CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TGAG-C-TAA--TTAACAGTATCT-----TAACAGTGAGG-GGACAAGAGG-ACCT-TTAA-------TTATGAT----GCCCTTAAGACAAACTCC---T--TTAC-TT--C--ACC-C DroEre_CAF1_left TACC---ATC--AG--ATGCA-AA-----TGTAAATT-CG-CACCATACTTTGCAG-TTCGAC-----CATCCAG----TACCGAATGTCGTTAATAAACT--AAAC-AC--G--GAA-- DroGri_CAF1_left CCAA-TGCAT--TC--AAAAA-CA--A--CGCAAGGA-CAATCATTAAATGACGAA-ACACCTAACG-TCATAAA----ATGA------CGTAGCGC---A--GGTC-AA--TGACGAAT DroMel_CAF1_left AAGA-C-TAT--CTCTCAATA-CA-----AAACAGAAGTA-TAAACATAAGCTCAG-CTCA-------TGCACAT----TTTCATCCTACGACTACT---A--AAAT-TC--T--AAC-G DroMoj_CAF1_left ATAC-A-TAC--A----AATG-CA-----TT-TAGTT-TA-TTATTCAACATAAGA-AATT-T-----CGATTGC----ATCCCACTTCCCTCTCAATTCAATTCAC-AT--A--CAC-- DroPer_CAF1_left TATC-G-AGT--AG--AGCCT-CA-----GGCCCGCG-GG-GCTCAAGACGGACAG-GGAG-C-----TGTAAAG----TGCAGATTGACCATTAAAATAT--GATC-TT--T--CAT-- DroPse_CAF1_left TATC-G-AGT--AG--AGCCT-CA-----GGCCCGCG-GG-GCTCAAGACGGACAG-GGAG-C-----TGTAAAG----TGCAGATTGACCATTAAAATAT--GATC-TT--C--CAT-- DroSim_CAF1_left TCAA-G-ACAGAAC--AGAAG-TA-----TAAGCATA-AG-GACCATG-CTAATTT-CCAC-C--CT-ATTTTAC----GACTAACATGCTAAATAA---A--TTTA-AA--T--AAT-- DroVir_CAF1_left ACCA-A-CTT--AT--AATAT-CA--A--CATTTGCC-AT-ATATAGAAA-A-ATA-TCCCGAATCA-GGCTTTA----AGCC------AAACACCT---A--TTAA-AACACGTCACTC DroWil_CAF1_left AGAA-C-CTC--TC--AAAAA-GG--A--TTCGTTTG-GC-ACACGAAAGCTATAT-CCTT-CAAGTTCCTATCAATCCTA--------CTAGCGCC-TCT--ATCCTAA--TGGA---- DroYak_CAF1_left AAACCA-AGAG-AA--ATGTA-GATGA--TTCCCACC--A-CATTTACT-GTCCAGATTCG-A-----CTAAAAG----ACTGTTGAAA---AT-AAATCC--AATC-TG--A--GAC-- DroSec_CAF1_left CTCA-A-GAC--AG--AACAG-AA--GTATAAACATA-AG-GTTCATGC-TAATTT-CCAC-C--C--ATTTTAC----GACTAAAATGCTAACGAAAT-T---TAA-AT--A--ATA-- DroAna_CAF1_left ATCAACAT--TCCCATTATTCATATTTATTAAT-CAATTAGCCCTCTCGGGCTTGCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroEre_CAF1_left GGGGTATT--TAACAAGCTTTAAATTTATTATT-CAATTAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroGri_CAF1_left TTTA--A---ACCTAAGCTTCACATTTATTATG-AAATTAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroMel_CAF1_left ATAAAATA--AGACAACCGTCATATTAATTATT-TAATTAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroMoj_CAF1_left ATTCCAATTCCCTCCTCCTTTTCATTTATTAAA-TTATGAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroPer_CAF1_left AGTCTTAA--ATTTAGTTTTCATATGTATTGGA-TAATTAGCCCTCTCGGGCTTGCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroPse_CAF1_left