj_CAF1_left ----TCAGATTTATT-TAAGTATATTTTTTCAACTTACTCTGTGCACTGTCTGTGGAGGTTGAGAGCAAGACAATCAGCAGACATATCACAAAGGCAATTCTCAGCAATCGCGGCGGCAA DroPer_CAF1_left GGGAGCCCCTTTGTTGTTGGC------AAAATACTTACTCTGTGCACTGTCAGTGGATGGTGAGAGCAAGACAATCAGCAGGCATATCACAAAGGCGACTTGCAGCAGCCGCGGCGA--- DroPse_CAF1_left GGGAGCCCCTTTGTTGTTGGC------AAAATACTTACTCTGTGCACTGTCAGTGGATGGTGAGAGCAAGACAATCAGCAGGCATATCACAAAGGCGACTTGCAGCAGCCGCGGCGA--- DroSec_CAF1_left -----AATGTTTAATTTCTTTTTACATTTTTTACTTACTCTGTGCACTGTCTGCGGAGGGCGAGAGCAAGACAATCAGTAGGCATATCACAAATGCGATTCGCAGCAACCGCGGTGG--- DroSim_CAF1_left TTGTTCATGTTTAATTTCTTTTTTCATTTTTCACTTACTCTGTGCACTGTCTGCGGAGGGCGAGAGCAAGACAATCAGTAGGCATATCACAAATGCGATTCGCAGCAACCGCGGTGG--- DroVir_CAF1_left ----GCATAATA-ATTAAT-TTTTTTCTGTCTACTTACTCTGTGCGCTGTCTGTGGAGGGCGAGAGCAAAACAATCAGCAGACATATCACAAAGACGATTCGCAGCAAACGCGGCGGCAA DroYak_CAF1_left TTGTTCATGTTCAATTTCTTTTTACATTTTTTACTTACTCTGTGCACTGTCTGCGGAGGGCGAGAGCAAGACAATCAGCAGGCATATCACAAATGCGATTCGCAGCAACCGCGGTGG--- DroGri_CAF1_left CTGTTTGTAATAATCTAGAGGCCAAAAGCATCATGACCAATATGCCCTTGCTGCATGTAAATTAT----GTCCAAGAGATATCTTAACGCA-TTACTAAATGTG---ATTTTTGTTA--- DroAna_CAF1_left --- DroEre_CAF1_left --A DroMel_CAF1_left --A DroMoj_CAF1_left CTG DroPer_CAF1_left -AA DroPse_CAF1_left -AA DroSec_CAF1_left --A DroSim_CAF1_left --A DroVir_CAF1_left CTG DroYak_CAF1_left --A DroGri_CAF1_left --T