CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ACCACACACATAC-ACATACACGTTGGCATTTCC-AGAT---T----AGCACATTTGCGAATATAGAGATA-GAAG-AAATTTGCCA-GAA-CTTTCTT--TTCGCATAT----TGCGGT DroEre_CAF1_left AACAGCGTCACAC-TCATACACAGGCATAGATAC-ACAC---A----CGCATAGGCAGATAAGCACATGTG-TATT-TGCAAATTAA-ATT-TGCTGGA--ATTTTCCTA----TGGACT DroGri_CAF1_left TCTTTTCCCATAT-GAATTATAAGTATGTGTGTT-GTGT---A----TGTATGCATACGTACACATACACATGCAT-ACATATTGAA-TTT-CATTTGA---TTAAATTT----TAATTA DroMel_CAF1_left AACAGCGTCACAC-AAATACACAGGCATAGATAT-ACAC---A----CGCATAGGCAGATAAGCACATGTG-TATT-TGCGAATTAA-ATT-TGCTGGA--ATTTTCCTT----TGGACT DroPer_CAF1_left ATCACACACACG-----AACGCATGGACAGGCAC-ATGT---G----TTCATGTGAATACAAACGCGATTA-AATT-TGCTGGAAATTTCCTTGCGCAT--ATTTATTCAATTTAGCA-- DroPse_CAF1_left ATCACACACACG-----AACGCATGGACAGGCAC-ATGT---G----TTCATGTGAATACAAACGCGATTA-AATT-TGCTGGAAATTTCCTTGCGCAT--ATTTATTCAATTTAGCA-- DroSec_CAF1_left AACAGCGTCACAC-ACATACACAGGCATAGATAT-ACAC---A----CGAATAGGCAGATAAGCACATGTG-TATT-TGCGAATTAA-ATT-TGCTGGA--ATTTTCCTT----TGGACT DroSim_CAF1_left AACAGCGTCACAC-ACATCCACAGGCATAGATAT-ACAC---A----CGAATAGGCAGATAAGCACATGTG-TATT-TGCGAATTAA-ATT-TGCTGGA--ATTTTCCTC----TGGACT DroVir_CAF1_left ATTAGAATTGCTGGAAATTTCTTTGCACATATAT-GTAT---A----TTGAA-TATGTATATGTGTATAGA-TGAC-ATGTATACAT-ATT-AAATTTT--ATTT-AAAT----TCTAGT DroWil_CAF1_left TACGCATATAGCC-GGACACACACACACACATAAGGCAG---A----TTAAATTTTTGCT-AGAATTTTCG-TTGCACATATTTAAT-GAT-TATTATC---TCCCTCCC----CTCTCT DroYak_CAF1_left AACAGCGTCACAC-ACATACACAGGCATAGATAC-ACAC---A----CGCATAGGCAGATAAGCACATGTG-TATT-CGCGAATTAA-ATT-TGCTGGA--ATTTTCCTT----TGGACT DroMoj_CAF1_left GATTTGCTGGAAT-TTTCT---TTGCACATATGT-ATTCAAATTGTATGCTTGTATGTGTATGTACAAACA-TACA-T-ATTGAATT-TCA---TTTGATTACGTTCTAA----TTAT-- DroAna_CAF1_left TCTCGATTTTCCATGATGATTACCTTT--CAGTTCTGCTACTGAAGATTTTTGACGATAGCAAAAATACCAAA-CCACTGAAA--AAAATCGAGAACTTTATAT--TTGTCATATTCCTT DroEre_CAF1_left CTTCGATTTGACATGATGATGATTTTT--CAGTTCTGCTACTGAAGACAGTTGACGAAAGCAAAAATACCAAAATCACTGA-A-CGAAATCGAG-TTTCCATCT--GGATTTTTAT--TT DroGri_CAF1_left TCTCGATTTTATATGATGATATCTATT--CAGTTCTGCTACTGAAGAATTTTGACGAAAGCAAAAATACCAAAATCACTGA----AAAATCGAG-AAATTATAT--AGGGTATTTT--TT DroMel_CAF1_left CTTCGATTTAACATGATGATGATTTTT--CAGTTCTGCTACTGAAGACAGTTGACGAAAGCAAAAATACCAAAATCACTGAAA-CAAAATCGAG-TTTCCATAT--GGAATTTTAT--TT DroPer_CAF1_left ACTCGATTTACCATGATGATTA-TTTT--CAGTTCTGCTACTGAAGAACTTTGACGATAGCATAAATACCAAA-CCACTGAAA---AAATCGAG-TTTGCTTTTAGAATGG--TTC--AA