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


DroAna_CAF1_left   GGCTCTCACACCGAGC---AGACGTGTTGG-CCTGG-CTAAAT-AAAACCCTA-A-ATAGTCTTAAAAAGAATTCTT----A-A--CTC-TTGTGAAAACTCT-TGCAATAATCTTTGGC
DroEre_CAF1_left   GTTCCGG--TGTGGCT---CTCA-CACCGAAC-AGA-CG--TG-TTGGCCTGC-C--T-AGAG-TAGAGTTCCAAAAGCTAG-TGCATTGTG-AT-TCCCCAA-AT-TGTGTTAACCCTT
DroMel_CAF1_left   GTGC-GG--CTCTCAC---ACCG-AGCAGA-CGTGT-TG--GC-CTGCCTAGA-A-TA-AGAA-TAACATTCAAATGGTCAG-TGCATTGTG-AT-GCCCAAA-AT-TGTGTTAAGCCAT
DroPer_CAF1_left   GTGACAA--AAGGTAC---AACG-GTCTTG-CAGTT-CCAGTG-CGGCTCTCA-C-AC-CGTA-CAGACATGTTTGT----C-TGCCAC-AA-AG-TACCATC-CA-TTCCAAGTTGTGC
DroPse_CAF1_left   GTGACAA--AAGGTAC---AACG-GTCTTG-CAGTT-CCAGTG-CGGCTCTCA-C-AC-CGTA-CAGACATGTTTGT----C-TGCCAC-AA-AG-TACCATC-CA-TTCCAAGTTGTGC
DroYak_CAF1_left   GTTCCGG--TGCGGCT---CTCA-CATCGA-GCAGA-CGTGTTGGCCTGCCTA-G-AG-TAGA-ATTCCAACAGCTA----G-TGCATTGTG-AT-TCCCAAA-AT-AGTGTTAACCCTT
DroGri_CAF1_left   CACC-GT--GCAGACGTTTGCTT-TGCCAA-C-AGAAACTCAG-CAAACAGTTGCAAA-AAGA-AATATAATACAAT----G-AACAATCAAGAG-TTCAAGTGCTATAATTTATGGTTA
DroVir_CAF1_left   ACACCGT--GCAGACGTGTTGTT---TTGA-C-ATAAATAAAA-CCAACCAAACAATA-CAGT-AAA--ATGCCAAA----TAATCAAACAA-AC--AAGTGCAAGTGCCAAACATTTTC

DroAna_CAF1_left   TGTAATAGTTTGGCTT-TTTTATAT-AA---GAGCTCCTAAATGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTATAAATTATTAGCTGGCTTTCGAGCAATAATTGAAAC
DroEre_CAF1_left   TGGCTAAGTTTGGTTGTTT-TATATAAG----AGTTCCTACACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTA-TTATCTAACAGCTGGCTTTCGAGCAATAATTGAAAC
DroMel_CAF1_left   TGGCTAAGTTTGGCTGTTT-TATATAAG----AGTTCCTTCACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTCATTGTTTACCAGTTGGCTTTCGAGCAATAATTGAAAC
DroPer_CAF1_left   ATTTTTTTGTGTGAAT-TCCATTGT-GA---AAGTA-TAAACCGGACACTTATCTATTTTTGATTGTTGCTCAGAAAGCCCTTATAATTAACCAGTTGGCTTTCGAGCAATTATCAAAGC
DroPse_CAF1_left   ATTTTTTTGTGTGAAT-TCAATTGT-GA---AAGTA-TAAGCCGGACACTTATCTATTTTTGATTGTTGCTCAGAAAGCCCTTATAATTAACCAGTTGGCTTTCGAGCAATTATCAAAGC
DroYak_CAF1_left   TGGCTAAGTTTGGTTT-TTTTATAT-AA---GAGTT-CCGCACGGACACTTATATAATTTTGATTGTTGCTCAGAAAGCCCTTACTATTTAACAGCTGGCTTTCGAGCAATAATTGAAAC
DroGri_CAF1_left   CTAGTGTGTTCTCCTG-ATGCCTGA-AACAGCCAAC-TACTATGGACGCTCATATAATTTTGATTGTTGCTCAGAAAGCCTTT--CACTTGACACTTGGCTTTCGAGTAATAATCGAAAC
DroVir_CAF1_left   CAAGTTACAACTCCAT-TTCCTTCC-TA---CCTCA-CAAAACGGACGCCTATATCATTTTGATTGTTGCTCAGAAAGCCCTG--CATTCAATACTTGGCTTTCGAGTAATAATCGAAAC

