CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GG------ACAAGAAGCC-GGGC-GTGCA-CCAGCCGCAGCGCGTCAGTATTCTGTTTATTTTCTTGG--TCAA-GTTTTAAGTGCCTTGT-CCCGCTTCT---GCTTCATTACCTGTTT DroEre_CAF1_left GC---TGGACAAGAAGCC-CGGT-GTGCA-CCAGCCACA----GCGTGTAAGTG--ATTTTCTTGTTTTGTCGT-GCTACGC--AGTGATA-GATTCGTCGTTTAAACCCCCTGCTGTCT DroGri_CAF1_left A--------TATTCTTTTATTTA-CCAAT-TAATAAT-AATATTCATTCATTACCTACCACCTAATCATAAATATGTGAGTGTGTTCTTCA-TGGTC-GTT---GCTATCAGTGCTCCAT DroMel_CAF1_left G---------ACGAGGGC-TTCCTGCTGG-ACAAGAA-GCCCGGCGTGCACCAGCCACAGCGTGTAAGTAATGTTTCCAGTTCCATCGTGC-TAAACATCG---TCTACCTCTGCTGTCT DroMoj_CAF1_left C--------AACCACAGCGTGTA-AGTGA-AAGCCCA-AACAATTACTCATTTACCTCTATAAATATTTGATAGTGTGTGTATGTATGTGT-TTCAC-GCT---TCCTCTAATGCTCCAT DroPer_CAF1_left A--------CAAGAAGCC-AGGT-GTACA-TCAGCCACAGCGCGTAAGTATAAATGAAACCCCTGTACCTCCAC-CCAACCATGCT-GCTCTCATTCTGCT---GCTACTGCTGCTGCAC DroPse_CAF1_left A--------CAAGAAGCC-AGGT-GTACA-TCAGCCACAGCGCGTGAGTATAAATGAAACCCCTGTACCTCCAC-CCAACCATGCT-GCTCTCATTCTGCT---GCTACTGCTGCTGCAC DroSec_CAF1_left G---------ACGAGGGC-TTCCTGCTGG-ACAAGAA-GCCCGGCGTGCACCAGCCACAGCGTGTAAGTAATGTTTCCAGTTCCATCGTGC-TACCCATCC---CCTGCCTCTGCTGTCT DroSim_CAF1_left G---------ACGAGGGC-TTCCTGCTGG-ACAAGAA-GCCCGGCGTGCACCAGCCACAGCGTGTAAGTAATGTTTCCAGTTCCATCGTGC-TACCCATCG---TCTGCCTCTGCTGTCT DroVir_CAF1_left C--------CACAGCGCGTAAGT-AATCC-CCCTAAA-CACTTACAATCATATTACTCATACACTTCATAAATATGCGAATGTGTGCGTGT-CTCTC-GCT---GCTGCCAATGCTCCAT DroYak_CAF1_left CCTGCTGGACAAGAAGCC-CGGC-GTGCA-CCAGCCACA----GCGTGTAAGTG--ATTTGCCAGTTTCTTCGT-GCTACTC--AGTTATG-GACTCGTCGCTTA---CCCCTGCTGTCT DroWil_CAF1_left G--------AAGCCAGGTGTTCA-TCAGCCACAGCGT-GTAAGTATTTCATTGTGCTCG-CCCCCCTCCCCCAA-TGTACCTACCCCTGCA-ACTGCTGTG---CTTACAACTGATGTCC DroAna_CAF1_left CCCAGCGCGTCGAAATGACTGTGACTTATGCGTAT----TTGAT-----GTCATATCACAGCCATTTTGACGAGTTTGGTGGAC-AGTGAAAG-TCATCGGCG-----CGAGAC-TCAAG DroEre_CAF1_left ATTAGCGCGTCAAAGTGACTGTGAACTATGTGGAT----TTGAC-----TTCATATCACAGCCATTTTGACGAGTTTGTTGGGC-AGCCCCA--TCATCGTGA-----AGTGTC-GGGCG DroGri_CAF1_left ATTGGCGCGTCAAATTGACTGTGAGCTATGTTGTTGCAGTTGTA----ATTCATATCACAGCCATTTTGACGAGTTTGATGTGGCAGCCACAA-TC-------TACTCATTGACCAAAAT DroMel_CAF1_left ATTAACGCGTCAAAATGACTGTGAGCTATGTGGAT----TTGAC-----TTCATATCACAGCCATTTTGACGAGTTTGTTGGAC-AGCCAGCC-TCATCAACG-TGGAAATGTT-GCGCG DroMoj_CAF1_left ATTTGCGCGTCAAATTGACTGTGAGCTATGTTTAT----GAGAT----TATCATATCACAGCCATTTTGACGAGTTTGATGTGGCAGCCACCA-ACTGCAAACAGCTAAGCGATGATCTG DroPer_CAF1_left ATTTACGCGTCAAAATGACTGTGAGCTATGTGTTT----TTGAT-----CTCATATCACAGCCATTTTGACGAGTTTGATGTGC-AGTCCCACTCCATCAATG-GCAGAGTGGA-GCTTT DroPse_CAF1_left ATTTACGCGTCAAAATGACTGTGAGCTATGTGTTT----TTGAT-----CTCATATCACAGCCATTTTGACGAGTTTGATGTGC-AGTCCCACTCCATCAATG-GCAGAGTGGA-GCTTT