DroPse_CAF1_left ACTCGATTTACCATGATGATTA-TTTT--CAGTTCTGCTACTGAAGAACTTTGACGATAGCATAAATACCAAA-CCACTGAAA---AAATCGAG-TTTGCTTTTAGAATGG--TTC--AA DroSec_CAF1_left CGTCGATTTTACATGATGATGATTTTT--CAGTTCTGCTACTGAAGACAGTTGACGAAAGCAAAAATACCAAAATCACTGAAA-CAAAATCGAG-TTTCCATAT--GGAATTTTAT--TT DroSim_CAF1_left CTTCGATTTTACATGATGATGATTTTT--CAGTTCTGCTACTGAAGACAGTTGACGAAAGCAAAAATACCAAAATCACTGAAA-CAAAATCGAG-TTTCCATAT--GGAATTTTAT--TT DroVir_CAF1_left TCTCGATTTAAAATGATGATATTTATT--CAGTTCTGCTACTGAAGAATTTTGACGAAAGCAAAAATACCAAAATCACTGA-A---AAATCGAG-TGTATAATA--CTAGTAACAA--AT DroWil_CAF1_left TCTTGATTTTCCATGATGATTAACTTT--CAGTTCTGCTACTGAAGAATTTTGACGACAAAACAAATACCA-AATCACTGAAAAGAAAATCGAG-TTAATTTTT--TTTTTTGCAC--GT DroYak_CAF1_left CTTCGATTTGACATGATGATGATTTTT--CAGTTCTGCTACTGAAGACAGTTGACGATAGCAAAAATACCAAAATCACTGA-A-CAAAATCGAG-TTTCCATTT--GGAATTTTAT--TT DroMoj_CAF1_left CTCGATTTTTATATGATGATAAATTGCCTAAGTTCTGCTACTGAATAATAATGAGGATAGCAAAAATACCAAATTCACTGA-C--AAAAATCGAGTTATAATGT--AGTTGCGAAT--TA DroAna_CAF1_left GTTTTTGCATATA-TTTTTTTGCACG---TTTTGT--GGTAGTTTTCCGTTCAACAATTA-GTCACTA--TCTC-CGTCC-CCTCTGCGCCCAG DroEre_CAF1_left GCACGCTCTTTTC-TGTAGTTGCGCCGCCCCCCTCTCTTTTACCCAATCCCATACATGCG-GGCACTC--GACC-TAACC-TCAAAAA-----A DroGri_CAF1_left TTTTTT-TTTTAT-AATTGACTTTTT---TCTTTGC-ACGTTCCTTTTTGTTACCAGTTT-CGCTTGT--GGCT-TTCTTACATACATACAC-A DroMel_CAF1_left GCACGCTCTTTTC-TGTAGTTGCGCC---CCACTCG-TTTTACCCACACCCTTACATGCG-GGCACTG--GACC-TAACC-TCAAAAAACAC-G DroPer_CAF1_left ATAAATAGGTTGT-TTCTTTTGTTGT----AAA-T--TTGCATGTACATATATTTATGTG-TATGCGGGTATGCGTACTT-TCATTGTTCAA-C DroPse_CAF1_left ATAAATAGGTTGT-TTCTTTTGTTGT----AAA-T--TTGCATGTACATATATTTATGTG-TATGCGGGTATGCGTACTT-TCATTGTTCAA-C DroSec_CAF1_left GCACGCTCATTTC-TGTAGTTGCGCC---CCAATCG-TTTTACCCACACCCATACATGCG-GGCACTG--AACC-TAACC-TCAAAAAACAC-G DroSim_CAF1_left GCACGCTCATTTC-TGTAGTTGCGCC---CCAATCG-TTTTACCCACACCCATACATGCG-GGCACTG--AACC-TAACC-TCAAAAAACAC-G DroVir_CAF1_left TGGACCTTTTTTT-GTATAATTCTTC---TTTTTTT-TTCTTTGCACGTTCCTTTTTGTT-GCCAGTT--TCGTTTGTGC-CTTTGTTACAC-A DroWil_CAF1_left TTCATTCTCAGTGTTC-CACA-TGTT---CAAATAG-TTTGTCCCTCTCCCCACAACTCATGTCAGGC--CATG-CGGTG-GCGACAGGTCT-A DroYak_CAF1_left GCACGCTCTTTTC-TGTAGTTGCGCC---CCTCTC--TTTTACCCACATCCATACATGCG-GGCACTC--GACC-TAACC-TCAAAAAACACGT DroMoj_CAF1_left GTTTTT-TTTTTT-AATGATAATTTT---TCTTTGC-ACGTTCCCTTTTGTTGCCAGTTT-CGTTTTG--TGCC-TTTGTTACACATACATA-C