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


DroAna_CAF1_left   TAGT-TCCATAAGAAAGACCCTTTATAGAGTATAATTTACACT--TT-TT-GTAACCATGTTAT-AAAAAGA---ATCTTCAAAA-AAAG-AAAAACCTAG---CTTTCGAATTGCCTCC
DroEre_CAF1_left   ATAA-AATCTAGCTACTTCTATTATCGTTGCACGTAGTTCACAG-AGCTT-CCAAAAAAG-TGG-TACTCCCA--CGC---AACC-CCAG-GAGTAGCTGG-GGCAGTT-GGATGCCTCC
DroMel_CAF1_left   CCCT-TAAAATATTAAT-ATTTGTATTATTTTCACAGTTCACAG-AGCTT-CCAAAAAAG-TGT-AACTCCCA--CGC---AACC-CCAG-GGCAACCTGGGGGCAGTT-GGATGCCTCC
DroMoj_CAF1_left   GTTA-CATAAAACTTTT-CTAGTTATAAAGCCATTTTA--TAAT-GGTTA-GCAAAAAAC-AGA-AGCT-TCTGGGGGAG-GAGGAGTAC-CCTGATCTGC---CCTCTGGATTGCCTCC
DroPer_CAF1_left   AGT--CAATCATGTGCAAAAAAACACTCGCGCAACTCCCACCATCCC-AT-CAGATACAT-GTG-ATGGTAT---GGT---AATG-GTAT-GGAAGCGCGGAATCTTGGGAAATGCCTCC
DroPse_CAF1_left   TCAA-TCATGTGCAAAA-AAGCACTCGC-G--CAACTCCCACCA-TCCCATCAGATACAT-GTGATGGTATGG--TAA---AATG-GTAT-GGAAGCGCGGAATCTTGGGAAATGCCTCC
DroSec_CAF1_left   CTTG-CTATTTGTACTATTTTCACATGAAGATCACAGTTCACAA-TGCTT-CCAAAAAAG-TGG-AACTCCCA--CGC---AACC-CCAG-TGCTACCTGG-AGCAGTT-GGATGCCTCC
DroSim_CAF1_left   CTAG-CTATTTGTACTATTTTCACATGAAGATCACAGTTTATAA-AGCTT-CCAAAAAAG-TGG-AACTCCCA--CGC---AACC-CCAG-GACAACCTGG-GACAGTT-GGATGCCTCC
DroVir_CAF1_left   CAAA-TAAGTAACTACGGAATTATAAATGAAGTAA-CTTAGCAGCTT-TG-TTTATGCAATAGG-CAAATAT---GTT---GGCA-AAAA-GTGA-AGCATTCACTCTGGAATTGCCTCC
DroWil_CAF1_left   TAGTTCCATGTTTAAGCACTCGAAACTGTAAGAACTTCTTCCAAATG-AA-ATTTGCAAAAAAT-TTTGGTT---GAC---CTTT-GGAA-T-CTCTTCCCGT-CTGCC-TTTTGCCTCC
DroYak_CAF1_left   TCAA-AATCTAGCTACTTCCATTATCTTTGCATGCAGATCGAAG-AGTTT-CCAAAAAAG-TGG-AACTCCCA--CGC---CACC-CCAT-GCCAAACTGG-GGCAGTT-GGATGCCTCC
DroGri_CAF1_left   TGTG-CAGATAATTTCAAGTAATGCCGAGATACATATCTCTCTA-TAAAA-GAAACTGAG-AGT-CCCAATGG--CAA---AAAG-TAAATCTCAAGGCAT-GGCCT-G-GTTTGCCTCC

