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


DroAna_CAF1_left   CATTTGCATTTCATAGT--CGTGGAAGTTCTGGGGCGTTCCG-GCTGGATTC---T--CATTGTCGTG-GCATAT-TGAACAC-GGTTCAC-GGCTCTTTCTGCTGT--ACTTGGGCCGC
DroEre_CAF1_left   TCGGCTTATTTGCATTA--CCATTGCCTTTGCCAGCCGAAAT-TCGAGGAAG---T--TGCGATTCTT-TCCATG-GCTTTTC-CGGATTT-TTCATTGT-TGCGGA-ATATTGGGCCGC
DroGri_CAF1_left   TGAGAGCAGTCTGACCT-----GCCCAACAGATATTCAAATT-CAAATTATGCGGAAGTCGTATTTTT-TTCTTT-TGGTTAC-T---CGACACTGTTCAACG--TTGAGTTTGAGCCGC
DroMel_CAF1_left   TCGGCTTATTTGCATTA--ATATTTTATTTGCTAGCCGAAAT-TCGAGGAAG---T--TACGATTTTT-CCCATG-GCTTTTC-CGGTTTT-CTCATTGT-TGAGGA-ATATCGGGCCGC
DroPer_CAF1_left   GGTTCCGGTTGTTTTTTGGTTTCAACGAGTACGAATACGAAT-ACGA--ACG---AATACGATTAGAT-GTAGTA--TGTATTTTGAGCAC-CATTCAGC--GTTGT--GCTTGGGCCGC
DroPse_CAF1_left   TTGTTTTTTGATTTCAA--CGAGTACGAATACGAATACGAAT-ACGAATACG---AATACGATTAGAT-GTAGTA--TGTATTTTGAGCAC-CATTCAGC--GTTGT--GCTTGGGCCGC
DroSec_CAF1_left   CG-GCTTATTTGCATTA--CCATTTTATTTGCTAGCCGAAAT-TCGAGGAAG---T--TCCGTTTTTT-CCCACG-GCTTTTC-CGGTTTTGCTCATTGT-TGC-GGAATATCGGGCCGC
DroSim_CAF1_left   CG-GCTTATTTGCATTA--CCATTTTATTTGCTAGCCGAAAT-TCGAGGAAG---T--TCCGATTCTTTCCCATG-GCTTTCC-G-GTTTTGCTCATTGT-TGC-GGAATATCGGGCCGC
DroVir_CAF1_left   GTTACAAACTGTAGTTA--AC-CTTTAACGAATATTCGCATT-CACATTCAA---A--TTTTTCTGAT-GTCCTGTTTTTGTT-ATTTGACAC-TTTCCAACGT-TG-TCCTTGGGCCGC
DroWil_CAF1_left   TAAATAAATATCGAATA--GAAAATGCATTCGCATTGCTTTTCAAAGTCGTA---G--TCAAGATTCG-TTTATT-GTTTGAA--TTGAAC-ACTGTTGAACGT-TG-AGCTTGGGCCGC
DroYak_CAF1_left   TCGGCTTATTTGCATTG--CCATTGCTTTTGCTAGTTGAAAT-TCGGGGGAG---T--TCCGATTCTT-TCCATG-GCTTTTC-CGGATT-TTTCATTGT-TGC-GGAATATTGGGCCGC
DroMoj_CAF1_left   CACTTCGATTATAATTC--ATATTCATAGT-TTTTTTTTGTT-TCTTTTATG--GAAGTCCAGATTCG-GTTTTG-GTTTCGG-TTGAG---TTAGTCCCACGT-TG-AGCTTGGGCCGC

