CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left G--GCAAGG-T-GTTG-CG-GTAATAAA--GAT-GGTTGAGCA----ACACTCAGAT-ACAGA-TAAAAATGTGCGCA-CGTAGATAC---A-G-ATACATT-TTCGGTCTAGCTCTTGT DroEre_CAF1_left AAATCTCCA-A-AGAA-AT-GCTGAAAT--ATA-CCA-CAATT----TCAAAGTACAATTTTC-CGCCAGAAGTCTGA-CTT-TTCTCG-TT-G-CTTTCTC-GC---TTTATCTCTTAA DroGri_CAF1_left C--CGTTACGTCATTC-TC-GTCGTCGT--CTT-TTT-GTTCA----TCGTCGAGCCGAATAC-ACAGTCAG-CGAAAACCT-CTCTGC-TT-G-CTTGCTT-TC---TTTGTCTCTTAG DroMoj_CAF1_left T--TTATTTAGTTCCATTG-GCTAAACAAATTG-CTTCTATTC----GAATGTATTT-AAATT-C--AATTTTACTCT-ATAAGCAAT---A-C-TATTCAT-AGT---TTGCTCTATTA DroPse_CAF1_left T--GCATTT-A-AGCA-TA-GGGAACAT--TGAGATA-TAAAG----TCTCACGCCAAGGTTT-TAATTAAGCCCAAC-AGTCAGAACT-GTAC-AAAACTC-TG----TTTTCTGTTAA DroVir_CAF1_left T--CTCTTAAT-ATCA-TT-CGGTTCAT--GAG-ACGCACAAA----A-ATGTTAAC-ACAAA-TTATATGAAAAATA-CGTCGATAT---T-C-AATGAAA-AGCAGTTCACATTACTA DroWil_CAF1_left A--TAATCAGTTTTGA-TT-CCAAAGAA--CAC-ATTGAAAAA----AGACATCGAA-ACGTT-CTAAATTGTTGAAG-ATTTTCAAG---C-A-GAGAAAA-GGCC-TTCGGGTTTTTG DroMel_CAF1_left G--CGTCCATAAAA-A-TAGTTCA--AA--CAT-GCAGACTCA---GATACTTCATA-TGTGCGCACAACTTG--TTA-GAACGCCTCTGTT-G-CTTCCTA-GC---CTCGTCTCTTGT DroPer_CAF1_left G--CGCTCGTAAAA-A----TAGT--TG--CAC-AACGGAGATACATATGTATCTGT-TTCTAAAGCAAGAAC--TCA-CATCTACTCGACG-AGCCAGCGCCGC---AAGTTCTTAGCA DroSec_CAF1_left C--AAAGAAATGCT-G----AAAT--AC--CAC-AATTTCACAGTATAATTTTCCGC-CAGACATCTATCTGA--AAA-CAAATCAGCTATT-A-CATTCTC-GT---TTTGTCTCTTCA DroSim_CAF1_left T--CTCCAAAGAAATG-CTGAAAT--AC--CAC-ATTTTCACA---GT-ATAATTTT-CCGCCAGACATCTGA--AAA-CAAATCAGTCATT-C-TATTCTC-GT---AATGTGTCTTGA DroYak_CAF1_left T--GCAAAGAAATG-C-GA-AAATTTAC--CAC-AATTTCCAAGTAAAATTTGTCTC-CA--CAAGCC--TGA--CAT-CAAATCAGCCATT-G-CCTTCTC-GT---CTTATCTCATTA DroAna_CAF1_left TGAGCATTTGGCAGCG-CATCGAAGC-AAGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTGGATTC DroEre_CAF1_left TGAGTGTTGGACATGC-GG-CACATC-GAGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTTTTTTT DroGri_CAF1_left TGTGCATTTGACAACG-GCCACTCAA-ATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTGATTTT DroMoj_CAF1_left CAATA-TTGGACGGCA-GAAGAGAAC-ATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTGACAAG DroPse_CAF1_left CAGCCATTTGGCGGCT-AT-TTAGGAAATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTGAATTG DroVir_CAF1_left CGATA-TTGGGCGACG-CCACGAAGC-ATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTGCTTTT DroWil_CAF1_left TGTCA-TTTGT-CTCAGTCGACAGAC-ATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTGGAAAT DroMel_CAF1_left TGAGCGTTTGACATA--ATCTACAAC-ATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTTTT-TT DroPer_CAF1_left CGCATTTGACA-ACG--CAGCAGAAT-ATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTGTGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTGAATTG DroSec_CAF1_left