CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroMoj_CAF1_left GGCATTCATATGCCAAT-ATGTCACC-ACATAAACAAAATCGT-GC-TAAAAA--A-AATAATTCAATAAAATATAATTAGAAAATAATA--TAAAACATA---------TCCAA----- DroPer_CAF1_left GCGCAC-ACTCGATAAT-AATTAACT-AGAA--TTCTCGGCAA-TAAATATGT--A-CATAAAAGAAGAAAATACTAAAAATAACAAAAGAGGGAAACACA---------GTGCG---G- DroPse_CAF1_left GCGCAC-ACTCGATAAT-AATTAACA-AGAA--TTCTCGGCAA-TAAATATGT--A-CATAAAAGAAGAAAATACTAAAAATAACAAAAGAGGGAAACACA---------GTGCG---G- DroVir_CAF1_left GCGTTT-TAAGCTGAAG-AATTCCCA-GCTTTGGCTAAATTAT-AATTTAACA--T-AATAATACTATGTGCTACGTGAAACAACAAATA--TGTTATAGT---------TTAAT----- DroWil_CAF1_left CTTTAC-CCCCCCGGTT-GACGATGATAAAA--AAAAAAGAAA-TACGAAAAC--AATTCAAATGAAATTCACTTAAAAGAAAAAAAAAGAACAAATTACT---------GTGTT---GC DroEre_CAF1_left GTT------CCAAGGTTCTT-TCGCC-TGAG--ACCTTTGAGCTTCCTGTGGA--A-AAGGAGATTATAATGTACAAATAATGTTGGAATAACCAGTTAAA---------CGCCATGGA- DroMel_CAF1_left TTC------TAAGGTTC-TTTCGCCT-TGAG--AACTTTGAGCTTCCTCTGGC--A-AAGGAGATTATAATGTACAAATAATGTTGCAATAACCAGTTGAA---------ACCAATGGA- DroSec_CAF1_left TTC------CAAGGTTC-TTTCGCCT-TGAG--AACTTTGAGCTTCCTCTGGC--A-AAGGAGATTATAATGTACAAATAATGTTGCAATAACCAGTTGGA---------TGCCATGGA- DroSim_CAF1_left TTC------CAAGGTTC-TTTCGCCT-TGAG--AACTTTGAGCTTCCTCTGGC--A-AAGGAGATTATAATGTACAAATAATGTTGCAATAACCAGTTGAA---------TGCCATGGA- DroYak_CAF1_left CTG-----------------TCGCC--TGAG--AACTTTGAGCTTCCTCTGGAATA-AAGGAGATTATAATGTACAAATAATGTTGGAATAACCAGTTAAGCAGAATAAACCCAATGGA- DroMoj_CAF1_left ATATTTACC-TGCAATTG-CCTATTTGCTAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCCTGTT-TTAAATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroPer_CAF1_left TGACGAAAA-CACGTTTT-GCTATTCGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT-----TTAGATACCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroPse_CAF1_left TGACGAAAA-CACGTTTT-GCTATTCGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT-----TTAGATACCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroVir_CAF1_left CTGTTTGCT-TGCAATTA-CTTATTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCTTGAT-TTAAATAATTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroWil_CAF1_left CGCCGCTTG-CAAAAAGATTCTTCTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTTTGTACTATAGATATCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroEre_CAF1_left ATATCGACC-GAGTCTTG-CTAATTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT-----TTTTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroMel_CAF1_left ATACC-----GAATCTTG-CTAATTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT-----TTTTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroSec_CAF1_left ATACC-----GAATCTTG-CTAATTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT-----TTTTAAAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroSim_CAF1_left ATACC-----GAATCTTG-CTAATTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT-----TTTTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroYak_CAF1_left ATACCGACCGGAATCTTG-CTAATTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT-----TTTTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT DroMoj_CAF1_left TTCCATCATAAATGCA-ATA-AAAA-AAT-GGAAAA--AT----------ATT----TTTAAAAAGAGAAAAGAAAAGGTCTCAAGATT--T-AGGCAGAAATCCTGCCCGCTTACAAAA DroPer_CAF1_left ATCCATCATAAATCCC-AAGAAGAG-CAA-ACAAGG--CG----------TAAAAA--ACTAGTTTTTCAATTGTGCGTGTAGAAGCCCGAA-AAAGAGATCACATCACAGCGGAAGGAA DroPse_CAF1_left ATCCATCATAAATCCC-AAGAACAG-CAA-ACAAGG--CG----------TAAAAA--ACTAGTTTTTCAATTGTGCGTGTAGAAGCCCGAA-AAAGAGATCACATCACAGCGGAAGGAA DroVir_CAF1_left ATACATCATAAATCCA-AAA-TAAAAGAA-AGAGTT--TT----------TTTTTT-TTTTTTGAATGCAATTTAATTTGCGAAAAACC--A-TAGCCGAAAAC---GTAAATCGTAA-A DroWil_CAF1_left ATCCATCATAAATCATAAACGACGA-CGA-CAAAAA--AA----------AAAAAA--ACAAGTTTTCTTCAATTTCAATTGTGCGTGTGTAGAGAGTTGGAAAAACAGATCACAAAAAC DroEre_CAF1_left AACCTTCAGTACCTTA-AAAAAAAA-AAA--------------------------------AAAAATCCAAAC-AAATCATAAAAGTCT--C-TGGAAAAACAAGTTTTT-CAATTGTGC DroMel_CAF1_left AACCTTCAGTACCACC-AACAGCAG-CAG-CAGCACCAAAAAAAAAAAAAAAAAAATGCGTAAAAATCCAAAC-AAATCATAAAAGTCG--A-AGGAAAAACAAGTTTTT-CAATTGTGC DroSec_CAF1_left AACCTTCAGTACCACC-AACAGCAG-CAG-AAAAAA--AA----------AAAAAATGCGTAAAAATCCAAAC-AAATCATAAAAGTCG--A-AGGAAAAACAAGTTTTT-CAATTGTGC DroSim_CAF1_left AACCTTCAGTACCACC-AACAGCAG-CAG-CAAAAA-AAA--------AGAAAAAATGCGTAAAAATCCAAAC-AAATCATAAAAGTCG--A-AGGAAAAACAAGTTTTT-CAATTGTGC DroYak_CAF1_left AACCTTCAGTAGCA-------CCAG-CAAAAAAAAA--AA----------TGAAAATGCCCAAAAAATCAAAC-AAATCATAAAAGTCC--A-AGGAAAAACAAGTTTTT-CAATTGTGC DroMoj_CAF1_left A-AAAATATATAAACA-AAA-----------TTTGCT DroPer_CAF1_left G-GAAGGAGAACACGACGGA-----------CCAGAA DroPse_CAF1_left G-GAAGGAGAACACGACGGG-----------CCACAA DroVir_CAF1_left A-CAAGTTTTTCAATT-GTG-----------CGTGTA DroWil_CAF1_left G-AGAACAAACCACCAGAAG-----------CGGAAG DroEre_CAF1_left GTCGCGGCAAGGAGCT-GGAGTAAAAAATGAGTGGAT DroMel_CAF1_left GTCGCGCCAAGGAGCT--------------------- DroSec_CAF1_left GTCGCGCCAAGGAGCT-GGTC--------AAAAAAAA DroSim_CAF1_left GTCGCGCCAAGGAGCT-GGCC-----------AAAAA DroYak_CAF1_left GTCGCGCCAAGGAGCT-GGAA----------CAGAGA