DroAna_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCCCACGAATCGAGGCCGTCCCAGTAGCGAATTTCAACAG---GGTGAGAGCTCGGC
DroEre_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCCCGCGTTTTGAGGGCGTCCCAGAAGCGAATTTCAACGGCTGGGTGAGAGCTTGGC
DroMel_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCCCGCCTTTTTAGCGCGTCCCAGATGCGAATTTCAACCGCTGGGCGAGAGCTTGGC
DroMoj_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCGTCTGCGGCAGAGGCGCTTAAGTAGCGAACTTGTGCGAACAATTGGCTTGCCTCG
DroPer_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCCCACATTTTGAGGGCGTCCCAGAAGCGAATTTCAACAGCCAAATGTCTCCGA-AC
DroPse_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCCCACATTTTGAGGGCGTCCCAGAAGCGAATTTCAACAGCCGAATTTCGAATGTCT
DroSec_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCCCGCGTTTTTAGCGCGCCCCAGAAGCGAATTTCAGCCGCTGGGTGAGAGCTTGGC
DroSim_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCTCGCGTTTTTAGCGCGCCCCAGAAGCGAATTTCAACCGCTGGGTGAGAGCTTGGC
DroVir_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCGCCTGCTTGAGAGGCGCTAAAGTAGCGAACTTCTGCTACAAGT-GCTGCAGATGC
DroWil_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCGGACAAATTTAGCGCGCCACAGAAGTCAATTTCAACGACAATT-GAGTTAGTTTT
DroYak_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCCCGCGTTTTGAGGGCGCCCCAGAAGCGAATTTCAACCGCTGGGTGAGAGCTTGGC
DroGri_CAF1_left   TGTGAGGATTGAACTCACGACCCCTGGTTTACAAGACCAGTGCTCTGCCACTGAGCTAAAGAGGCTCTCCTTTTATGAGCGCAAAAGTAGCGAACTTCAGCAAA-GAACTTGAGGCAGTC

DroAna_CAF1_left   T---TGCATTGTGT--ATCTTTGTATCTGCG-AGTAGAACACAAAAGATA-A-CTG-GCAACAG--ATGAAG-A-ACTCGAACATATGTTGACACAG
DroEre_CAF1_left   T---TGCATTGCACGGGTGCTATATCTTTGT-ATCTGCTCGCCGAACACA-A-AAG-ATAGCTG--TCGCAG-A-ACAAGAACAT-----ATGTTGA
DroMel_CAF1_left   T---TGCATCGTACGGTTACTATATCTTTGT-ATCTGCTCGAAGAACACA-A-AAG-ATAGCTG--TCGCAG-A-ACAAGAACAT-----ATGTTGA
DroMoj_CAF1_left   A---GTCGTGT-TGTCGCCATATCTTGTATCTTGTATCTTGTATCTTTGC-GGCTT-GTATCTG--GCGC-G-A-ACACATGTTG-----ACACAGT
DroPer_CAF1_left   A---AGAGCTGCGCTTGCAGTATGTAGGTACCAATTTTGTATCTTTTTGT-A-CGA-GTATCTGCGACACAA-A-AGAT-AGCAT-----GCGA-CA
DroPse_CAF1_left   CCGAACAAGAGCTGCGCTTGCAGTATGTAGG-TACTAA-TTTTGTATCTT-T-TTG-TACGAGT--AT-CTGCG-ACACAAA-AG-----A-TAGCA
DroSec_CAF1_left   T---TGCACCGTACGGTTGCTATATCTTTGT-ATCTGCTCGAAGAACACA-A-AAG-ATAGCTG--TCGCAG-A-ACAAGAACAT-----ATGTTGA
DroSim_CAF1_left   T---TGCACCGTACGGTTACTATATCTTTGT-ATCTGCTCGAAGAACACA-A-AAG-ATAGCTG--TCGCAG-A-ACAAGAACAT-----ATGTTGA
DroVir_CAF1_left   A---AGCTTGTATCTTGTATCTTGTATCTGCGACACACACAGATAGCAGCGA-ACA-TATGTTG--ACACAG-T-TGTC-GCCTG-----CTGCTGA
DroWil_CAF1_left   T---TTCCACCATCAACCTGCTGCCCTCTCCCCTGTACAAATTTTTAGTT-T-ATA-TCTCAAGTTGAAGAT-A-GAAC-AACGA-----CAAA-AG
DroYak_CAF1_left   T---TGCATTGCACGGGTACTGTATCTTTGT-ATCTGCTCGAAGAACACA-A-AAG-ATAGCTG--TCGCAG-A-AGAAGAACAT-----ATGTTGA
DroGri_CAF1_left   G---TGCTGCAAA-GAGAGCTTGTTGTATCT-TATATCTGATAGTTTGCT-G-TATCTGTGGCA--ACACAT-GTTGACACAGTT-----GTCGCCT