DroAna_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCTGAAGCAGTTCTCAAGCCTTGCC-CTCACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATTGCCTTTTGTTGGTAGCACTGAC
DroEre_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCAGAAGCAGTACTCAAGCCTTGCC-CTCACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATCACCCATTAACCGAAGCACTTTC
DroGri_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTTGTAAGCAGTGCACAAGCCTTCCT-CTTACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACCCAATTTCCATATCTAT-TAGTAAAGAG
DroMel_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCAGGAGCATTATTCAAGCCTTGCC-CTCACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATCACCGATTATCCGAAGCACTTTC
DroPer_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCAGAAGCAGTGCTCAAGCCTTGCC-TTCCCAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATTGCCTCTGATTCGTCTCACTCTC
DroPse_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCAGAAGCAGTGCTCAAGCCTTGCC-TTCCCAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATTGCCTCTGATTCGTCTCACTCTC
DroSec_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCAGGAGCAGTATTCAAGCCTTGCC-CTCACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATTACCCATTATCCGAAGCACTTTC
DroSim_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCAGGAGCAGTATTCAAGCCTTGCC-CTCACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATTACCCGTTATCCGAAGCACTTTC
DroVir_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTTGTAAGCAGTGCACAAGCCTTCCC-TTTACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATTTCCATTTATCCAAAAATTGAAT
DroWil_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTAGTATGCAATGCTCAAGCCTTTCCCCTAACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATTGTCACACACAC-A--TACTTAC
DroYak_CAF1_left   AATTGCTGGAATCAAGTTGCTGACTTCAGAAGCAGTACTCAAGCCTTGCC-CTCACAGGCTACACAGTCAACTTAATTCCAGGAACTGCAACGCAATCACCCATTATCCGAAGCACTTTC
DroMoj_CAF1_left   AGTTGCTGGAATCAAGTTGCTGACTTTGTAAGCAATGCAAAAGCCTTCCC-CTTACAGGCGACACAGTCAACTTTATTCCAGGAACTGCAACGCAATTAATACACACAC-ACACACTCAC

DroAna_CAF1_left   ACACC-CATATCC-ACACCCAC-ACACTTGAACACTT-CG-ATTCGAC--ACTAAACACGTTGGAACG-GAAACGGATA-CG-GAAA-TGGA-AACGCAC---T-A
DroEre_CAF1_left   ACTCC-TGACCTT-TGAACTCG-ACACTAGCACTTAT-GG-AAGCGGTT-GTGGAAATCGGTTTCACG-CTCGCACACA-CA-CACA-CGTA-A-TTGGT---T-A
DroGri_CAF1_left   AAACAACCACATC-ACAACATC-ACCATCGCGCACC--CGATTTAATT--TCACATTGTTATTCAC-A-TTCACATTCA-CT-TGAC-TTGA-CTTGAATTTGA-G
DroMel_CAF1_left   ACTCG-TGACCTT-TGAACCCG-ACGCTGGCACTTT--GAAACGGAAA--CGGAAACACACACTCACA-CACACGTAAT-TTGGTTA-GTCT-G-ATATC---G-A
DroPer_CAF1_left   CGGCT-CTATG----GAACACGCACTTAGGCCCGATTCGATTCACATT--ATTCAAATTCAACGCACG-GAAACGGATA-CG-GATA-CTGA-AACGAAC---T-A
DroPse_CAF1_left   CGGCT-CTATG----GAACACGCACTTAGGCCCGATTCGATTCACATT--ATTCAAATTCAACGCACG-GAAACGGATA-CG-GATA-CGGA-AACGAAC---T-A
DroSec_CAF1_left   ACTCG-TGATCTT-TGAACCCG-ACGCTGGCACTTT--GAAACGGAAA--CGGATACGGTTTTGAA-A-ATCGGTTTCA-CG-CACA-CACA-CTCACAC---ACA
DroSim_CAF1_left   ACTCG-TGACCTTTTGAACCCG-ACGCTGGCACCTT--GAAACGGAAA--CGGAAACGGTTTTGAA-A-ATCGGTTTCA-CG-CACA-CACA-CTCACAC---A-C
DroVir_CAF1_left   ACACA-CAGCACT-TTTACACG--CACTTTTCAATT--TA-ACTTTTAACACTTTGTAAAAACTTT-A-CGTCTAGACTTGA-CGTT-GAGT-TTAATGA---A-C
DroWil_CAF1_left   TCTCT-CTCTCTC-TCACTCGC-ACTGTTGCACTTA--CATATATTAT--TATTATTATT-ATTAC-GTTAAA----CA-CT-TTAT-GCAA-CGGAAAC---G-A
DroYak_CAF1_left   ACTCG-TGACCTT-TGCACTCG-ACACTAGCACTTT--GTAATGGAAA--CGGTTGTGGAAATCGG-T-TTCACGCACA-CA-CTCA-CTCAACTCACTC---A-C
DroMoj_CAF1_left   ACACA---CTCA---CACTT------TGAACACTTT--GCATCGAATA--GAAACACTTG-ACACG-T-CGAATTGAAT-TT-AACTAGCGA-TATCGTT---G-T