CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ATAATAATCGC--AAGATCAACGA-AAGAAGT-----AATTCAAACCCTACGCCGCGAT-AATTTCAGTTT-TTTG-T-T-TCAGTTTGAAAATA-AT---AATAAACG-CTGAG-AGAA DroEre_CAF1_left CGATAGAC-TG--CCCCACAAAAA-TACAATA-----AAAAAAAACGAAACTTACGCCGCGCCGTGACGAA-CATTTT-G-GTTTTTGTT-TCAGTTC---AAAAGACC-TAACG--ATA DroGri_CAF1_left TGTTGTGTGTG--TCAGTTGAACA-AATATAT-----ATTATTAC-ATATATATATATA-CGTATATTTATGTATA-TAT-AT-AGCTATCTATATAC---ATATAGACGAAAT--CTAG DroMel_CAF1_left ATAC-AATGAAAAACTTACGCC-GCGCCGTGC-----CGAATATGATTTATGGTTTTTG-TTTCAGTTGAA-AATA-T-A-TATATATAC-ATATATA---ACGAGGCC-TAACG--ATA DroMoj_CAF1_left GCGTTGTTGTT--GCGGTTTTGTT-CAGTTAC-----AAAGAAAAGTAAAAGAAAAAAA-GGCAAAAAGAA-AATA-T-A-AATACGTAAAAATAAAA---AAGAAAAG-TATCT-ATAG DroPer_CAF1_left GTCGCTGCCAC--GCCCACGCCCA-GACTGCC-----TACGCGACCGCGACGGGCTGAA-AAAGAAACGATTAAAC-G-A-TAAACCGAT-ATATGCG---ACAACGAT-AAACGATTAA DroPse_CAF1_left GTCGCTGCCAC--GCCCACGCCCA-GACTGCC-----TACGCGACCGCGACGGGCTGAA-AAAGAAACGATTAAAC-G-A-TAAACCGAT-ATATGCG---ACAACGAT-AAACGATTAA DroSec_CAF1_left AATACAATGAAAAACTTACGCC-GCGCCGTGC-----CGAATATGATTT-TGGTTTTTG-TTTCAGTTGAA-AATA-T-A-TATATGTAC-ATATATA---ACGAGGCC-TAACG--ATA DroSim_CAF1_left CTGCCCCACAG--AAATACAATGA--AAAACT-----TACGCCGCGTCGTG---CCGAA-TATGATTTTGGTTTTT-G-TTTCAGTTGAA-AATATATATAACGAGACC-TAACG--ATA DroWil_CAF1_left GAAAACCAAAA--AAAAACAAAAA-CCAAGAT-----GAAGAAAAGTTTAA---TAAAA-AAATAAATATATTTAC-A-T-AGTTCCTTC-AGTTTCGAGTTTAAGAAC-AAATG--AAA DroYak_CAF1_left AAAACCAAAAA--ACAAGAACTAACGCCGCGCAGTGCCGAACATTATTT-TG----GTT-TATGTTTCAGT-TCAA-A-A-TATATAAAT-ATATATA---ACGAGACC-TAACG--ATA DroVir_CAF1_left TGTTCGTTGTT--CGTTGCCGCCA-AATGTAA-----TTTGAGTTCTTTCAGTTCAAAC-AAACAAACAAAAAATA-T-A-TAAATATAA-TAAAGA----ATATATAT-GTATA--TAG DroAna_CAF1_left AAATGCATCCT-T---TGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCT-GA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroEre_CAF1_left AAATGCATCCT-T---TGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCT-GA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroGri_CAF1_left CATATCATCTTTG---AGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCT-GAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroMel_CAF1_left AAATGCATCCT-T---TGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCT-GA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroMoj_CAF1_left CATAGCATCCT-CTTGAGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCT-GA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroPer_CAF1_left CTGAGCATCCT-T---TGAAGGTTTTGGGTTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCT-GA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroPse_CAF1_left CTGAGCATCCT-T---TGAAGGTTTTGGGTTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCT-GA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroSec_CAF1_left