CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TATTT--ATA-ACA-A-AAGCTGCTAG-ACCATATA-CTAAGCAGT---TTATTAATCTAATCA-TATTTAAGGGA--AACTAGAACGAAGCAAGCTATGATGGGCACTT--CGCCAGGG DroEre_CAF1_left TACTG--TTA-CTTTAAATAGTTAATCGGCTGATAATGGAATCAAC---CCC---CGAGATGAT-TTCAGATGAGA--AATCTGCGC--AGCGAGCACTTAAGGGGTTTT--TTCCTCGG DroGri_CAF1_left GCCAA-TCAT-TTGCT-TATC--ATGCTTCTATAAATAGCATCATTTTAAGT---TGATGTGAA-A-CAACCCTGT--TCATTGTTC--GCCAAGCATAAGTTGGGTGTA--TTTTCGGC DroMel_CAF1_left --CAAGAAGT-GCTTAGTAGTTTAATCGGCTGATAATGGATTTAAC---CCC---CATGATGAT-GTCGGATGAGA--AATCTGCAC--AGTGAGCAAATAAGGGTCTTT--TTTCCCGG DroPer_CAF1_left TAATA--AATATCA-A-CAGAAGAACC-ATATAACA-TGATTCAAC---TCCTATATAAACCAA-GTGGAAAGCTC--TCCTCCAAC--AAAAACCCTTAATGGGGCCAT--TGTCGGTG DroPse_CAF1_left TAATA--AATATCA-A-CAGAAGAACC-ATATAACA-TGATTCAAC---TCCTATATAAACCAA-GTGGAAAGCTC--TCCTCCAAC--AAAAACCCTTAATGGGGCCAT--TGTCGGTG DroSec_CAF1_left AGAAG--T-G-CTT-AATAGTTTAATCGGCTGATAATGGATTCAAC---CCC---CATGATGAT-GTCAGTTGAGA--TATCTGCGC--AGTGAGCAGATAAGGGTCTCTTTTTTTCCAG DroSim_CAF1_left CAAGA--AGT-GCTTAATAGTTTAATCGGCTGATAATGGATTCAAC---CCC---CATGATGAT-GTCAGCTGAGA--TGTCTGCGC--AGTGAGCAGATAAGGGTCTTT--TTTCCCGG DroVir_CAF1_left CTA-A-TCAT-TCGCT-TATC--GTGAGTTTATAAATAGATGCATATATATA---AAAGTTGTG-CTTTTCTCCTA--GCGTTGTGC--TCCAAGCATAAACTGTGTAAT--TTGCCGCT DroYak_CAF1_left AGTAAAACCT-GTTAAATAGTTTAATCAACTGATAATGGAATCA-----CCC---CAAGATGAT-GTCATATGAGA--TAGCTGCGC--AGTGAGCACATGAGGGGTTTT--TTTCCCGT DroMoj_CAF1_left GGCTA--ATC-AGT-CGCCTATCTTACGTTTTAGCTTT-----TTC---CGTAAAAGAGCTTTTGGCGAAAAGTCACGGAATGGCCA--TGCGTGCTCAAGCATTGTATT--TTTCCACG DroAna_CAF1_left CG-CTTCCAAGAGCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGGTTCATCTTTTTTTGCTTTTCTTTT-T---A--T DroEre_CAF1_left CGAATCTCAATAGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGCATAAAAACTTTTTTTTAATTTGAATTT------ DroGri_CAF1_left TGGCCGCCAACTGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGGATTACTTTTTTGCGCTTTTATTATATTT----- DroMel_CAF1_left CGAGTTCCAATAGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGCATCTAACTTTTTTTTTTTGTTTAAATAAATAGC DroPer_CAF1_left CGTTTTTCAAGAGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGCATATATCTATTTTTCCCATTTTTTCTCTCT--C DroPse_CAF1_left CGTTTTTCAAGAGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGCATATATCTATTTTTCCCATTTTTTCTCTCTCTC DroSec_CAF1_left CGAGTTCCAATAGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGCATCAAACTTTTTTTTGTTTAATTATAA------ DroSim_CAF1_left CGACTTCCAATAGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGCATCAAACTTTTTTTTGATTTATTAATC------ DroVir_CAF1_left AGATTTTCAACCGCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGAATGAATTTTTTTTGTTAATTTATTTTTT----- DroYak_CAF1_left CGAGTTCCAACTGCCTCCGTGGCGCAATTGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGCATCAAAGAAATTTTTTTTACTTGTTTTGTTTAC DroMoj_CAF1_left CGGCCCTCAGTTGCCTCCGTGGCGCAATCGGTTAGCGCGTTCGGCTGTTAACCGAAAGGTTGGTGGTTCGAGTCCACCCGGGGGCGAGACACTTTTTTTTTTTTTTTTTTTTTTT----- DroAna_CAF1_left TTAATTTTTTATTTTAATGGCTTCCCTAGTGT-GTACTCG-ATTATTGTTGAA-A-TTATTAGCTTTGT-G---------T-GTCGAATTCTAATGGCAAAAATTAAGT--GAA DroEre_CAF1_left -----------AATAAATAGCTTCTCTAATGT-CGTTG-G-TTCAT-GA-GCTTT-TGTTTATTGCTTT-TGTGC-GGCGAATTTAAAGTGTGCA-A-T--TA---GTA-AAGG DroGri_CAF1_left -----------TTCGTAATTATTAAATACATTTAACGT-GTGCTAA-GT-GACTC-AGCGCATACATATTACACC-TAATTATTTTATTTGTTAT-TTAAAAG---CAT---TA DroMel_CAF1_left TT--CTATAATGTTTTTAGTTCATAAAGCTTT-TGCT-TA-T-TGCTTT-TGTGC-GACGAATCTAAAG-TGTGC-A--ATTAGTGAAG-----------------GGA-AATC DroPer_CAF1_left TCTTTTTTTAATTATTGGCAAATGGCTTTTTT-TAATGTT-TTCTT-AAAATA-T-ATTTATTTGTTTA-T---------T-CGTTTATTGTGTAGCGAATTT---TAA-TGAT DroPse_CAF1_left TCTTTTTTTAATTATTGGCAAATGGCTTTTTT-TAATGTT-TTCTT-AAAATA-T-ATTTATTTGTTTA-T---------T-CGTTTATTGTGTAGCGAATTT---CAA---TG DroSec_CAF1_left -----------TACAAGCAGCTTCTATAATGT-TTTTG-G-TTCATAAA-GCTTT-TGTTTATTGATTT-TGTGT-GGCGAATTTAAAGTGCGCA-A-T--TA---GTGAAGGG DroSim_CAF1_left -----------AATTAATTATTATATTTATTATTATAA-ACAGCTT-TT-ATAATGTTTTTTGTTCATA-ATTCC-TTTGTTTATTGATTTTG-T-G-T--GG---CGA-ATTT DroVir_CAF1_left -----------TATGTGCTCATAAATATTTTGAGGCAA-TTTGCAA-AT-GCTAG-ATAACACACAGAATACATA-TTATG-TTTAATTTTCTAT-TTTA-TT---TAT-TGTT DroYak_CAF1_left TT--TTAATTTAATAAATAGCTTCCCTAATGT-TTTTGGG-TTCATAAA-GCTTT-TATTTATTGCTTT-TGTGT-GGCGAATTCAAAGTGTG---------C---AAT-TAGT DroMoj_CAF1_left -----------TTATAAATTGCTTGCAATAAACATTTA-A-AGTCA-TC-ATGAA-ATTTTTATTGTATTTAATAATTATTATATATTTTGTATA-A-AT-AT---GCA-CTTC