CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left --TGGGAGTCAG--TCACAGATT--AG----TCTGAATTGAGTTC-----TAC-CCGAAGGCAGCAAGCACATCGCACTAAAAAGGCTGGCCACGAGAGTTTTCAATGCCA-T-CAGG-C DroEre_CAF1_left --GT--AGTCAG--TCACAGATT--AG----TCTGAATTGAGTTC-----TGCCTGGAAGGCAGCAAGCACATCGCACTAAAAACGCTGGCCACGAAAGGTTTCAATGCCAAC-CAGG-C DroMel_CAF1_left --GT--AGTCAG--TCACAGATT--AG----TCTGAATTGAGTTC-----TGCCTTAGAGGCAGCAAGCACATCGCACTAAAAACGCTGGCCACGAAAGGTTTCAATGCCAAC-CAGG-C DroMoj_CAF1_left --GA--TTAGTC--TGAATTGAGTTCT------AC-----GCACCTCAGAGTTGAGGTTTGCAGCAAGCACATCGCACTAAAATTGCTGGCCACGAAAGCTTTCAATGCAA-C-ATGGCC DroPer_CAF1_left --TC--ACAGAT--TAGTCTGAAT-TGAGTTCTGC-----GTTGCCC----GGAGGCTTTGCAGCAAGCACATTGCACTAAAACAGCCGGCCACGAAAGTTTTCAATGCAA-C-AAGG-C DroPse_CAF1_left --TC--ACAGAT--TAGTCTGAAT-TGAGTTCTGC-----GTTGCCC----GGAGGTTCTGCAGCAAGCACATTGCACTAAAACAGCCGGCCACGAAAGTTTTCAATGCAA-C-AAGG-C DroSec_CAF1_left --GT--AGTCAG--TCACAGATT--AG----TCTGAATTGAGTTC-----TGCCTGGGAGGCAGCAAGCACATCGCACTAAAAACGCTGGCCACGAAAGGTTTCAATGCCAAC-CAGG-C DroSim_CAF1_left --GT--AGTCAG--TCACAGATT--AG----TCTGAATTGAGTTC-----TGCCTGGGAGGCAGCAAGCACATCGCACTAAAAACGCTGGCCACGAAAGGTTTCAATGCCAAC-CAGG-C DroVir_CAF1_left CAGA--TTAGTC--TGAATTGAG--TT----CTGC-----GCACCTCA--GGCAAGGTTTGCAGCAAGCACATCGCACTTAAATTGCTGGTCACGAAAGTTTTCAATGCAA-C-ATGGCC DroWil_CAF1_left --GA--GTTCTG--CTTTCCACT--GC----CTCCAAAGGAGGGT-----AGCT--TATAGCAGCAAGCACATCGCACTAAAACGGCTGGTCACGAAAGATTTCAATGCAT-CCGT-A-A DroYak_CAF1_left --GT--AGTCAG--TCACAGATT--AG----TCTGAATTGAGTTC-----TGCCTGGGAGGCAGCAAGCACATCGCACTAAAAACGCTGGCCACGAAAGGTTTCAATGCCAGC-CAGG-C DroGri_CAF1_left --GT--TCTGCGCACCACCTCCG--AG----GAG----------------G----GATTTGCAGCAAGCACATCGCACTAAAATTGCTGGTCACGAAAGATTTCAATGCAACG-CGCGTC DroAna_CAF1_left GGCG--GTTGC------TG---GG-C---AAC---GGCAA-C-ACCT-G---GGCAGGATTTCTGGTACTCTCGCCCTGTAATCATACAGGTTTCCTGCTAGAAAATAGAGCCTC-GCAC DroEre_CAF1_left GGCG--GTCCC------CGAG--G-G---AAC---GGCAA-C-GCCT-GGT-AGCAGGATTTCTGGTACTTTCGCCCTGCAATCACACAGGTTTCCTGCTGGGAAATGGAGCCGC--AAC DroMel_CAF1_left GGCG--GTCAC------CGGG-GG-C---AAC---GGCAA-C-ACCT-GGT-AGCAGGATTTCTGGTACTTTCGCCCTGCAATCACACAGGTTTCCTGCTGGGAAATGAAGCCGC--AAC DroMoj_CAF1_left GGCG--GCA---G-------G-TT-A---TGC---GGCAA-CAGCCA-TGC-TGCAGCATTTCTGGTACTTTCGCCTTGTGATTACACAAGTTTCCTGCTAGGAAATGAAGCTCCACGAC DroPer_CAF1_left GGCA--GTCAGAC---GCGAG-CGCC---GAT---GGCAA-C-GCCA-AGC-CGCAGTATTTCTGGTACTTTCGTCCTGCAATCACACAGGTTTCCTGCTAGGAAATTAAGCCTC-CGAC DroPse_CAF1_left GGCA--GTCAGAC---GCGAG-CGCC---GAT---GGCAA-C-GCCA-AGC-CGCAGTATTTCTGGTACTTTCGTCCTGCAATCACACAGGTTTCCTGCTAGGAAATTAAGCCTC-CGAC DroSec_CAF1_left GGCG--GTCAC------CGGGGGG-C---AAC---GGCAA-C-GCCT-GGT-AGCAGGATTTCTGGTACTTTCGCCCTGCAATCACACAGGTTTCCTGCTGGGAAATGAAGCCGC--AAC