CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CAAGGACGAGTCCCTGTTGAGGCGCGTCATCAAGCCGCTGGAGGGTCTTCTGGTGAACCACAAGCGAATCATCATGAAGGACAGTTCCGTAAGTG----AAACATTTTCAA-------CA DroEre_CAF1_left CAAGGACGAGTCTATGCTGCGACGTGTGATCAAGCCGCTAGAAGGTCTGCTGGTCAACCACAAGCGCATTATTATGAAAGACAGTTCGGTAAGTT----TGGCACTCAGTTGC--CGTTT DroGri_CAF1_left CAAGGACGAGTCCATGCTGCGTCGTGTCATCAAGCCGCTGGAGGGTCTCCTCATCAACCACAAGCGCATCATCATGAAGGACAGTTCCGTAAGTT----TGCTAGGAACAAGG--TGTTC DroMel_CAF1_left CAAGGACGAGTCTATGCTGCGACGTGTGATCAAGCCGCTAGAAGGTCTGCTGGTCAACCACAAGCGCATTATTATGAAGGACAGTTCGGTAAGTT----TGACATCCAGTTGC--CGTTT DroPer_CAF1_left CAAGGACGAGTCGATGCTGCGTCGTGTGATAAAACCGTTGGAGGGTCTGCTGGTCAACCACAAGCGCATCATAATGAAGGACAGTTCGGTAAGTG----TTCAACAGTGTTTCTACACTT DroPse_CAF1_left CAAGGACGAGTCGATGCTGCGTCGTGTGATAAAACCGTTGGAGGGTCTGCTGGTCAACCACAAGCGCATCATAATGAAGGACAGTTCGGTAAGTGTT--CAACA--GTGTTTCTACACTT DroSec_CAF1_left CAAGGACGAGTCTATGCTGCGACGTGTGATCAAGCCGCTAGAAGGTCTGCTGGTCAACCACAAGCGCATTATCATGAAGGACAGCTCGGTAAGTT----TGGCATCCAGTTGC--CGTTT DroSim_CAF1_left CAAGGACGAGTCTATGCTGCGACGTGTGATCAAGCCGCTAGAAGGTCTGCTGGTCAACCACAAGCGCATTATCATGAAGGACAGCTCGGTAAGTT----TGGCATCCAGTCGC--CGTTT DroVir_CAF1_left CAAGGACGAGTCCATGCTGCGACGCGTTGTCAAGCCCTTGGAGGGCCTTCTTATCAATCACAAGCGCATCATCATGAAGGACAGCTCGGTAAGTT----GACTATACTTCAGA--TTTTC DroWil_CAF1_left -----ATGAGTCCATGTTGAGACGTGTGATAAAGCCCTTGGAGGGTCTGCTGGTCAACCATAAACGCATCATCATGAAGGACAGTTCGGTAAGTTTATTGGAGAACCTTTTTT--TTATT DroYak_CAF1_left -AAGGACGAGTCTATGCTGCGACGTGTGATCAAGCCGCTCGAAGGTCTGCTGGTCAACCACAAGCGCATCATTATGAAGGACAGCTCTGTAAGTT----TGGGAACTGGGTT-----TAT DroMoj_CAF1_left -AAGGACGAGTCTATGCTGCGTCGCGTGATCAAGCCACTGGAGGGCTTGCTAATCAACCACAAACGCATCATCATGAAGGACAGTTCGGTATGTT----GCACAGTATTATGA--GATTT DroAna_CAF1_left ------AAA-C------T-TACCCCATGATATTAAGCCGGCAGATGCT-CG-AATC--T--CCACGCGCATTTGTGACTATGATTGGGAACAGTAATGCTCCTGATGTGTGTATGTTGTT DroEre_CAF1_left ------ACGAA------G-TACCCCATGATATTAAGCCGGCAGGTGCT-TGCAATC--C--CCACGGGCACCTGTGACTATGATTGGGAACAACAAAGCTTCTGATGTGTGTATGTTGGG DroGri_CAF1_left ------TTA-C------T-TACCCCATGATATTAAGCCGGCAGACGCTTGT-AATTTAA--CCAGCGGCGTCTGTGACTATGACTGGGAACAGTAAAGCCGCTGATGTGTGTATGTTGGA DroMel_CAF1_left ------GCGAAG---TAG-TACCCCATGATATTAAGCCGGCAGGTGCC-TGCAATC--C--CCACGGGCACCTGTGACTATGATTGGGAACAGCAAAGCTGCTGATGTGTGTATGTTGGG DroPer_CAF1_left ------TCGATTCCCCAT-GACCCCATGATATTAAGCCGGCAGACGCC-CGTATCC--C--CCATAAGCGTCTGTGACTTTGATTGGGAACAGTAAAGGTGCTGATGTGTGTATGTTGGG