AGTCTTAA--GTTTAGTTTTCATATTTATTGGA-TAATTAGCCCTCTCGGGCTTGCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroSim_CAF1_left ATATTCAA--AGACAACCGCCATATTAATTATT-TAATTAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGGCTATTGGTTTAAGTTTTCAA DroVir_CAF1_left ATCAACA---ACCTGATAATCACATTCATTATT-TAATTAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroWil_CAF1_left -TCTAAT---ACTACTTTGTCAAATTTATTATATATTTAAGCCCTCTCGGGCTTCCAAAAATTGCCTTAGCGGACGGTATTTCACGTCCCCTGGGCGGGG-TATTGGTTAAAGTTTTCAA DroYak_CAF1_left CTATTTGT--AAATATCTTTTAAATAAATTGTT-TAATTAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroSec_CAF1_left -TATTCAA--AGACAACCGACATATTAATTATT-TAATTAGCCCTCTCGGGCTTCCAAAAATTGCCGTAGTGGACGGTATTTCACGTCCCCATGGCGGGG-TATTGGTTAAAGTTTTCAA DroAna_CAF1_left CTAGCAATAACCGCACCTCAGTAGAACTTCATCGGTTACGGTATTGCCACTGCGCAAAGATAACGAATGCCAGTA-CGG-CTGGCTTACTCCATTCGAGAGCGGCCAGAATCGGTTG DroEre_CAF1_left CTAGCAATAACCGCACCTCAGGAGGACTTCATTGGTTACGGTATTGCCACTGCGCAAAGATAACTAAACGCTGGCATTC-G-ACTCTACTGTATGCCGGCGCTGTTAGAAGCAGTTG DroGri_CAF1_left CTAGCAATAATCGCACCTCAGTAGAACTTCATTGATTACGATATCGCCTCTGCGCAAAGATAACCAAACACTGCTAAAA-TACAACTACTCTATGCACACACAGCCAGAACCAGT-T DroMel_CAF1_left CTAGCAATAACCGCACCTCAGGAGGACTTCATTGGTTACGGTATTGCCACTGCGCAAAGATAACTAACCTCTGCCATTT-TTACCATATACCATGCCGGCGCTGCCAGAAGCAGTT- DroMoj_CAF1_left CTAGCAATAATCGCACCTCAGTAGAACTTCATTGGTTACGATATCGCCTCTGCGCAAAGATAACCTAACTCGCCTAAGC-AACGGCTACTCCATGCGCGCCCAGTCATAACCAG-TT DroPer_CAF1_left CTAGCAATAACCGCACCTCAGTAGAACTTCATCGGTTACGGTATTGCCACTGCGCAAAGATAACCTGACACTCGAAATC-ATTGCTTTCTCCATGCCGGCGCAGCCAGAA-CTGGTT DroPse_CAF1_left CTAGCAATAACCGCACCTCAGTAGAACTTCATCGGTTACGGTATTGCCACTGCGCAAAGATAACCTGACACTCGAAAGC-ATTGCTTTCTCCATGCCGGCGCAGCCAGAA-CTGGTT DroSim_CAF1_left CTAGCAATAAACGCACCTC-GGAGGACTTCATTGGTTACGGTATTGCCACTGCGCAAAGATAACTAAGCTCTGCCATTT-TGACTCTATACCATGCCAGCGCTGCCAGAAGCAGTTG DroVir_CAF1_left CTAGCAATAATCGCACCTCAGTAGAACTTCATTGGTTACGATATCGCCTCTGCGCAAAGATAACCTAACATAGGCAAAACAACGACTACTCCATGCGCGTACAGCTACAACCAG--T DroWil_CAF1_left CTAGCAATATTCGCACCTCAGTTG-CCTTCATTGGTTACGAAATTGCCGCTGCGCAAAGATAACATAGCATGGCCAAAC-AGCACTTACTCCATGCCGGCGATACTATAACCAGTTG DroYak_CAF1_left CTAGCAATAACCGCACCTCAGGAGGACTTCATTGGTTACGGTATTGCCACTGCGCAAAGATAAGCAAGCACTCGCATTC-G-AGTCTACTCCATGCCGATGCTGCCAGAAGCAGTTG DroSec_CAF1_left CTAGCAATAACCGCACCTCAGGAGGACTTCATTGGTTACGGTATTGCCACTGCGCAAAGATAACTAAGCCCTGCCATTT-G-ACTCTATACCATGCCAGCGCTGCCAGAAGCAGTTG