CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AGTGGTGTT---TGGGGA-ATA-ATTCGTA-TTTCGAATGTATTTCTTTACAAATGATTATG---GG-AAAAAAGTT-------G-TTCCTTACATCATTTT-TAATTTAAAA-TTA--- DroEre_CAF1_left AAACAATAAATTTGAAGGTATT-CAG------TT-TCGTAGGGA--AAA-----TAAATATTTATAT-AC-AGTGAA-------T-TATGTAACTCTCC----TCACCTAGAA-ATTGGG DroMel_CAF1_left AGTGT---TGATAAATAT-AAG-TTATTCA-GTT-GTACATTGT--AAAGTGTTGTATTTTG---AT-AT-AGTGGT-------T-TATGTAATTCTTT----TGACCTATAA-ACAA-- DroMoj_CAF1_left CTTGGTTTC--TATACGA-CATATAA--AA-TAT-ATGTGTTTA--CTATACAAATTAAGCAG-ATT-AC-TAAATA-------A-ATGTCAATAGTCA-TATTGATTTTAAA-TTAAAA DroPer_CAF1_left TGTGTCATA--TAGCTGA-AATAACACCCTCAATGGTG-AGATC----AGATCTATAAATAA---AA-GT-AGAGTC-------G-CTGAGAAAATATC----AGATATACAA-ATATAT DroPse_CAF1_left AGCTTCATA--TAGCTGA-AATAACACCCTCAATGGTG-AGATC----AGGTCTATAAATAA---AA-GT-AGAGTC-------G-CTGAGAAAATATC----AGATATACAA-ATATAT DroSec_CAF1_left TTTAAAGTTGATAACTAG-AAG-TTATTCA-GTT-GTGCAGTGC--ATTGTTGTATTTTTAT---AT-AG-TGTCGT-------T-TATGTAATTCTTT----AGACCTATAA-ATA--- DroSim_CAF1_left TG--------ATAACTAA-AAG-TTATTCA-GTT-GTGCAGTGC--AAAGTGTTGTATTTTTAT-AT-AG-TGTGGT-------T-TATGTAATTCTTT----TGACCTATAA-ACAGAG DroVir_CAF1_left GAATAATTT--GATTTTT-ATTA-TC--GA-ATT-ATTCAATTG--ATAAGTACATTTTTCAA-TAT-AG-AAATCT-------T-GCAACGACTGATGGTATTTATTATTAT-TGATAA DroYak_CAF1_left GTAATTG---GAAGCTAT-TCATTTTCACA-GGG-CAAAGAATT--AGCT---T---TATTTTACAT-AT-AGTAAATTATGTAAATTTTTTAACCTAT----ATTTGTTCAAGACATAA DroGri_CAF1_left GTTATAATA---A-TGAT-ACG-GTATTTA-ATTGAT-TTGCTT--TTATT-AATA-GCTTT---GAATA-TT-TTC-------T-TGATCTATTCTACTTT-TTATATAAAA-TTG--- DroAna_CAF1_left -A---AA---TT-AAAAAGAAAAA--T--AAA-AAGTA-TTTCCAAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCGCT DroEre_CAF1_left AAAGGCATAAAT-AAAAACAAAAACGAAAAAA-GATAACTTCTTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCGCG DroMel_CAF1_left -AAGGCCTCAAC-AAAAACAAAAA--A--AAA-AGGAA-TTCCTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCGCG DroMoj_CAF1_left AAATAA--TAAT-AAAAGCTAAAT--A--TAATACACT-GATCCTAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCCAA DroPer_CAF1_left GTAGCT-----T-AAAA--ATAAA--A--AAA--GATA-ACGTTAAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCCA- DroPse_CAF1_left GTAGCT-----T-AAAAATAAAAA--A--AAA--GATA-ACGTTAAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCCA- DroSec_CAF1_left -----GGGC----AATATATAAAA--A--AAA-TTGAT-TCTCTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCGCG DroSim_CAF1_left CAAGGCGTTAAC-AAAAATAAAAA--A--AAC-TTGAA-TCTCTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCGCG DroVir_CAF1_left