CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CACCTAAGGCTGGACGAC-C-AAAGAAACTAATTGCAACC-TTTATA-T-TGGTATATT--A--TT-TGAAACTTTAC--ATTTCCAA-GTCA----CT--TTAGCTTGATGAACATTTT DroEre_CAF1_left G-AAAAGTCACCTAAGGCTG-G-ACGACCAAAGAAACTAATTGC-AA-C-CGCTACAGT--A--TC-TTT-TGTTTTC--ACTCGCAA-CTTC----ACAGTGTGCATGTTGAATATTTT DroGri_CAF1_left TAAGGC-TGGACGACCAAAG-A-AACTA-ATTGCAACCTCTATA-AA---ATATAGATCGAT--TT-ATC-ATTTTTCATTTAACCAA-AACT----GA--TGCCTATGTTGAACATTTT DroMel_CAF1_left GGAAAAATCACCTAAGGCTG-G-ACGACCAAAGAAACTAATTGC-AA-C-CGCTCCATA--A--TA-TTTTAATTTTC--ACTCGCAA-CTTT----AC--TGAGCATGTTGAATATTTT DroMoj_CAF1_left CAAAGAA--ACTAATTGCAACC-TCTATACGATATAGATTTTGT-TTTC-TTTTTAAGT--T--TG-AACCATGCACT--AGAAATTT-TATA----AT--TGAAATTGTTGAACATTTT DroPer_CAF1_left TTGCAACCACAATAAGGTAT-C-AACTC-GTGGAGTGTACACAC--A-C-TTTGTCACTT-T--TTTCAC-TTTTGTC--ACTTCCGT-CACT---GGT--TGGCCATGTTGAACATTCT DroPse_CAF1_left TTGCAACCACAATAAGGTAT-C-AACTC-GTGGAGTGTACACAA--A-C-TTTGTCACTT-T--TTTCAC-TTTTGTC--ACTTTCGT-CACT---GGT--TGGCCATGTTGAACATTCT DroSec_CAF1_left GGAAAAGTCACCTAAGGCTG-G-ACGACCAAAGAAACTAATTGC-AA-C-CGCCACAGA--A--TA-TTTGAAGTTTC--ACTTGCAA-CTTC----AC--TGAGCATGTTGAATATTTT DroSim_CAF1_left GGAAAAGTCACCTAAGGCTG-G-ACGACCAAAGAAACTAATTGC-AA-C-CGCCACAGA--A--TA-TTTGAAGTTTC--ACTTGCAA-CTTC----AC--TGAGCATGTTGAATATTTT DroWil_CAF1_left -------TCACCTAAGGCTG-G-ACGACCAAAGAAACTAATTGC-AA-CCCGCCATTTG--GTTAA-AGTTAAT-TCT--TCTCACTAGCTTGTTGGTT--GTTGCTTGTTGAACATTTT DroYak_CAF1_left AGAAAAGTCACCTAAGGCTG-G-ACGACCAAAGAAACTAATTGC-AA-C-TGCCCCAGT--A--TC-TGATTAATTTC--ACTTGCAA-CTTC----AC--TGAGCATGTTGAATATTTT DroVir_CAF1_left AACTAATTG--CAACCTCTA-T-ATGAT-ATAGATATATATATA-TA-T-ATATATTGCGAC--GG-TTATCAAATCG--AGAACTTG-TGCT---TTT--TATATACGTTGAACATTTT DroAna_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTT-GTTGGT-------AAC----CA-ATTTTTTTGTGAAAAAGCGACCATACCGACAATCGCCATTCAATTTTAAAATTCTGA DroEre_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTC-GATCGA-------AAC----C--TT---CTT-TGAAAAAGAGACCATACCGACATTCGCCATTCAATTTTAAAACTGCAG DroGri_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTTATATATATTGT-------ATA----TA-GAGTTTAGGTTCAAAAGCGACCATACCGACAATCGCCATTTAATTTTAAAATACTGG DroMel_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTT-AATCGA-------AAC----C--TT--TCTT-TGAAAAAGAGACCATACCGACATTCGCCATTCAATTTTAAAACTGGAG DroMoj_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTTATATAGAATGT-------TTG-GTGT--AT---ATGTTGAAAAAGAGACCATACCGACAATCGCCATTTAATTTTAAAATTTTAT