CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CGGACTTA-A---------ATATC---ACACTTCGAGCAGTCGGCATAATTAAAAT---TTCAACGC-AA-ATATTTGTA-----TATCAAGGGG-GGT-------ACTTGG-AGCATG- DroEre_CAF1_left TTATCTTG-A---------GTTAT---TCCACA--A-------TAACAAGGATGTGAAGGGTGA-GA-AT-A-AAATTAAAACCATATGTAACAA-AAT------GCTCCGAAATGCTG- DroGri_CAF1_left TTTGTGCG-C---------TACTA---AATTAAT-TAC-----AAAGCAATTTAAAAAGCACAGCTGCCA-AAAATGACA-----AAATATGCGG-ATG----------ATTATGAACAG DroMel_CAF1_left AATACGTA-T---------TTTAG---TTTCAC--T-------TGGAAGTTACAAAGTCATAGG-TT-TG-C-TTATCTTAAGTCATTCATGCAG-CTA------TACGAGATATGCTG- DroSec_CAF1_left ATTATTGA-TTTAGCTGTGTGTGC---TTATGT--T-------TTATCTTAAGTCATTCAACAA-TA-AC-A-ACG---------ATGCGAGTAA-ACC------AATTAGTAATGCTG- DroSim_CAF1_left TTAGCTGT-G---------TGTGC---TTATGT--T-------TTATCTTAAGTCATTCAACAA-TA-AC-A-ACGATGTGAAGTAAGCTAAAAA-ACC------CATTAGTAATGCTG- DroVir_CAF1_left AATTTGTG-C---------GGCAC---TAA--A--T-------TAATTACAAAGCAATTTGAAA-GC-AC-A-GCTGCCAATAATGAATTCATCT-GCA------GATGATTAAGGCCAC DroYak_CAF1_left TTATCTTT-A---------GTCAGTCAACAATA--A-------CAACGATGTGAAG---A--AT--A-AGAA-T-AA----ACCATATGTAAGAA-ACC-------ATTATATACACTT- DroMoj_CAF1_left ACTAAATT-A---------ATTAC---GAAGCAATTTGAGCTGACTGTTG-CCAA-AA-ATAAATTC-AT-A-TCCAGCTGATTAGGGCCACTAA-TGC-----AGATATGTAAATATT- DroPer_CAF1_left TTGAGGGA---------------C---TAACTGTGCAGAGTCAGCATAAT-GGAA-TT-TTCCAGGC-AA-A-TATTTGACGACAAACACACACGGGGCGGTGGAGAGGGGGAGAGGGG- DroPse_CAF1_left TACCCCTTGA---------GGGAC---TGACTGTGCAGAGGCAGCGTAAT-GGAA-TT-TTCCAGGC-AA-A-TATTTGATGACAAACACACACG-GTG----G-GCGGGGGAGAGGGG- DroAna_CAF1_left A-AGCATGAC-TAACTAAAA-CAAT-A-T--ACTACGATAT-AA-AAAATAAA----AATA---AA----AAAAAAATTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroEre_CAF1_left A-TATTGAAC-GAAGATGAA-CAAA-C-A--TTTT------------ATAAAA----TAAA---AA----CAAAAAGCTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroGri_CAF1_left T-TTTTGCAA-TCTAAATAGTTAAT-T-T--AGTTTGATGTGGTAATCAAAAT----TAAC---AA----CAAAAAATTAACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroMel_CAF1_left A-TACTGCAA-AAATATGAA-CAAA-T-A--TTTTTC--------AGAAATAAAAAAAAAAAACAA----CAAAAAGTTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroSec_CAF1_left A-TATTGCAA-TAACATGAA-TGAA-T-A--TTTTTT--------ATTAAAAAAAAAAGGA---AA----CAAAAAATTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroSim_CAF1_left A-TATTGCAA-TAACATGAA-TGAA-T-A--TTTTTT--------ATTAAAAA----AAAA---AA----CAAAAAATTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroVir_CAF1_left T-TAAGGCAT-GTAAATTAC-TAAA-T-A--TATTTC--------CTTAGAAA----AAAA---AA----TAAAATATTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroYak_CAF1_left A-AATGCTGATATT---GAT-ATAA-A-ATGAAT-----------AAAATAAA----AAAA---AT----CAAAAAGTTTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroMoj_CAF1_left