DroSim_CAF1_left GGCG--GTCAC------TGGTGGG-C---AAC---GGCAA-C-GCCT-GGT-AGCAGGATTTCTGGTACTTTCGCCCTGCAATCACACAGGTTTCCTGCTGGGAAATGAAGCCGC--AAC DroVir_CAF1_left GGCG--GCAAACG---GCAAG-CG-G---TGC---GGCAA-CAGCCA-TAC-TGCAGCATTTCTGGTACTTTCGCCTTGTGATTACACAAGTTTCCGGCTAGAAAATGAAGCTCCGCGAC DroWil_CAF1_left GGCG--GCGGT-C---GAGGG-GA-C---CGC---AACAAGC-CAAA-CAG-TACAGTATTTCTGGTACCTTCGCCCTGTAATCACACAGGTTTCCTGCTAGGAAATGAAGCTAC--ACG DroYak_CAF1_left GGCG--GTTCC------CGAG--G-C---AAC---GGCAA-C-GCCT-GGC-AGCAGGATTTCTGGTACTTTCGCCCTGCAATCACACAGGTTTCCTGCTGGGAAATGGAGCCGC--AAC DroGri_CAF1_left GTCGTCATCGTCGTTGGCAAC-AA-CAACAATAACAATAA-C-A-GCAGCGAGGCAGGATTTCTGGTACTTTCGCCCTGCGATCACACAGGTTTCCTGCTGGGAAATGAAACTCCGCGAC DroAna_CAF1_left GAAGCGAAACAACATGGCTTG--G-CCGATTCTCAGA-C-CTTCCC-GGGGCAAAAT--AAGAGAGTA----ATCAGATACTC---GTTGTGTGTGCC-CCAG-ATGCTGGATT----G- DroEre_CAF1_left AA------ACAGC-ATGCTCG--G-CCAATTCTCAGA-C-CTTCCC-GGGGCAATGGTTCGTGGAGTA----ATCAGATACTC---GTTGTGTGAGCC-CCAG-ATGCTAGTTTGCAAC- DroMel_CAF1_left AA------ACAGC-TGGCTCG--G-CCGATTCTCAGA-C-CTTCCC-GGGGCAATGGTTTGTGGAGTA----ATCAGATACTC---GTTGTGTGGGCC-CCAG-ATGCTAGTTTGCAAC- DroMoj_CAF1_left AC------ACAAT-CACCTTT--CAGCT-TTTGAGCGTT-GT-TACGGCAACAAGGGAGC---TTTGACCAAATC---TCAGACCTTCCCGGGGCAAT----C-ATAAGAGTAATC-AGA DroPer_CAF1_left AC------ACAGG-CACCTCT--CGATGCACTGCATGTT-GT-AACAAC-ACAAGGAGGC---TTG-GCCAAATC---TCAGACCTTCCCGGGGCAAA--GTAAGAGTAATCAGAT-AC- DroPse_CAF1_left AC------ACAGG-CACCTCT--CGATGCACTGCATGTT-GT-AACAAC-ACAAGGAGGC---TTG-GCCAAATC---TCAGACCTTCCCGGGGCAAA--GTAAGAGTAATCAGAT-AC- DroSec_CAF1_left AA------ACAGC-TGGCTCG--G-CCGATTCTCAGA-C-CTTCCC-GGGGCAATGGTTTGTGGAGTA----ATCAGATACTC---GTTGTGTGGGCC-CCAG-ATGCTAGTTTGCAAC- DroSim_CAF1_left AA------ACAGC-TGGCTCG--G-CCGATTCTCAGA-C-CTTCCC-GGGGCAATGGTTTGTGGAGTA----ATCAGATACTC---GTTGTGTGGGCC-CCAG-ATGCTAGTTTGCAAC- DroVir_CAF1_left AC------ACAAT-CACCTCT--CGGCT-TTTGTATGTT-GT-TACAGCAACAAGGGAGC---TTTGACCATATC---TCAGACCTTCCCGGGGCGTT--GTA-AAAAGAGTAATC-AG- DroWil_CAF1_left CC------AAACC-CCTTTCG--G-ATGAATTGGCATGT-TG-TACAAAA-CACACAAGCTTCG---ACCAATTC---TCAGACCTTCCCGGGGCAAAGAGAG-TAATCAGATACTCGT- DroYak_CAF1_left AA------ACAGC-AGGCTCG--G-CCAATTCTCAGA-C-CTTCCC-GGGGCAATGGTTTGTGGAGTA----ATCAGATACTC---GTTGTGTGAGCC-CCAG-ATGCTAGTTTGCAAC- DroGri_CAF1_left AA------ACGAT-CACCTTTAACAGCAAATCGCTTGTTGTG-CACACAAACAAGGGAGC---TTTGACCAATTC---TCAGACCTTCCCGGGGCTTT------TATAGAGT--AATCA- DroAna_CAF1_left -TAA DroEre_CAF1_left -TGA DroMel_CAF1_left -TGA DroMoj_CAF1_left TACT DroPer_CAF1_left -TCG DroPse_CAF1_left -TCG DroSec_CAF1_left -TGA DroSim_CAF1_left -TGA DroVir_CAF1_left -ATA DroWil_CAF1_left -TAT DroYak_CAF1_left -TGA DroGri_CAF1_left -GAT