TGAGCGTTTGACATA--AGCCAGAAC-GAGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAATTTTTTAT DroSim_CAF1_left TGAGTGTTTGACATT--CACTACATT-ATGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTTTTTTT DroYak_CAF1_left TGAGCGTTGGACATG--CGCCACAAC-AAGGTAGCGTGGCCGAGCGGTCTAAGGCGCTGGTTTAAGGCACCAGTCTCCTCGGAGGCGTGGGTTCGAATCCCACCGCTGCCAAGTTTTTTT DroAna_CAF1_left T-ATT--TTGTTTATTTTGTTAC--TTTAT-----TG-AATTAT-TTGTTCTTTCTGAT--CGCTCTTACGTAGTTCTCCAAGC-GGGAGA-------------C-TTGGAAAA---AAT DroEre_CAF1_left T-TTA--TCCCTTAT-TTGCCAT--AATTT-TT--AT-TCTTCCGATCTTCG--CCA-ACGATTGTCAAG----CAAG-AAGAA-CA-AGA-------------A-ACGTACAA---GAA DroGri_CAF1_left T-TTA--TTTTTCAATTTATTTT--AA-AA--T-ATT-CTCTCA-ATATTA---AC--AAGCAATGGA------TCTTCTCAGA-CT-T-T-------------A-TT--TCTA---GCA DroMoj_CAF1_left A-ACT--TTTTATTCTATTTTTA--AAATTTAT-ATA-CATTTT-TCTCACA--TTTGAAATCATTAAAC----GA-T-CGTGT-CT-GCT-------------C-TTTCTATC---TCA DroPse_CAF1_left A-TTT--TTTGTAAATTTTCCAG--ATTTT-CT--AT-CTTTTTCAATAGCT--ACG-TAGCGATCC--G----ATCG-GCGAT-CG--GC-------------A-TTGAAGAA---GAA DroVir_CAF1_left TTTATTCTTGTTAAAAACCTGTT--TGCAT-----AA-CTGAAA-TTGTCTGCTGCTGA--TCATCGCTCGCACAAATTATGGA-CTCGTT-------------T-GCTTA-GA---ATC DroWil_CAF1_left A-ATT--TTTTGTATAATTCCCT--TTAGG--T-TTT-CTTTTT-ATTTGTG--TTTTTCATCTATTTTG----TG-TTTTTGT-GA-TCA-------------C-TTGTAGTT---GAA DroMel_CAF1_left T-TTG--TTTACAATTTACTTTG--TATTT--T--TC-CGATCAGTTCCAAC--AAC-AGTTGT---------------------AA--GACAC----TCAAGAA-ATTAACCA---GAA DroPer_CAF1_left C-TTT--TTTGTAAATTTTCCAG---ATTT--TCTATCTTTT-TCAACAGCT--ACG-TAGCGATC-CGA----TC-GGCGATCGGC--GATCGGCATTGAAGAA-----GAAT---CTT DroSec_CAF1_left T-TTT--TCTT-AGTATTGTATT---TTGT--AT-T--TTTT-CGATCAGTG--CCA-ACAACAAC--GG----TC-TTCAAGC-AA--GACGC----TCGAGAA-ATGAACAA---GAA DroSim_CAF1_left T-TCT--TCTTTGTATTTTTCCG--ATCAG--T--GC-CAACAACAACGGTC--GTC-AAGCA-----------------------A--GACGC----TCGAGAA-ATGAACAA---GAA DroYak_CAF1_left T-TCA--TCCCCATAATAGCCTTATTTTGT--A--TT-TTTTCCGATCTTTG--CCA-TCTG-TTG--TG----TT-GTCAAGC-AA-GAAC-T----A--AAGAATCGTACAAGAAAAG DroAna_CAF1_left CAGA--AATAGA-ATGAAATATCACCCCTAAGC--AG-CGAAAGATAC DroEre_CAF1_left CCTATTCTCCCCCTCCC---C-CTCC----TAC--GGACAGATACATC DroGri_CAF1_left ACTGTGAACATGCTGCTCGCA-CTGG----CAT--TTCGTTAGATCAC DroMoj_CAF1_left CTGATTATCGAG-CTGTTGAAGCACAC--ATTG--AG-CAACAATACA DroPse_CAF1_left TCTTAGAACACACAAGTCGGA-AAAA----AAA--GTAATTCCACCCC DroVir_CAF1_left AGAG--GCAATG-ACAAAAC-----------GT--AA-TAAACACGCG DroWil_CAF1_left AAGATTTACGTAATTCTGTTTGTAGGC--ATT------ACACAAAAAC DroMel_CAF1_left CCTATTCCCACCCTATA---A-TATC----AACGCACTAATACATCTT DroPer_CAF1_left AGGACA----CACAAGT---C-GGAA----AA------AAGTAATCCC DroSec_CAF1_left CCTATT----CCCCACC---C-TATA----ATA----TCAACGCCCTG DroSim_CAF1_left CCTATTCCCACCCTATA---A-TATC----AAC-----AACGC-ACTG DroYak_CAF1_left AAGTAG----AACCTAT---T-TCAA----CC------CTCGAACGCC