CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TCGGCTCT-------GGATTCATAAACGTGAAACG-CA----TGACAATGCACTTTG-GGAA---TTTAAATGA-AC-CA-G--TT-A-GG-TTCC-G-AAACCA-AGACATTTAATA-- DroEre_CAF1_left TGCTAACG-------AGACTCTTTAA--TGTCATGACA----AT-GCACTTCCTGAATTTCA---ATGAGTAGG-TAACT----ACAGTAG-GTGC-A--AAAT--AAAGTCCGTAAA-- DroGri_CAF1_left TCCGATGA-------CATTGCACATT--TGAAATG-AC----AGTAAACACAAATTA-AAAT---GCAAGGCAC-ATTTG----CCTATTC-GATT-C-GATTTG-AATTTCCTGACA-- DroMel_CAF1_left CGAG--------ACCACACTCTTTAA--TGTGATGACA----AT-GCACTTCTTGCATTTCA---ATGAGTAGT-CAACT----ACGGTAG-GTGC-A-CAATT--AAAGTTGGTAAA-- DroPer_CAF1_left CCGGTTTT-------TTTTATGTTTT--TGGATCGTATGCGCGTTTGTCA-TGACGATGCAC---TT----TGGATAACAATGAGCCGTAG-TATA-A--AAAT--GTTGGCCCACAA-- DroPse_CAF1_left GTTTTTTT-------TTTTATGTTTT--TGGATCGTATGCGCGTTTGTCA-TGACGATGCAC---TT----TGGATAACAATGAGCCGTAG-TATA-A--AAAT--GTTGGCCCACAA-- DroSec_CAF1_left CTAACCAGACCGGCCACACTCTTTAA--TGTCATGACA----AT-GCACTTCTTGCATTTCA---ATGAGTAGT-CACCT----ACGGC-----------AGGT--AGAGTTGGTAAA-- DroSim_CAF1_left CTAACGAGA----CCACACTCTTTAA--TGTCATGACA----AT-GCACTTCTTGCATTTCA---ATGAGTAGT-CAGTTACCTACGGT-----------AGGT--AGAGTTGGTAAA-- DroVir_CAF1_left GCACATTT-------G-AATCTACAA-TAAATACA-CA----TTACAATG-CCAGGCACAT----TCAGTCAAT-AAATC----GAATTTC--GTGAA-ATTGGTCATTTTTAAAGCA-- DroWil_CAF1_left ACACATAA--------GTCATGACAA--TGCATTT-CT----TT-AAAATACAAACGAAAAA---AAAATTACT-ATGCC----A-AGCAC-ATTT-T-GACCA--AGAGTTGGTTGACC DroYak_CAF1_left CTAACGAG-------ACTCTTTTTAA--TGTCATGACA----AT-GCACTTCTTGCACATCA---ATGAGTAGG-TAACT----ACAATAG-GTGG-A--AAAT--AAAGCCGGTAAA-- DroMoj_CAF1_left CGTTGCA--------CATTTCGAATG--ACAAACA-AA----AA-TTACTATG-----CAAAGCACA-ATTGGT-CAGCA----AATTGAGTTTTG-TGGTGTA--AGAAATGGAAACGC DroAna_CAF1_left -TCAGT-CGAAA-ATTGTAAAGGCCAATAAAAATGGCCAAATCACGACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATACCCCGCATCTCC DroEre_CAF1_left -TGTTACCAAAC-CTTGTAAGGGCCAATAAAAGAGGCGTATTCACGACGGGGATGTAGCTCAGATGGTAGAGCCCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroGri_CAF1_left -ATGGG-CCAAG-TTTATGTGGCCCAATAAAATGCAGTCGGATACAACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroMel_CAF1_left -TGTTACCAAAC-TTTGTAAGGGCCACTATAAGAGTGACATTCATGACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroPer_CAF1_left -CCAAAGCACGCACTTTTTAGGGCCAATATATTGGGCTTATCCACAAGGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroPse_CAF1_left -CCAAAGCACGCACTTTTTAGGGCCAATATATTGGGCTTATCCACAACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroSec_CAF1_left -TGTTACCAAAC-CTTGTAAGGGCCACTAAAAGAGGCGTATTCACGAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroSim_CAF1_left -TGTTACCAAAC-CTTGTAAGGGCCACTAAAAGAGGCGTATTCACGAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroVir_CAF1_left -GTTGA-CAAAG-CTTGTATGGGCCAATAAATGCTGGGCATGTACAACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroWil_CAF1_left -ATTTACCAAAC-TTTGTAAGGGCCAAGAAATCACAGCAAATCATCACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroYak_CAF1_left -TGTTACCGAAC-CTTGTTAGGGTCACTAAAAGAGGCGTATTCATGACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCC DroMoj_CAF1_left AGTTGT-GGACG-CTTTTGTGGGCCAATAAATGCCCAGGAGATACAACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATACCCCGCATCTCC DroAna_CAF1_left AAA------TGA-TTT--TTTAAAT-ATATATATATT-T-TTTAA---ATA-----TA-TG-ATTTTGTTTTAAGGTGTTATTTAAGATTT-GATAATC-----T---T-GAGAAATTTT DroEre_CAF1_left AAT------TGG-TTT--TTTTAGT-TTTTCTTAAGC-C-TAATCAAATAT-----TT-T---A-AGAGGATATTGAG----GATTATT-G-AGGACATT-CTTT-------------AA DroGri_CAF1_left AGG------ATA-AAC--CCAATTTTTTATCTTTTTT-T-TTTTA---ATA-----TTTCAAATTTATTCTTTTGCATTTGCAGGCGAACAAAGTGATG-----G---A-CATGCCTCTG DroMel_CAF1_left AAA------GGA-TTT--TTTCCAT-ATATTT-TACTTTTTTATAACCCTT-----AA-CA-AATTTTATATGAATAT----TGATGCC-A-TACTAAA--AAAA---A-AACAAGCATA DroPer_CAF1_left AAAAG-GA-GGA-CTACAGGTCCAT-ATTTTTGTTAA-A-TTTCTTTCCTTTTGTAAT-CT-ATAAAAATGTTTTCTT---TTGATTGC-A-GACCAACAAAATGATAGAATCCCCTTTG DroPse_CAF1_left AAAA-----GGA-CTACAGGTCCAT-ATTTTTGTTAA-A-TTTCTTTCCTTTTGTAAT-CT-AAAAAATTGTTTTCTT---TTGATTGC-A-GACCAACAAAATGATAGAATCCCCTTTG DroSec_CAF1_left AAA------GGA-TTT--TTTCCAC-ATATTTTGCTT-T-TTATAACCCTT-----AA-CG-ATTTTTTTAAGAATAT---TGGATGGC-A-TATTTAAA-ATAA---A-AACAAGCGTA DroSim_CAF1_left AAA------GGA-TTT--TTTCCAC-ATATTTTGCTT-T-TTATAACCCTT-----AA-CG-AATTTTTTAAGAATAT---TGGATGGC-A-TATTGGA--AGCA---T-AACTTCCTAT DroVir_CAF1_left AGG------AGT-AAT--ATAATAACTTTTTGTTGT--T-TTTTT---TAA-----TT-AT-TAACGAAATTAAAAAGGATCTACTGTTTG-CATTTGC-----A---G-GCCAACAAAG DroWil_CAF1_left AAGGA-AGAGGA-CTT--GGTCCTT-TTTTTTGACAA-T-TTTTTGAAATC-----AT-TT-TTTTTTTTGTATATT----ATTTGTGC-A-GACCAATAAAGTCATGGAATCGCCATTA DroYak_CAF1_left AAA------GGA-TTT--T-TTTTT-AACCGTAATAA-A-ATATTTTATAT-----AG-C---T-TAACTTCCCTTTT----AATATTA-T-AC-ATTTT-TTTA-------------TC DroMoj_CAF1_left AGGATATTTGTAATTT--TTTATAT-ATTATCTTTTT-T-TTTTAATTACT-----AA-GC-AATTCTGAGTGATTTC---CCATTTTT-A-TTTTTTTC-TCAA---T-TGCAGGCTAA DroAna_CAF1_left -TAAA-A-ATAATTTCTATACTTATT--GCAGACC--AA-TAA-AATGA DroEre_CAF1_left AA-GAACAATATTTTAAATAGCATGACTTCC------CTTTTC-ATTTT DroGri_CAF1_left -TTATCC-ACTGGACAGTCCATCATC--GCAG------T-CAA-GGCGA DroMel_CAF1_left AGTTCCT-ATTTAATATAATACAATT--TAT------AA-TAA-TTAGA DroPer_CAF1_left -CTCTCC-ACGGGCCAGTCCATTATC--GCA------GT-CAAGGCCAC DroPse_CAF1_left -CTCTCC-ACGGGCCAGTCCATTATC--GCA------GT-CAAGGCCAC DroSec_CAF1_left ACTTCCT-ATTTAATATTATACATTT--T-A------TA-ATA-ATTAT DroSim_CAF1_left TTAATAT-TATATATTTATAATAATT--AGA------TT-AGA-TTATA DroVir_CAF1_left -TGAT-G-GACATGCCTCTGCTGTCC--ACTGGGCAGTC-GAT-TATCG DroWil_CAF1_left -CTTTCG-ACTGGACAATCCATAATA--GCT------GT-CAA--AGCA DroYak_CAF1_left TA-TTCC-AAATTGATAATTAGATTA--GAT------TA-TAA-TATTA DroMoj_CAF1_left TAAAGTG-ATGGATCTGCCGCT-GCT--AGC------AA-CTG-GCCAG