AAATGCATCCT-T---TGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCT-GA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroSim_CAF1_left AAATGCATCCT-T---TGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCC-AA-AGCATGTAAATGCATTATTTGGTACGACATTCCAGAACGTACAATCTTCCC DroWil_CAF1_left ACAAGCATCCTTT---TGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAAATTTCTAAA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCTC DroYak_CAF1_left AAATGCATCCT-T---TGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCT-GA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroVir_CAF1_left AGCATATCCTT-G---AGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCT-GAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCC DroAna_CAF1_left GAATGCAAG-A---AAATGCG-AATAAACA----AACGATATACATATAT-ATATGCAATTTTT--GTGATTGTGCAACAACTGACATAATTTCTCAAAAA-ACTGA-TTATTAATTCA- DroEre_CAF1_left GAATGCAGG-AA---AATGCG-ATAAATGA----AATATGCAATTTTTGT--GAT-AGTGCGATT-ACCGATTCTCAAACTGATTTTTAA-ACTGAATAGAAATAAA-TAAGGTTACTT- DroGri_CAF1_left GAATGCAAG-AAATAAATGCTGAATAAACA----AACAAAAAATGAAAACCAAAAATAATC-TA--AGAAATATGCAATTTTTGTGTGAA-TAGTGTGATTTTCAAT-TATTTATAAAG- DroMel_CAF1_left GAATGCAGG-AA---AATGCG-ATAAATGA----AATATGCAATTTTTGT--GAT-AGTGTGAAATACTGATTCTCAAACTGATTTTTAA-AAGAAATAGCAATAAA-TAAGTTTACTC- DroMoj_CAF1_left GAATGCAAC-AACTAAATGCTGAAACAATA----TATATGC-AATTTTTG-TGAATAGTGTGAC--TTGCCAATATATATAAATATATATTTACAGTTTAT-TTATT-TATTCTATATAT DroPer_CAF1_left GAATGCAAG-ACAAATATGCGAAT-AACTA----AATGAAATATGCAATTTTTGTGCTAGT-GT--GATACAATTTCTCAAACTGATTTATAATTTACAACTACAAC-TAAACAACTAA- DroPse_CAF1_left GAATGCAAG-ACAAATATGCGAATAAAACA----AATGAAATATGCAATTTTTGTGCTAGT-GT--GATACAATTTCTCAAACTGATTTATAATTTACAACTAAAAC-T--ACAACTAA- DroSec_CAF1_left GAATGCAGG-AA---AATGCG-ATAAATGA----AATATGCAATTTTTGT--GAT-AGTGTGAAATACCGATTCTCAAACTGATTTTAAT-ATTAAATAGCAATAAA-TAAGTTTACCC- DroSim_CAF1_left GAATGCAGG-AA---AATGCG-ATAAATGA----AATATGCAATTTTTGT--GAT-AGTGTGAAATACCGATTCTCAAACTGATTTTTAA-ATTAAATAGCAATAAA-TAAGTTTACTC- DroWil_CAF1_left GAATGCAAG-AA---AATGCT-GAATAACATCAAATCAATCAAACAATAA--TAA-ACCTCTATATACATATA-TAGGTACATATGTATA-TATGTAC-TCAAAATA-TAATGATATGC- DroYak_CAF1_left GAATGCAGG-AA---AATGCG-ATAAATGA----AATATGCAATTTTTGT--GAT-AGTGTGATATACGATATACCGATTCTCAAACTGA-TTTTCAAAC-AAAATA-CAAATAAATAA- DroVir_CAF1_left GAATGCAAACAAATAAATGCTGAATATGCG----AACATAACGAATATCT---AT-ATATAAAAATATGCAATTTTTGTGAATAACTAGT-GTGATTTTCTATAACATTGAATATTTTC- DroAna_CAF1_left ATTAGA-CCTTTACG DroEre_CAF1_left GTAAGCTACATACTT DroGri_CAF1_left AGTATT-TTTAACAA DroMel_CAF1_left TTAAGC-TAACCACT DroMoj_CAF1_left GTTTTA-AAATTAAA DroPer_CAF1_left ATAAGT-TA-CTCTA DroPse_CAF1_left ATAAGT-TACTCTAA DroSec_CAF1_left TTAAGC-TAATCACT DroSim_CAF1_left TTAAGC-TAACCACT DroWil_CAF1_left A-ATTT-TTACGTGT DroYak_CAF1_left GTTTACTTTTAAGCC DroVir_CAF1_left AAATTA-TTGAGTTA