CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroAna_CAF1_left   CAAG--AC------TT-TCAAATTTTATTCACTGAACGAACCAGTTTAATATTTTTGG-CCTATTGCTTGTCGGCTATGTGGCTGAAG-----GTACCCTCGGA-GTGTGCATGCTTTCA
DroEre_CAF1_left   AGAT--ACAAT-AATA-ACAATCCGATTTTATTCACGCAACCTGTTTTATTT-TTGAC-CCTTTGGCAGTTCAGG---TCA-CTGAAG-----TTGGCCTCTTTGCC-GCGCTTGTTTCA
DroGri_CAF1_left   TTCA--ATGTG-T-TTGTTTGAACTTGTTTGCCGAACCGGCTGGCAAATTGC-CCAGC-CTTG-----TATTTAT---TCCCTAAATTCAAAAGTCATT-TTTGGCC-GACCTGCGTTCA
DroMel_CAF1_left   ACTC--AAATAGATAC-AATATACGATTTTATTCAAGCAACCAGTTTTATTT-TTGAC-CC-TTGGCAGTTGAGG---TCG-CTGAAG-----TTGGCCTCTCTGCC-GCTTAAGTTTCA
DroMoj_CAF1_left   TCCT-TTCGTT-T-TC-TGATTTTGTTTGGCTGTGGCCGGCTCGTATGTTAC-T-CAA-CTAAC-GCACATGTTG---CCA-AGCATA--A--AAGCCATTTCTGGCTCCGTAGCCCTCA
DroSec_CAF1_left   AGAT--ACAAT-A-GC-ACAATCCGATTTTACTCAAGCAACCAGTTTTATTT-TTGAC-CCTTCGGCAGTTTAGG---TCGCCTGAAG-----TTGGCCTCTTTGCC-GCCCACGTTTCA
DroSim_CAF1_left   AGAT--ACAAT-A-GC-ACAATCCGATTTTACTCAAGCAACCAGTTTTATTT-TTGAC-CCTTCGGCAGTTCAGG---TCGCCTGAAG-----TTGGCCTCTTTGCC-GCCCATGTTTCA
DroVir_CAF1_left   CTTT--CTGAT-GTCT-GCACGAACTTGTTTGTCGAGCCGGCTGACATATTT-CTCAT-TCCGTGCGCATGCAGC---AAGCACAAAA-----GCTAACTCAAGCCC-A-GTAGTTCCCA
DroYak_CAF1_left   T-AGATACAAT-A-GC-ACTATCCGATTTTATTCAAGCAACCTGTTTTATTT-TTGAC-CCTACGGCTGTTCAGG---TCG-CTGAAG-----TTGGCCTCTTCGCC-GCGCTTGTTTCA
DroPer_CAF1_left   TAAA--TAGAC-TTTG-ATTTTATT-CACTGAACCAGTTTCCTTGGCC-CCT-CGCCAGCTGGGGGCTGAGCCGG---GCCTCTGAAG-----TTGACCTTTGG-TCGGGGACAATTTCA
DroPse_CAF1_left   TAAA--TAGAC-TTTG-ATTTTATT-CACTGAACCAGTTTCCTTGGCC-CCT-CGCCAGCTGGGGGCTGAGCCGG---GCCTCTGAAG-----TTGACCTTTGG-TCGGGGACAATTTCA

DroAna_CAF1_left   GCTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGGATGATTAATTTTTTTGTATA-TT-TTTTTAACTTTCAATTCT
DroEre_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGGTG-ATTAATTTTTTGTA-TT-TT-AAATTTAATT--TTACTT
DroGri_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGATG-ATTTACTTTTTGCAATT-GC-TTTTTT-AAATATAA-TT
DroMel_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGGTG-ATAAACTTTTTT-T-TTAGT-TTTTATACAATTCGTATT
DroMoj_CAF1_left   GCTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGGGG-ACAACTTTTTTTAA-TT-TT-TTTTTTTTAATTTTTACA
DroSec_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGGTG-ATAAATTTTTTTTT-GT-AT-TTAAATACAATTTTTATA
DroSim_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGGTG-ATAAACTTTTTTTT-GT-ATTTTAAATACAATTTTTAAA
DroVir_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACATGAT-ACAATTATTTTTTAAAT-TT-TCAATGATAATTATTGCT
DroYak_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACAGGTG-AAGTACTTTTTTG--CA-TC-TTAAATTTAATTATTACT
DroPer_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACATGAT-TGGGATTTGATTTA-TC-TC-GAATTCTACCAAACTTTT
DroPse_CAF1_left   ACTGTTTCCGTGGTGTAGCGGTTATCACATCTGCCTAACACGCAGAAGGCCCCCGGTTCGATCCCGGGCGGAAACATGAT-TGGGATTTGATTTA-TC-TC-GAATTCTGCGAAACTTTT

DroAna_CAF1_left   -TAAAATTATTGCCTTTTAATAATAAAATT-GACTGCATT-TTGTAGC--A-TATAT-TATTACCGGTG-ACATTTA-TTTGGGAGTC
DroEre_CAF1_left   CTTGAAGAA--AT-TCTATTACTAAATTTCACTATTATATAAGTGCAATAAGGTATT-TGAGTTT---T-AGTTGAA-ATGCATAGAC
DroGri_CAF1_left   TAGGGCATT--TG-CGTTGATAATCGTTTT-ATTTATA---AATATTTTAATGTATTTCACTTATAATTTACATAAT-AGGCACGTTT
DroMel_CAF1_left   TTA-AGAAA--CC-ACCAGACTAAATGGCT-GAGTTCTCC-TCTAACGATATTTAGG-TATAAAGTATT-TGAGTATTAATTGAAATT
DroMoj_CAF1_left   AAT-TTTAA--TT-TATAAATACGTTTG-GGATAACTTTTTATTT--TAATTAAATT-CAATATAATAA-TTTAATA-ATAAATATTA
DroSec_CAF1_left   TTAACACAA--TT-TTTATATTAAGAAGCC-ACCAGACTA--ATGTTCGAGTTCCTT-CTTTAATGCAA-GTAGCATATTCTAGCAAT
DroSim_CAF1_left   TTAACACAA--TT-TTTATATTAAGAAGCC-ATCGAGTTC--CTTCTTTAATGCAAG-TAGCATATTCT-AGCAATA-AAGGATTTAA
DroVir_CAF1_left   TCATTTACT--TA-AATTTAATAATAGAAG-TCAGGAAAT--ATAAATAAATAAATG-CATAGCGAACT-TTTA-AA-TGTTTAATCT
DroYak_CAF1_left   TTTTG-AAG--GC-ATCAAACTAATGGTTA-AATTCCTCT-TTTGAAGCTATTA-GT-AAATATGAAACGTGAATAA-CCTTCTTTTG
DroPer_CAF1_left   TTT-GTTTA--GC-TACTTATTTAA-AT-AGCTGAATTCCAAGTTAACGAAGGAT---TTTAATATACA-TAAGTCT-ATGTTTATGG
DroPse_CAF1_left   TTT-GTTTA--GC-TACTTATTTAA-AT-AGCTGAATTCCAAGTTAACGAAGGAT---TTTAATATACA-TAAGTCT-ATGTTCGTTT