DroSec_CAF1_left ATCAACGCGTCAAAATGACTGTGAGCTATGTGGAT----TTGAC-----TTCATATCACAGCCATTTTGACGAGTTTGTTGGGC-AGCCAGCC-TCATCAACG-TG-AAAAGTC-GTGCG DroSim_CAF1_left ATCAACGCGTCAAAATGACTGTGAGCTATGTGGAT----TTGAC-----TTCATATCACAGCCATTTTGACGAGTTTGTTGGGC-AGCCAGCC-TCATCAACG-TG-AAAAGTC-GTGCG DroVir_CAF1_left ATTGGCGCGTCAAAATGACTGTGAGCTATGTTGTTGCATTTGCC----ATTCATATCACAGCCATTTTGACGAGTTTGATGTGGCAGCCACAA-ACTGCAATCAGCTATACGACAATCTT DroYak_CAF1_left AGTAACGCGTCAAAATGACTGTGAGCTATGTGGAT----TTGAC-----TTCATATCACAGCCATTTTGACGAGTTTGCTGGCC-AGTCTCA--TCATCGTGA-----AAAGTC-GGCCG DroWil_CAF1_left ATGGTCGCGTCAAAATGACTGTGAGCTATGTTAAC----CGGTCAGAAATTCATATCACAGCCATTTTGACGAGTTCGATGGGC-ATACGAA--TCTTCATAA-----AAATAATGCA-A DroAna_CAF1_left TGG-AT---GC--TTAGGAA---AGT-G-TTTTGCGA-TAAA--GTGTGTTAATCCTTTGGCCCTT-TTATTAC--AGATTGAGAAGGCCAA--GATTCTCAT-----TGC--CAACACG DroEre_CAF1_left TGCAAGTG-AAT-TTTTAAGA-CTAT-G-TACCAGAACATGA--T---CTCAT-CCATGAACCA--CCT---GG--CTGCTCTTCTCCACC---GCA--GATTGAGAATGC--C---AAA DroGri_CAF1_left TACAAA-AAAAAAAAAAAAAA-AA-AAAAAAACCT-T-CGAC---CACGTGAC-TCATACGCTGACATC---AGGCCCTGG--CGTCATGA---GCT--GGA------TGA--A---TGG DroMel_CAF1_left TGCAAG-TGAGTCTTTCAAGA-CCAA-G-TAAAAGAA-TCTC-ATGATCTCAT-ACATGGGTGCTCTTC---TC--CATCGCAGATTGAG----AAT--GCCA-----GAA--T---CCT DroMoj_CAF1_left TGCAAC-ATTTCTCTTCATGTGTTCAATTAAATAA-T-TTAA---AATATGAT-CCTTATCATTACAAA---TCTAAATTGAACCATGAGA---TCA--TAT------TAAACC---AAT DroPer_CAF1_left TCC-AG---TGTTGTACAATC-GAAA-C-GAACGCGC-GTGA--CTTTGCAAAGAAACCATAAATG-AAA--AC--AAAAATTCAATTATT---TCA--AAAG-----TGC--G---AAT DroPse_CAF1_left TCC-AG---TGTTGTACAATC-GAAA-C-GAACGCGC-GTGA--CTTTGCAAAGAAACCATAAATG-AAA--AC--AAAAATTCAATTATT---TCA--AAAG-----TGC--G---AGT DroSec_CAF1_left TGCAAG-TGAAT-TTTCAAGA-CCAA-A-TAACAGAA-TCTC-ATGATCTCAT-ACATGGACCATACAT---GG--CTGCTCTTCTCCATC---GCA--GATT-----GAG--A---ATG DroSim_CAF1_left TGCAAG-TGAAT-TTTCAAGA-CCAA-A-TAACAGAA-TCTC-GTGATCTCAT-ACATGGACCATACAT---GG--CTGCTCTTCTCCATC---GCA--GATT-----GAG--A---ATG DroVir_CAF1_left CTCTAT-AATTTGTTAAATAGTTTAAGTTCAATATTA-CCAAAACGACGAGCC-TATGTTGTCGACCAC---GT--GACTCAGACTCAGAC---GCT--GAC------ATC--A---GGC DroYak_CAF1_left TTCAAGTGCATT-TTTTATGA-CCAA-C-TAACCGAACATAA--G---CTCAT-CCATAAACCA--CCT---GG--CTGCTCTTCTCCACC---GCA--GATTGAGAATGC--C----AA DroWil_CAF1_left AATCTTTG-AAA-A-TTCTATGAAATGT-GAAAT-GATATGT-G----AAAAT-CAAATTGATTGA-GT---TT--TGTATCCTTTGTTAGATTGAA--AATG---C-AAA--A---ATT DroAna_CAF1_left C DroEre_CAF1_left A DroGri_CAF1_left A DroMel_CAF1_left G DroMoj_CAF1_left C DroPer_CAF1_left A DroPse_CAF1_left G DroSec_CAF1_left C DroSim_CAF1_left C DroVir_CAF1_left T DroYak_CAF1_left A DroWil_CAF1_left T