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


DroEre_CAF1_left   AAATAA-ATTCA-ATCA-CGCTTACAAGTAAAAAT-ATTT--ACCCTCTAAAACCAA---TACA-ATCCGA-ATTCGCTC-TAAATT---TAACTAATTTCTTAAATA--CTAAAA---A
DroMel_CAF1_left   GTTAAA--CACAATGCT-TTAA---AAATCACAAA-ATAA--AACAACACATTGTTATAATACT-TAC-----TCTATAA-AAACAAAAATAACTCTTTAAAAATTGC-TTAAATA---A
DroPer_CAF1_left   TTAAAT-ACTT--AATT-ACTA---AATATTCGGA-ACTA--CCTCGCTAACAAAATAATAATT-AATAGATGCATCTAT-TTAATT---CTTCAACTAAAAAGACAA--TGAAAAAGGA
DroPse_CAF1_left   GCTTAA-ATACTTAAAT-AATA---AATATACGGA-ACTA--CCTCGCTAACAAAATAATAATT-AATAGATGCATCTAT-TAAATT---CTTTAACTAAAAAGACAA--TGAA-----A
DroSec_CAF1_left   ACCCAG--CGCACTGCA-TTAC---AAAAAATAAA-AGAA--CACATAGATAATAGT---TACC-CTCT-A-AACCTCTA-AAACTCTTACAAAAATAA-CTAATTTATTAAAATA---A
DroSim_CAF1_left   TTTAAA--CACACTGCA-TTAC---AAAAAATAAA-AGAA--CACATAGATAATACT---TACT-CTCTAA-AACCAAAA-TAAATCTTACAAAAATAA-CTAATTTC-TTTAATA---A
DroWil_CAF1_left   TGTTTA-AAATA-GTTG-AAAT---TATTTAAATA-TTCTATCAAAAAACGTTCACT-TACATG-AATTTA-ATAATTTA-TTG---GAATTGAAGTCCAACTATAGT-AGAAAAA--CA
DroYak_CAF1_left   TTATAA-GCTTAATTCACGCTT---CAAACAAGTA-ATAA--TACGCCCCA---GAACAATACA-ACC-----TTTTTACTCTCTAAATTTAACTAATTTCTTAAATA-AGTAAAA---A
DroAna_CAF1_left   AAGACTAACATCAGACT-TAAT---GAACTTCAAAGTTTG--TTCCATTTTAAAC-A--AGTTTCTTACTC-AGTTTCTT-AATAAA--CCAAAAATTATTTAATTTT-TTAAACC--AA

DroEre_CAF1_left   TTAAAAA--CCAAAAAA--GTTCGTTGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTCGTGACTCC-AGGAAAACCAAA
DroMel_CAF1_left   CTAAAAA--CAAAAAAATTAATTTATGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTCGTGAGTCA-ATGAAAATCAAA
DroPer_CAF1_left   G-AAACA--AACAAAAAATTACTTTTGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTGTTGAAAGTTTCCCAAAAATAA
DroPse_CAF1_left   G-AAACA--AACAAAAAATTACTTTTGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTGTTGAAAGTTTCCCAAAAATAA
DroSec_CAF1_left   C-TAAAA--ACAAAAAAGTTAATTATGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTCGTGTTTTA-ACGAAAATCAAA
DroSim_CAF1_left   C-TAAAA--ACAAAAAAGTTATTTATGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTCGTGTTTTA-ACGAAAATCAAA
DroWil_CAF1_left   G-AATCA--AAAAAAAAGATACTTATGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTGTTGGGTGG-ATCTGCCTATAG
DroYak_CAF1_left   TTAAAAA--CCAAAAAAATTATTTATGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGATGCTTCGTGAGTCA-AGGAAAATCAAA
DroAna_CAF1_left   A-AATATTGCAAAAAAAATTTATTTTGCATCGGCCGGGAATCGAACCCGGGCCGCCCGCGTGGCAGGCGAGCATTCTACCACTGAACCACCGAGGCTTCTTGGAAGA-GTCCAATCCAAC

DroEre_CAF1_left   TTC---CCATCACAC-TAAGCTGTTT-CTAAAAATAGCCTAAGCTAGCGATCATGAAAAACTTGC--TCGGTCT-CATG-AGTGGAGTGAGCTGCAGATCAGC-----GATC
DroMel_CAF1_left   TTC---CCACCACAC-TAAGCTGTTT-CTAAAAATAGCCTAAACTAGCGATTATGAAAAACTTGC--TTGGTCA-CACG-ATTCGAGTGAGCTGCAGATCAGC-----GATC
DroPer_CAF1_left   CAC---CAATCTCGAGAGAGAGCCCA-CAAAAGACCATCTATCCATTCAAATAGTTGCTGCGTCT--AAAAATA-ACCGAACAAGAAATAACAACAACTGAGA-----AAGT
DroPse_CAF1_left   CAC---CAATCTCGAGAGAGAGCCCA-CAAAAGACCATCTATCCATTCAAATAGTAGCTGCGTCT--AAAAATA-AACCAACAAGAAATAACAACAACTGAGA-----AAGT
DroSec_CAF1_left   TTC---CCACCACAC-TAAGCTGTTT-CTAAAAATAGCCTAAACTAGCGATTACTAAAAACTTAC--TTGGTCT-CATG-AGTCGAGTGAGCTGCAGATCAGC-----GATC
DroSim_CAF1_left   TTC---CCACCACAC-TAAGCTGTTT-CTAAAAATAGCCTAAACTAGCGATTACGAAAAACTTGC--TTGGTCT-CATG-AGTCGAGTGAGCTGCAGATCAGC-----GATC
DroWil_CAF1_left   GAGCACTCAGATTTCCTAAACATT-G-GCAAAGGCATCACAAACAAGTCTAAAAATAAAACAACCATTTGAACAACGAC-AATCAGCATACACTAACAACATGCAGCATAAA
DroYak_CAF1_left   TTC---CCACCACAC-TAAGCTCTTT-CTAAAAATAGCCTAAACTAGCGATCATGAAAAACTTGC--TCGGTCT-CATG-AGCCGAGTGAACTACAGATCAGC-----GATC
DroAna_CAF1_left   TTC---CCACATCTG-GCATCGCGCTTCCATAGCTGGGTCTAAAAATAGCCCAAAACTAGCGACT--AACAGCG-AAAC-TTGCTTAGTC-AGATAAGCCAAC-----TCAG