DroPer_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTT-GATCGG-------AAC----C--CT----G--GTAAAAAGCGACCAAACCGACAATCGCCATTTAATTTTAAAATTTGTC DroPse_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTT-GATCGG-------AAC----C--CT----G--GTAAAAAGCGACCAAACCGACAATCGCCATTTAATTTTAAAATTTGTC DroSec_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTT-GATCGA-------AAC----C--TT--TATT-GGAAAAAGAGACCATACCGACATTCGCCATTCAATTTTAAAACTGGAG DroSim_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTT-GATCGA-------AAC----C--TT--TCTTTGGAAAAAGAGACCATACCGACATTCGCCATTCAATTTTAAAACTGGAG DroWil_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTTCTTA-TTAGATTGGCAAAAACAAA-CAAGA--TTTTTGGAAAAAGAGACTATACCGACAATCGCCATTCAATTTTAAAAGTAAT- DroYak_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTCGCTT-GATCGA-------AAC----C--TC----TTTTGAAAAAGAGACCATACCGACATTCGCCATTCAATTTTAAAACTGGAG DroVir_CAF1_left AAAATTATAGCACGAGTGTTCGGTCTAGTCACTTTATAT-AGATAA-------TGG----TA-TA--TTGTTTGAAAAAGCGACCATACCGACAATCGCCATTTAATTTTAAAATACTGG DroAna_CAF1_left TGCTAAAAATCACTT--ACAATTTGATGAATTGATT---CTTCGTTGAGATGGCCAAGAT-CCTGAGACACACTTTGCCCAGTGATGGA-T-ATATTT-T----TGG DroEre_CAF1_left TGCCT-ATAACACTT--ACTCTGCATTT----GTTG---TTGATTTGTAGTTGCGTCGAA-GTGGCCAGGATCTTGAGACACACTTTGC-C-CAGTGATGTGAGATA DroGri_CAF1_left CTGGGTTTGACTGCAACACACACAAAACACTGCAAA--ACACTGCAAAATTCACCATTTT-ATATTCTTTTCTTTACTTGCCACAATTT-T-GAGAC--------AC DroMel_CAF1_left TGCCCAATATCACTT--ACTCTTGATTTTTTGATTT-AATTGATTTGAAGTTGCGACGAT-GTGGCCAGGATCTTGAGACACACTTTGC-C-CAGTGAT-------G DroMoj_CAF1_left AATTTTCGAACACTGGAAATGAAACACTGAAAGTGA---AACACT-GATAGTGAAAC-AC-TGGAACTGAAACACTCCTCCTTTGTGCT-AGTTG-CCCC-----AA DroPer_CAF1_left TTCTTTTTCTGCGAC--ACACACACTTTATCGCCAT------TCTTGTACACTTGTTGGC-GGGGCTGCAATCCTGAGACACACTTTGC-C-CAGTGATGAG--GAT DroPse_CAF1_left TTCTTTTTCTGCGAC--ACACACACTTTATCGCCAT------TCTTGTACACTTGTTGGC-GGGGCTGCAATCCTGAGACACACTTTGC-C-CAGTGATGAG--GAT DroSec_CAF1_left TGCCCAATATAACTT--ACTCTTGATTTTTTGATTG---TTGATTTGTAGTTGCGACGAT-GTGGCCAGGATCTTGAGACACACTTTGC-C-CAGTGATG-----TG DroSim_CAF1_left TGCCCAATATCACTT--ACTCTTGCTTTTTGGATTG---TTGATTTGAAGTAGCGACGAT-GTGGCCAGGATCTTGAGACACACTTTGC-C-CAGTGATG-----TG DroWil_CAF1_left TTCAATTGCATAGTC--ACTCACTAAGTTTGGTTGG---CTAACTTTTTGGGTTGATATG-GTTACCAAAATTATGAGACACACTTTGC-C-CAGTGATGA----GA DroYak_CAF1_left TGCCT-ATAACACTT--ACTCTTCTCTTTTGCATTACTGTTGATTTGTAGCTGCGTCGAA-GTGGCCAAGATCTTGAGACACACTTTGC-C-CAGTGAT-------G DroVir_CAF1_left AATATTGGAATTGAA--ACACTGGAATACTGGAACA---CTGTCACACTGAAACACTGGAATATCTGAGCTGCGTTATTTTCTCTGGTAGC-CA--CAAT-----TT