DroAna_CAF1_left   CAAATAAGTGATCCTGACAACATTTTAAGTGTGAAATATTCTTTTAAAGG--GTGAGTAAA-TAGTTATAG-AT-AT-TATTATACAAG-ACTTTGTTTATGTTAATTATATTTAATAAT
DroEre_CAF1_left   CAGATAAGTGATCCTTACAACGCTGA-AGATTTGACTGCATTTCGTGTTG--GTAAGTAAA-CATGAAAAATACATTATA-AATAGATA-ATTATAAAATACATTATAAGGAAGCTGGTA
DroMel_CAF1_left   CAGATAAGTGATCCCCTCAACGCTGA-CGATTTCAAAGCACTTCGTTTTG--GTAAGTTAA-GATTTATTTCATTAATTA-TGTTTAAA-AAATATATAGAGATTTCAAATTTAATTACT
DroPer_CAF1_left   CAAATAAGTGATCCCAACAACATTTT-AGTGTGAAATACTTGACTCAAAG--GTAAGTGA-AAATAGTT-T-TCTTA-TT-TATTTATT-TAAGCACTTGTCCTTTCTGGGTTTCGGTTC
DroPse_CAF1_left   CAAATAAGTGATCCCAACAACATTTT-AGTGTGAAATACTTGACTCAAAG--GTAAGTGAAAAATAGTT-T-TCTTA-TT-TATTTATT-TAAGCACTTGTCCTTTCTGGGTTTCGGTTC
DroYak_CAF1_left   CAGATAAGTGATCCTTACAACATTGA-AGATTTGACTGCG--TTTCGTGTTGGTAAGTAA--AAATGTT-T-TTTAT-TT-TTAAAGGTCC-TAGAAAATACACA-TTGAAAAGCTGATA
DroGri_CAF1_left   CAAATAAGCGATCCTAACTACAATTA-CTCAAA--CATTAACCCACATGC--TCAAGTAAG-TAGCGGATA-AATTG-GT-TTTAAACT-CAATC-CA--TCATTAATGTGGCACATTTC
DroVir_CAF1_left   CAAATAAGCGATCCTAACTACGTTTA-CCTAAT--ATTATTATCATGGTC---CAGGTAAG-TACCTTTTT-GTACC-CT-TTTA-AG--C-TAC-CA--TTATATAATATATTATTTAT

DroAna_CAF1_left   ATTTTTATTAGA-----ATATT--AGAGTAGAA--CAC-CTTA
DroEre_CAF1_left   GCTTTACATGAA-----CGAAT--AAAATACTT--TTCAGATT
DroMel_CAF1_left   TTAAATAAAAAG-----CATTG--CTAATTATA--CATACGAT
DroPer_CAF1_left   ATTTGTATGGTT-----TTTAT--ACCCATAAA--CTCCCTTA
DroPse_CAF1_left   ATTTTCATAGTG-----CTTAT--ACCCATAAA--CTC-CCTT
DroYak_CAF1_left   ACTTTAAATTAACGAATAAAAT--ACTTTTTAC--AATAGTCA
DroGri_CAF1_left   TGCACTATTTTG-----ATTTTTAATTTAAGCT--TTCACATT
DroVir_CAF1_left   ATATTTATGTAT-----CAAAATATAATAAGCAATTATGTATA