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


DroAna_CAF1_left   TCTTTTG-GTAGTTTCAG-CA-AAC--AAGAAAGCGCCACCTACTGTTATTTCCGTACGACTGCTTTACTTTCA-CGCAAG---------CAGTGTGCTTTAGTACGAAAAATAACCCTA
DroEre_CAF1_left   ACT-----------TGTG-CA-CTG--CTTGCAGCGCATCAATGAGGTCAAGCAGTGTAAATAGATGTACAGTACAGATGTACAGATGTATGGGAAGCACTAAGGTGAAATCTTGCCA-C
DroGri_CAF1_left   ATTGTTT-AGTGCGCCAT-CTAGCGTTTAAAGTTTACAGTGAGGCAGCTTTACGTACTTGGC-----A-TTAACAGTGCGT--------TG-CTTTGCTTTAGTAGTTAAGTTATTCA-G
DroMel_CAF1_left   GG-CTTG-AAGC-TCGTG-CA-CTG--CTTGCATCGCAACAATGGGGTCAAGCAGTGCGTGCGTATGTACAAATTTTTTGT--------TGAGGAAGCACTAAAGTAAAGTCGTGCCA-C
DroMoj_CAF1_left   CTAG-ACATAAC-A-AAC-AT-TTA--GCTGCAGC-CAACTTTGCTCTCAATTGATTGTGCATGTTGCTGTCAC-TGTTCT--------ACACCTTGTCTTAATACGGACATTTTTTG-G
DroSec_CAF1_left   TGGCTTG-AAAC-TCGTA-CA-CTG--CTTGCATCGCAACAATGCGGTCAAGCAGTGCGTGCGTGTGTACATTT-TGTTGT--------TGAGACACCACTAAACTAAGGTCTTGCCA-C
DroSim_CAF1_left   TGGCTTG-AAAC-TCGTT-CA-CTG--CTTGCATCGCAACAATGCGGTCAAGCAGTGCGTGCGTGTGTACATTT-TGTTGT--------TGAGACAGCACTTAACTAAAGTCTTGCCA-C
DroVir_CAF1_left   TTGTCAT-ATAA-ACTAAAAA-GTG--CAGCCAACTTAACTTAAAAATCAATACACATACAC---AGCGTTCGC-TTTGCA--------ATGCTATGCTTACATACTAAAAATTTTCG-G
DroYak_CAF1_left   TTTGAAG-CTTG-GCCGT-AT-AGG--CTTGCATCGCCTCCACGAGAGCAAGCAGTGTGTTCGTATGTACATTC-CGTTGT--------GTGAGAAGCAGTAATCTAAAGTCTTGCCA-C
DroPse_CAF1_left   ATTGTTA-TCGACAAAAG-CTGAAA--TGTATGACACTGAAAAGATAATACACAAACCAAACCATTGC----AC-CCAAGC--------TCGCGACGTAGAAGTTGCATAATTATCAC-A

DroAna_CAF1_left   GCAGT-CTGCATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------T-ATGGAGCA--AT-TG-TAACGCTCC--
DroEre_CAF1_left   ATGCGTGAACATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------TACTGGAACACAAT-TA-GAGTGTTTC--
DroGri_CAF1_left   CAATGTGCCAGTGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCATGAGTTCGAATCTCGTCGGGGCC------TAT-TGTGGAAAC-CGC-AATTGATAA--
DroMel_CAF1_left   ATGCGTGAATATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------TATTGGAACACGAT-TT-GAGTGTGCC--
DroMoj_CAF1_left   TTGTGGAGTAACGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------TACACAGTTGAATA-TC-CGCAAACTGA-
DroSec_CAF1_left   ATGCGTGGACATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------TATTGGAACACGAT-TT-GAGTGTGCC--
DroSim_CAF1_left   ATGCGTGGACATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------TATTGGAACACGAT-TT-GAGTGTGCC--
DroVir_CAF1_left   TCATGCGCAAATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCCTATGGGACGCGTACAATTAA-TTGTAGTTGTGTTT
DroYak_CAF1_left   ATGCGTGAACATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------TACTGGAACACAACTTT-GAGTGTCCC--
DroPse_CAF1_left   ACATGGCCACATGGCGCCGTGGCTTAGTTGGTTAAAGCGCCTGTCTAGTAAACAGGAGATCGTGAGTTCGAATCTCGCCGGGGCC------TTTC--T--ACAA----------------

DroAna_CAF1_left   ATTTACTTTTTTTTTATTT-TAC-CTA--ATCTTATTTTAAATAAACTTTACT-TTTAAATTTA--TATAAATGAAAATTATTCTTCTCTTTGGAT-TAGGAAC-CACAAGAAAAATCT-
DroEre_CAF1_left   ACTAACCTTTTTTCCTATTACTA-CAC--CATAAGCTATTTTTTAAAT--AC---AAAGTAAAT--CATTAATCTTTCATTACTTATGCGATTCCTGGTT-TAGCTGCATGAGCCGAAA-
DroGri_CAF1_left   AATTGTGTTCTTTTTTTAA-CAA-ATA--TTTTATTTTATATTTTTTAATATA-ATCCCAAATA--TCTAATCTA-CTACTTTTAACTAGCTGCATATTATTGA-ACACCATACAAA-T-
DroMel_CAF1_left   AGTAATATTTTTTCTATTA-TAT-TTT--CTATTTCTATCAAGCTATTATTTT-TATATACTAA--ATTAATCTTACC-GTTTAGCAGCATGAGCCGAAAGCCA-ACAAAGCGCTTCCT-
DroMoj_CAF1_left   TGTGGATTATTTTTTTATT-TTT-TTA--TTTTTTACAGAATACAATG-TGGA-CTCCAAGCGA--ACCGGATATAAAACATACTTCGCACCC-ACGCAGACAA-GCAATAAAGGAA-T-
DroSec_CAF1_left   AGTAATATTTTTTCTATTA-TAT-TTT--CTATTTCTATTAATCTTTTATTTT-CATATATCAT--TCCAAACTAAACTTACTATACTTTCTTAATTCACGTTT-TAGCTGCATGAGCA-
DroSim_CAF1_left   AGTAATATTTTTTCTATTA-TAT-TTT--CCATTTCTATTAGTCTTTTATTTT-CATATACTGA--AGTATACTACCTAAACTAATCTTACTATACTTTCTTAA-TTCACGTTTTTTGC-
DroVir_CAF1_left   GCGTCCTAAATTTATTTTA-ATA-TAT--TAATATTTATTTTTTAATAGCGTC-AATCAACCGAAAAGAAAACTGAACTTAACAAGCAAAAGCCAAA-ACAAAT-GTTAAGGGAATGCAA
DroYak_CAF1_left   ATAAACTTTTTTGCTTACA-TAC-ACCAACCATGCTAAACAAGCTTA--TTTTTTAAAAACTA---AAT---TGAATCATTATAATCTTACTTTACTTATGTAA-TTCCTGGTTTAGAT-
DroPse_CAF1_left   GAAATA---------TTGG-TATATTT--CC--TTTTTGCCAACTCT----TT----------------------------TTCCTCTT-------------------------------

DroAna_CAF1_left   AAAACATT
DroEre_CAF1_left   GCCAATAA
DroGri_CAF1_left   ACAGATAC
DroMel_CAF1_left   TACAAGAA
DroMoj_CAF1_left   GCAATTTT
DroSec_CAF1_left   AAAA-GCC
DroSim_CAF1_left   TGCA-TGA
DroVir_CAF1_left   CTTTGCTG
DroYak_CAF1_left   TCCAGAGA
DroPse_CAF1_left   TTTGTTAG