TAATAA--AAAT-AAAT--AATTA--A--TAAAATGCT---GCTCAGGTTCCACCGAGACTTGAACTCGGATCGCAGGATTCAGAGTCCTAAGTGCTAACCATTACACCATGGAACCTGT DroYak_CAF1_left ATAAATAAAAAC-AGACAAAAAAA--A--AAG-ACAAC-TTTCTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATAGAACCGCG DroGri_CAF1_left -----TA-T-TGAAAATACAAAAA--T--AAT-CGGTA-TAAATCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCCCG DroAna_CAF1_left ATGGTCGGTCACTGC---CAGA-TCGTTCCCTTCGACTT--CCG--GC-GCCTAAAATAGA--------CTTT-AAAAAGTTGAGAAATTT-----GATGGA--GCTGAGGTAGGCA-CA DroEre_CAF1_left CTGATCAGCCGTCGC---CAAA-TCGTTCCCTTCGATTT--CCG--CT-ACCAAAAAT--A--------CCCG-A-CGGCCGAAGAAAGTT-----GATTGA--GCTGAGATAGGCA-GA DroMel_CAF1_left CTGATCACCCGTCGC---CAAA-TCGTTCACTTCGATTT--CCG--CT-ACCAAAAAT--A--------CCCG-A-CGGCTGAGGAAAGTT-----GATTGA--GCTGAGATAGGCA-GA DroMoj_CAF1_left CTGATCAGTGATCGC---CGAG-AAACAAAACTTGAATTCTTTGTATC-ATCTATTTT--A--------TTCA-A-TGCCTCTCAGTGACTCATGATATTTC----AAAATTATTTT-TA DroPer_CAF1_left CTGGGCGAGGGCCAT---CAAA-GAGCTCTG--TTCGAT--TTC--CA-ATGAAAGAT--C--------ATAG-C-TAGATCACGAAAACA--AGAAGAC-A--AGAGAGGCC--CC-AA DroPse_CAF1_left CTGGGCGAGGGCCAT---CAAA-GAGCTCTG--TTCGAT--TTC--CA-AAGAAAGAT--C--------ATAG-C-TAGATCAAGAAAACA--AGAAAACAA--AGAGAAGAAGCCACAA DroSec_CAF1_left CTGATCTCCCGCCGC---CAAA-TCGTTCCCTTCGATTT--CCG--CT-ACCAAAAAT--A--------CCCG-A-CGGCCGAGGAAAGTT-----GATTGA--GCTGAGATAGGCA-GA DroSim_CAF1_left CTGATCACCCGCCGC---CAAA-TCGTTCCCTTCGATTT--CCG--CT-ACCAAAAAT--A--------CCCG-T-CGGCCGAGGAAAGTT-----GATTGA--GCTGAGATAGGCA-GA DroVir_CAF1_left TAGATAAGCGACCAC---AAAC-AAACAAAAATTTTGCCGTTTTCCAT-TTCTATTTT--A--------ATCA-A-AATACAACTTGTTCCCAAATATACAA----CAATTAATGCA-CA DroYak_CAF1_left GTGATCGGCGATCGC---CAAA-TCGTTCCCTTCGATTT--CCG--CT-ACCAAAAAT--A--------CCCG-A-GGGCCGAAGAAAGCT-----GATTGA--GCTGAGATCGGCA-GA DroGri_CAF1_left GTGATCAAGAATCGACAGCAAACAAGCAAAATTTTATTA--CTT--TGCATTAAAATA--ATACAAATTCTTGAA-CTGCTGAGGTAAACA-----AATTCAAAATTTAAATAAACG-GT DroAna_CAF1_left AAAATATCTCGTG----C--AAAAACAATGT---GTATGGCA DroEre_CAF1_left AAAGAAAGATGAA--ATC--GGTGTAAAGTA--AACATTTGC DroMel_CAF1_left AAAGAAAGATGGA--ATC--GGCGTAAAGCA--AACATTTGC DroMoj_CAF1_left CGACTAGACAGACATCGTATTATGCAAATAA--AGTGTAGAT DroPer_CAF1_left CAAGAAAGAAGAA--AAC--AATGAGAAGAAGCCACAAAAAG DroPse_CAF1_left AAAGAAAGAAGAG--AAC--AATGTAAAGCA--A-GG-CAAA DroSec_CAF1_left AAAGAAAGATGAA--ATC--GGCGTAAAGCA--AACATTTGC DroSim_CAF1_left AAAGAAAGATGAA--ATC--GGCGTAAAGCA--AACATTTGC DroVir_CAF1_left CCAAAATTCTGAGACAGATATTTGGGAATTA--CATATATCA DroYak_CAF1_left AAAGAAAGATGAA--ATC--GGTGTAAAGCA--AACATTTGC DroGri_CAF1_left TCAATAAGTGGCA--ACA--GTTTTTCAACA--ATC-GACAC