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


DroEre_CAF1_left   CGGTC-CCCGAGGGAACGGCAACGCCTGGTAGCAGGATTTCTGGTACTTTCGCC-CTGCAATCACACAGGTT--TC-CTG-CTGGGAAATGGA-GCCGCA------AC-AAACAGC-ATG
DroGri_CAF1_left   T-----ACTTTCGCCCTGCGATCACACAGGTTTCCTGCTGGGAAATGAAACTCCGCGACAAACGATCACCTTTAAC-AGCAAA-TCGCTTGTTGTGCACA------CA-AACAAGG-GAG
DroMel_CAF1_left   GGTCA-CCGGGGGCAACGGCAACACCTGGTAGCAGGATTTCTGGTACTTTCGCC-CTGCAATCACACAGGTT--TC-CTG-CTGGGAAATGAA-GCCGCA------AC-AAACAGC-TGG
DroMoj_CAF1_left   CTGGT-ACTTTCGCCTTGTGATTACACAAGTTTCCTGCTAGGAAATGAAGCTCCACGACACACAATCACCTT--TC-AGC-TT-TTGAGCGTT-GTTACG------GC-AACAAGG-GAG
DroPer_CAF1_left   TCTGGTACTTTCGTCCTGCAATCACACAGGTTTCCTGCTAGGAAATTAAGCCTC-CGACACACAGGCACCTC--TC-GATGCA-CTGCATGTT-GTAACA------AC-A-CAAGG-AGG
DroPse_CAF1_left   TCTGGTACTTTCGTCCTGCAATCACACAGGTTTCCTGCTAGGAAATTAAGCCTC-CGACACACAGGCACCTC--TC-GATGCA-CTGCATGTT-GTAACA------AC-A-CAAGG-AGG
DroSec_CAF1_left   GTCAC-CGGGGGGCAACGGCAACGCCTGGTAGCAGGATTTCTGGTACTTTCGCC-CTGCAATCACACAGGTT--TC-CTG-CTGGGAAATGAA-GCCGCA------AC-AAACAGC-TGG
DroSim_CAF1_left   GTCAC-TGGTGGGCAACGGCAACGCCTGGTAGCAGGATTTCTGGTACTTTCGCC-CTGCAATCACACAGGTT--TC-CTG-CTGGGAAATGAA-GCCGCA------AC-AAACAGC-TGG
DroVir_CAF1_left   C-TGGTACTTTCGCCTTGTGATTACACAAGTTTCCGGCTAGAAAATGAAGCTCCGCGACACACAATCACCTC--TC-GGC-TT-TTGTATGTT-GTTACA------GC-AACAAGG-GAG
DroWil_CAF1_left   TCTGGTACCTTCGCCCTGTAATCACACAGGTTTCCTGCTAGGAAATGAAGCTAC-ACGCC---AAACCCCTT--TCGGATGAA-TTGGCATGT-TGTACA------AA-A-CACAC-AAG
DroYak_CAF1_left   CGGTT-CCCGAGGCAACGGCAACGCCTGGCAGCAGGATTTCTGGTACTTTCGCC-CTGCAATCACACAGGTT--TC-CTG-CTGGGAAATGGA-GCCGCA------AC-AAACAGC-AGG
DroAna_CAF1_left   TGCTG-G-----GCAACGGCAACACCTG--GGCAGGATTTCTGGTACTCTCGCC-CTGTAATCATACAGGTT--TC-CTG-CTAGAAAATAGA-GCCTCGCACGAAGCGAAACAACATGG

