CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroGri_CAF1_left C-AC-TGTGATATGTAAC--GAT---TT-AA--TG--------AACGCATATCACAACGATCGTTCCTT-TTAG-C-----GAGTGACCCATAACGACTTTAACA-CATATATCAG---G DroWil_CAF1_left -------TGATATATAAC--GGT---GA-AT--CT--------AACGCATATCACAACGATCGTTCCTT-TTAG-C-----GAATGGCCCAGAAAAAAACGACGATGAAACTTGAA---C DroAna_CAF1_left A-TATGTAACG---------AGG---GATAAACGCAT-ATCACAACGATCGTTCCTTTTAGCGAATGGT-CCTTAG----AATATTTTAC---------ATTTTT-TTTCGAATAGTCAC DroEre_CAF1_left A-AA-GGAAAA---TCAC--TGT---GATAT--GTTAGGGAACAACGCATATCACAACGATCGTTCCTT-TTAG-C-----GAACGGCCC---------GTCAAA-TTAGGGGATCACTT DroMel_CAF1_left A-AA-GGAAAA---TCAC--TGT---GATAT--GTTAGGAAACAACTCATATCACAACGATCGTTCCTT-TTAG-C-----GAATGGCCC---------GATGAA-TTTGGGGATCACTT DroMoj_CAF1_left TTAA-CGCATA---TCAC--AAC---GAT-C--GTTC-CTTTTAGCGCATGGCCCATTCATCGAGTTTGCATTT-T-----GAACTTTCA---------TAAAAA-CTTTTCATAGATGT DroPer_CAF1_left G-TT-C---------CTTTTAGCGTATGGCC--CCTAGGAAGTTG-GGAGCTA---ATCAATGACACTG-GGAT-GGATGTGAGGGTGGG---------TATGGG-TGTTGGTGTTGGTG DroPse_CAF1_left A-CG-ATCGTT---CCTTTTAGCGTATGGCC--CCTAGGAAGTTG-GGAACTA---ATCAATGACACTG-GGAT-G-----GATGT-GAG---------GGTGGG-TGTGGGTGTTGGTG DroSec_CAF1_left A-AA-GGAAAA---TCAC--TGT---GATAT--GTTCGGGAACAACTCATATCACAACGATCGTTCCTT-TTAG-C-----GAATGGCCC---------GATGAA-TTTGGGGATCACTT DroSim_CAF1_left TAAA-GGAAAA---TCAC--TGT---GATAT--GTTG-GGAACAACTCATATCACAACGATCGTTCCTT-TTAG-C-----GAATGGCCC---------GATGAA-TTTGGTGATAACTT DroVir_CAF1_left T-AT-GTAACG---------GTT---AATGAACGCAT-ATCACAACGATCGTTCCTTTTAGAGCATGAC-CCAA-T----TTATATATAG---------TATACG-AGAATATCAGATAT DroYak_CAF1_left A-AA-GGAAAA---TCAC--TGT---GATAT--GTTAGGGAATAACGCATATCACAACGATCGTTCCTT-TTAG-C-----GAACGGCCC---------GTTAAA-TTGGGGGAACACTT DroGri_CAF1_left AATATTATATACACTATAT---AATCGCTGCGTATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAGAAATCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCT DroWil_CAF1_left TTTGCTATTGATGTCCTTA---AACTGGCGATAATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAGAAATCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCC DroAna_CAF1_left ATTTGAAATTCTTGTTAAT---AAGCGCCGCAATTGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAGAAGTCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCT DroEre_CAF1_left AACTGGATTTGCTAACTCT---TGGTGCTGCTGATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAAAAGTCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCG DroMel_CAF1_left AACATAATTTCTTGACTCG---TGGTGCTGCTAATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGACCGGAAAAATCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCG DroMoj_CAF1_left ATATATATATATTATATAT---AGGCGCTGCTTATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAGAAATCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCT DroPer_CAF1_left TGGGTGTGGTTGTGGTAGG---TAGTGCTGCAAATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAGAAATCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCA DroPse_CAF1_left TGGGTGTGGTTGTGGTAGG---TAGTGCTGCAAATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAGAAATCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCA DroSec_CAF1_left AACTTGATTTCCTGACTTG---TGGTGCTGCTAATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCGGAAAAGTCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCG DroSim_CAF1_left AACTTGATTTCTTGACTTG---TGGTGCTGCTAATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCGGAAAAGTCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCG DroVir_CAF1_left ATA--TATGGTCAGATTAT---AGCCGCTGCTTATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAGAAATCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACCT DroYak_CAF1_left AACTCGATTTCTTGACCCGTAATGGTGCTGCTAATGCCACAACGAACTTCAATGGTTGTCTAGCTTTATGATCAGAAAAGTCACCTAAGGCTGGACGACCAAAGAAACTAATTGCAACTG DroGri_CAF1_left CTATAA-AATATAGATCGATTTATC-----AT-TTT-TC--ATTTA--A-CCAAAACTGATGCCTATGTTGAAC-ATTTTAAAATTATAGCACGAGTGTTCG-----G-TCTAGTCACTT DroWil_CAF1_left -GCCAT--TTGGTTAAAGTTAATTC-----TT-CTC-ACTAGCTTG--T-TGG---TT--GTTGCTTGTTGAAC-ATTTTAAAATTATAGCACGAGTGTTCG-----G-TCTAGTCACTT DroAna_CAF1_left TTATATTGGTAT--A-TTATTTGAAACTTTACATTTCCAAGTCACT--TTAGC---TT--GATGAACATTTTAAAATTATAGCACGAGTGTTCGGTCTAGTC-ACTTC-GCTTGTTGGTA DroEre_CAF1_left CTACAG-TATCT--T-TT-GTTTTC-----ACTCGC-AACTTCACAGTG-TGC---AT--GTTGAATATTTTAAAATTATAGCACGAGTGTTCGGTCTAGTC-ACTTC-GCTCGATCGAA DroMel_CAF1_left CTCCAT-AATAT--T-TTAATTTTC-----ACTCGC-AACTTTACT--G-AGC---AT--GTTGAATATTTTAAAATTATAGCACGAGTGTTCGGTCTAGTC-ACTTC-GCTTAATCGAA DroMoj_CAF1_left CTATAC-GATAT--A-GATTTTGTT-----TTCTTT-TTAAGTTTG--A-ACC---AT--GCACTAGAAATTTTATAATTGAAATTGTTGAACATTTTAAAA-TTATA-GCACGAGTGTT DroPer_CAF1_left CAATAA-GGTAT--C-AACTC-GTG-----GAGTGT-ACACACACT--T-TGT--CAC--TTTTTTCACTTTTG-TCACTTCCGTCACTGGTTGGCCATGTTGAACAT-TCTAAAATTAT DroPse_CAF1_left CAATAA-GGTAT--C-AACTC-GTG-----GAGTGT-ACACAAACT--T-TGT--CAC--TTTTTTCACTTTTG-TCACTTTCGTCACTGGTTGGCCATGTTGAACAT-TCTAAAATTAT DroSec_CAF1_left CCACAG-AATAT--T-TGAAGTTTC-----ACTTGC-AACTTCACT--G-AGC---AT--GTTGAATATTTTAAAATTATAGCACGAGTGTTCGGTCTAGTC-ACTTC-GCTTGATCGAA DroSim_CAF1_left CCACAG-AATAT--T-TGAAGTTTC-----ACTTGC-AACTTCACT--G-AGC---AT--GTTGAATATTTTAAAATTATAGCACGAGTGTTCGGTCTAGTC-ACTTC-GCTTGATCGAA DroVir_CAF1_left CTATAT-GATAT--A-GATATATAT-----ATATAT-ATATATTGC--GACGG---TT--ATCAAATCGAGAACTTGTGCTTTTTATATACGTTGAACATT--TTAAAATTATAGCACGA DroYak_CAF1_left CCCCAG-TATCT--G-ATTAATTTC-----ACTTGC-AACTTCACT--G-AGC---AT--GTTGAATATTTTAAAATTATAGCACGAGTGTTCGGTCTAGTC-ACTTC-GCTTGATCGAA DroGri_CAF1_left TAT--ATATATT-GT DroWil_CAF1_left TCTTATTAGATTGGC DroAna_CAF1_left ACC---AAT-TT-TT DroEre_CAF1_left ACC--TTCT-TT-GA DroMel_CAF1_left ACC--TTTCTTT-GA DroMoj_CAF1_left CGG--TCTAGTC-AC DroPer_CAF1_left AGC--ACGAGTG-TT DroPse_CAF1_left AGC--ACGAGTG-TT DroSec_CAF1_left ACC--TTTATTG-GA DroSim_CAF1_left ACC--TTTCTTT-GG DroVir_CAF1_left GTG---TTCGGT-CT DroYak_CAF1_left ACC--TCTTTTG-AA