DroPse_CAF1_left ------TTGATTCCCCAT-GACCCCATGATATTAAGCCGGCAGACGCC-CGTATAC--C--CCATAAGCGTCTGTGACTTTGATTGGGAACAGTAAAGGTGCTGATGTGTGTATGTTGGG DroSec_CAF1_left ------GCGAA------G-TACCCCATGATATTAAGCCGGCAGGTGCT-TGCAATC--C--CCACGGGCACCTGTGACTATGATTGGGAACAGCAAAGCTGCTGATGTGTGTATGTTGGG DroSim_CAF1_left ------GCGAA------G-TACCCCATGATATTAAGCCGGCAGGTGCT-TGCAATC--C--CCACGGGCACCTGTGACTATGATTGGGAACAGCAAAGCTGCTGATGTGTGTATGTTGGG DroVir_CAF1_left ------AAA-T------CGTACCCCATGATATTAAGCCGGCAGACGCATGT-ATTTTAA--CCAGCTGCGTCTGTGACTATGACTGGGAACAGTAACGCTGCTGATGTGTGTATGTTGGA DroWil_CAF1_left GGTCCATTTCT------T-TACCCCATGATATTAAGCCGGCAGTTGCT-CGAAATT--TAACCAAGAGCAGCTGTGACTATGACTGGGAACATTAAAGTCGCTGATGTGTGTATGTTAAA DroYak_CAF1_left ------ACGAA------C-TACCCCATGATATTAAGCCGGCAGGTGCT-TGCAATC--C--CCACGGGCACCTGTGACTATGATTGGGAACAACAAAGCTGCTGATGTGTGTATGTTGGG DroMoj_CAF1_left -------GTAAG---CTA-TACCCCAAGATATTAAGCCGGCAGTCGTTCGT-ATTTTAA--CCAGCGGCGACTGTGACTATGACTGGGAACAGAAATGCCGCTGATGTGTGTATGTTGGT DroAna_CAF1_left G--CAACTCCT-C--A-ATACTGCTTCAACAAAGAAT-TTTCAGTCGA--CAGCTTTTTAATCATAA-AA-TATT-CTAGGAAATGAAACTAAAGGGTAC DroEre_CAF1_left CA-GCGCTCTT-A--TACTGCGCGCTTGACAAAGAAT-ATTCGGTCGA--CATTTCCTCTACCAAAAATTAACCC-CTTATGGTATCA--ACTAA--CAG DroGri_CAF1_left ATTGC--GCTT-T--ATCTGCGCATCTGACAAAGATTTATTCAGACTA--CAAAACATAAAAATTGA-CA-CATA-AATATTTAATTG--AACAAGCAGC DroMel_CAF1_left CA-GCGCTCTT-A--TCCTGCGCGCTCGACAAAGAAT-ATTCGGTCGA--CATTTCCTCTAGCAAAG-GA-CCCC-CTTATGATATCA--ACTAACAACC DroPer_CAF1_left CA-GCGCTCTT----TCCTGCGCACTCGACAAAGAAA-TTTCAGACTA--CACTTCCAAGCCCGACC-GA-ATTCGAAATCATCTTCG--ACACAACTTG DroPse_CAF1_left CA-GCGCTCT--T--TCCTGCGCACTCGACAAAGAAA-TTTCAGACTA--CACTTCCAAGCCCGACC-GA-ATTCGTAATCATCTTCG--ACACAACTTG DroSec_CAF1_left CA-GCGCTCTT-T--TCCTGCGCGCTCGACAAAGAAT-ATTCGGTCGA--CATTTCGTCTAGCAAAA-GA-CCCC-CTTATGATATCA--ACTAATACCT DroSim_CAF1_left CA-GCGCTCTT-T--TCCTGCGCGCTCGACAAAGAAT-ATTCGGTCGA--CATTTCGTCTAGCAAAA-GA-CCCC-CTTATGATATCA--ACTAACACCT DroVir_CAF1_left GTTGC--GCCT-T--GCTTGTGTATCCGACAAAGTTATTTTCAGACCA--CAAATTCCAACTAAAAA-AA-TATA-TATTTACTTTAA--TACATCACAA DroWil_CAF1_left CA-GCGTATTCTTTACCCT--GCGCGTTCGACAAAGT-AATTTCAGACCACATTTC--AACCCAAAA-AA-TACT-AAAACGAGTAGA--A-ACTTATTT DroYak_CAF1_left CA-GCGCTGTG-A--TCTTGCGCGCTTGACAAAGATT-TTTCGGTCGA--CATTTTCTCCAGAAAAA-AA-CCCC-CTTTTGATGTCC--ACTAACAGCC DroMoj_CAF1_left G--TTGCGCCC-A--CCATGCGTATCTGACAAAGTAATTTTCAGACGA--CATATTCTATATATATT-AA-AACT-AGCAAATATATA--GTTCGTACAT