CAAATATGTT-TAACATATT-TTGATATA--CAAT--------TTAAAAAAAT----AAAT---TAATTTAAAAAAAACTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroPer_CAF1_left GTAGTGAA-C-GAAAACATA-AGCC-G-A--AAAA--------ATAGAAAAAT----ATTT---TA----CAAAAAATGTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroPse_CAF1_left GTAGTGAA-C-GAAAACATA-AGCCCA-A--AAAA--------ATAGAAAAAT----ATTT---TA----CAAAAAATGTACTTGTGCGTCGGCCGGGAATCGAACCCGGATCAACTGCT DroAna_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCCGTTGAATAGTGCCGGAATTTTAAGCCCCATGGGTCTC--GTTCTCTTC----CCAACTCCGAGAGAGTAGTGTTCTATTTA DroEre_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCCCTTGGAGATGCGGAGAATTTTAGCCCCTATCACTCACCCCTCTACTCT-GTTCTGATTGGAAGTGAAGCGTGTTCTAAAAA DroGri_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCACATGAATATAGTCGGAAAT-GTTCTCAACATA-AGTCGCTTGACACTA-AAACTAAAACAAATACTGCTCTAAATATAGTA DroMel_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCCCTTAAAAATAGTGAGCAAGTTAACCCCTATCACTCACGCCTTTACTCT-CTTCTGATTGGAAGTGAAACGTGTTCTAAAAA DroSec_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCGCCTTGAGGAGATTGAGAAAGTTAACCCCTATCACTCACGCCTTTACTCT-CTTCTAATTGGAAGTGAAACTTGTTCTAAAAA DroSim_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCGCCTTGAGGGGAATGAGAAAGTTAACCCCTATCACTCACGCCTTTACTCT-CTTCTGATTGGAAGCGAAACTTGTTCTAAAAA DroVir_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCCGTTGTTTTCAAAACTAAAATTTCTCAATAACAGCCACTGCCGTTATTC-CAATCTAATCAAGCCGTT--CTAAACATAATA DroYak_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCACTTGGAGGGATCCAGAATTTTAGCCCCTATCACTCACCCCTTTACTCC-CTTCTATTGGGAAGTGAAACGTGTTCTAAAAA DroMoj_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCGCTTGAGATGCTGCCGAAAAGTTCTCAATATAAATAAGTAGAAAGTAAAGTTCTCTAAGCAGCCTCTCCCTG-TAGCTATGT DroPer_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCACTTGAAAGATCGGGGAATTTCTACCCGCAAGAACCGCACGACTGCGGAATGCCGGAATTGGACTGAAACCA-ACCCAACGT DroPse_CAF1_left TGGAAGGCAACTATGCTGACCATTACACCACCGACGCCACTTGAAAGATCGGGGAATTTCTACCGCCAAGAACCGCACGACAGCGGAATGCCGGAATCGGACCGAAACCA-ACCCAACGT DroAna_CAF1_left TAG--AACAGG--CGGCAGTCGCGCTTCAAACCCATGAATA DroEre_CAF1_left TAG--AACGAG--CGATAACCACGCTT---AG-CAAG-TCT DroGri_CAF1_left TTG--TTATCAGTCCCGCTTGAAAAAC---AA-AAGA-GAA DroMel_CAF1_left TAG--AACAAA--CGATAGCCACGCTT---AG-CAAG-TCT DroSec_CAF1_left TAG--AACAAA--CGATAGCCACGCTT---AA-CAAG-TCT DroSim_CAF1_left TAG--AACAAA--CGATAGCC-CGCTT---AG-CAAGTCTT DroVir_CAF1_left ATGCCAACAGT--CTCGCTTTGGAATA---TG-CAGA-ACC DroYak_CAF1_left TAG--AACAAA--CGATAAGCGCGCTT---AG-GAAG-TCT DroMoj_CAF1_left AAA--TACAAA--TTTGTCGCCTCTGA---GG-CTTA-TCT DroPer_CAF1_left TCT--ATAAAT--AGATCGTACGGCAC---GA-CATG-CAA DroPse_CAF1_left TCT--ATAAAT--AGATCGTACGGCAC---GA-CATG-CAA