DroEre_CAF1_left   CTC-GGCCAATTCTCAGACCTTCCCGGGGCAATGGTTCGTGGAGTAATCAGATACTCGTTGTGTGAGCCCCAGATGCTAGTTTGCAACTGACTGGAGGAGAAGG-AGCCAAAGGCGGCTG
DroGri_CAF1_left   CTTTGACCAATTCTCAGACCTTCCCGGGGCTTT----TATAGAGTAATCAGATACTCGTTGTGTGTGCCCCAGATGCTAGATTGTAACTGACTGAGGAAGGCGA-TGATAATGATAAT-G
DroMel_CAF1_left   CTC-GGCCGATTCTCAGACCTTCCCGGGGCAATGGTTTGTGGAGTAATCAGATACTCGTTGTGTGGGCCCCAGATGCTAGTTTGCAACTGACTGGAGGAAAAGA-AGCCCAAGGCGTCTG
DroMoj_CAF1_left   CTTTGACCAAATCTCAGACCTTCCCGGGGCAATC---ATAAGAGTAATCAGATACTCGTTGTGTGTGCCCCAGATGCTAGATTGTAACTGACTGAAGAAGAGTA-TGTGACCGTTGG--T
DroPer_CAF1_left   CTTGG-CCAAATCTCAGACCTTCCCGGGGCAAA----GTAAGAGTAATCAGATACTCGTTGTGTGTGCCCCAGATGCTAGTTTGTAACTGACTGAAGGAGGTGA-AGAGCCGGGACG--T
DroPse_CAF1_left   CTTGG-CCAAATCTCAGACCTTCCCGGGGCAAA----GTAAGAGTAATCAGATACTCGTTGTGTGTGCCCCAGATGCTAGTTTGTAACTGACTGAAGGAGGTGA-AGAGCCGGGACG--T
DroSec_CAF1_left   CTC-GGCCGATTCTCAGACCTTCCCGGGGCAATGGTTTGTGGAGTAATCAGATACTCGTTGTGTGGGCCCCAGATGCTAGTTTGCAACTGACTGGAGGAGAAGG-AGCCCAAGGCGTCTG
DroSim_CAF1_left   CTC-GGCCGATTCTCAGACCTTCCCGGGGCAATGGTTTGTGGAGTAATCAGATACTCGTTGTGTGGGCCCCAGATGCTAGTTTGCAACTGACTGGAGGAGAAGG-AGCCCAAGGCGTCTG
DroVir_CAF1_left   CTTTGACCATATCTCAGACCTTCCCGGGGCGTTGT-AAAAAGAGTAATCAGATACTCGTTGTGTGTGCCCCAGATGCTAGATTGTAACTGACTGAAGCGATGAATATAGCCGCTGGG--C
DroWil_CAF1_left   CTTCGACCAATTCTCAGACCTTCCCGGGGCAAA------GAGAGTAATCAGATACTCGTTATGTGTGCCCCAGATGCTAGATTGCAACTGACTGAAGAACTGAC-CAGGAATGACAG--A
DroYak_CAF1_left   CTC-GGCCAATTCTCAGACCTTCCCGGGGCAATGGTTTGTGGAGTAATCAGATACTCGTTGTGTGAGCCCCAGATGCTAGTTTGCAACTGACTGGAGGAGAAGG-AGCAAAAGGCGGCTG
DroAna_CAF1_left   CTT-GGCCGATTCTCAGACCTTCCCGGGGCAAAAT--AAGAGAGTAATCAGATACTCGTTGTGTGTGCCCCAGATGCTGGATTGTAACTGACTGTAAGCGACG--AGACAAATAC-GCTG

DroEre_CAF1_left   -GGGA-TCCCCTCTGATCCCGGCGATCTAGGAAA-G-TGGTGTATGAGGTGCG-GTGCCCA---------ACGAAA-CCAATACGAACCGGATCC-AGCGACACCGAC-T-----G
DroGri_CAF1_left   ATGGA-GATGTGGT---TGGC--TAGG-AATACAAT-TTAAATATAT-GAA---TTGTTTAA--GTTACACAAAAA-TTAAATTACATATTAATA-TGCACCAA--TT-A--CTAA
DroMel_CAF1_left   -GGGA-TCCCCTCT---GACT--GAATGATGTAG-G-TGCCCAACGA-AACCA-ATACATACCGGATCCAGCGACA-CCGAC-TGTTGCGGCACC-AGCACCAA--TG-A-----A
DroMoj_CAF1_left   -TAGG-AGAATTCA---A-CA--TAGCATATACA-G-TAAT-AAAGA-TC-GGACAAATCGAAAGCTTAACGAAAA-CCAATACGAACCGGAACC-AGCGACA---CCGA------
DroPer_CAF1_left   -AACA-TGGGCGGA---GGGC--CACGCATGATA-G-GTGGGTATGA-GC-CATGGGAATGGGAGTAACAACAAAA-CCAATACGAACCGGATCC-AGCGACAC--CG-A--CT-G
DroPse_CAF1_left   -GACA-TGGGCGGA---GGGC--CACGCATGATA-G-GTGGGTATGA-GC-CATGGGAATGGGAGTAACAACAAAA-CCAATACGAACCGGATCC-AGCGACAC--CG-A--CT-G
DroSec_CAF1_left   -GGTA-TTCGCTCT---GACT--GAATGAGGTAT-G-TGCCCAACGA-AACCA-ATACGTACCGGATCCAGCGACA-CCGAT-TGTTGCGGCACC-AGCGCCAA--TG-A-----A
DroSim_CAF1_left   -GGGA-TTCGCTCT---GACT--GAATGAGGTAT-G-TGCCCAACGA-AACCA-ATACGTACCGGATCCAGCGACA-CCGAT-TGTTGCGGCACC-AGCGCCAA--TG-A-----A
DroVir_CAF1_left   -AGGA-TTGGACAA---ATTG--AATCATGGTAA-G-ATGCTAATGT-ATCAGACAAGACGCTTAACAATTGGTAA-CCAATACGAACCGGAACC-AGCGACA-------------
DroWil_CAF1_left   -TTATAGTGGAGTA---G-----GAAT-AGGGAA-G-TATA-TATGA-AT-TA-TAACTAAATGTAAAGATGGCAA-CCAATACGAACCGGAACC-AGCGACAC--CG-A--C---
DroYak_CAF1_left   -GTGG-GATG-A-TTCCCTCT--GATCTCGGTGA-T-CTGCGACTGA-ATGAG-GTGCCCA---------ACGAAA-CCAATACGAACCGGATCC-AGCGACACCGAC-TGTTGCG
DroAna_CAF1_left   -AGGA-CTTCCACC---TGGT--TGAGGAGTTAA-ATATCGTTAAAA-AA-GATGAC---AACAAAACCAATACGAACCGGA-TCCAGCGACACCGACTGTTGC--AGCA-----C