CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left A---AGCC-T--AC-ACAC--AACACAACAAC-CATA-CTAAATATGGT-TGGAAAAGGGGAGGTTGCTGCAGTGCG-----AG--TTA-CGCCTT--CGCCTTCGGATAT-TATTA-GC DroGri_CAF1_left GAG--TGAAT--AT-TTCT--TCT---AGTTGCCTCG-CACTGCG--CA-AGCCTCCACATTTATTTATGAACTCTT-----GG--GGG-CGCTTTGTGTCTATTTTTAGC-TTGAC-TG DroMel_CAF1_left CGCAAGCC-C--AC-ACAC--AAC---ACAAC-CATA-CTAAATATGGT-TGGTAATGGGGAGGTTGCTGTAGTACG-----AG--GTA-CGCCTT--CGCCTTCGGATAT-TATTA-GC DroMoj_CAF1_left ATGGACAC-G--AA-TATG--CGC---ATTC--AAGTATTTCAGCTTTT--CAGTTTTTTTAGCTTTTGTCGATTGG-----GG--TTGCCTTCGT--ATTGCATTGCAAC-TTGCT-GT DroPer_CAF1_left GGCA-CTG-C--GC-AAGT--CCC---ACACA-CATG-CCATACTCCTG-CCTCCACC-ACACCAGGCCATAAAAGG-----GGGGGAA-TGACT---ATTAATAGCAATC-TGTGC-TC DroPse_CAF1_left GGCA-CTG-C--GC-AAGT--CCC---ACACA-CATG-CCATACTCCTG-CCTCCACC-ACAGCAGGCCATAAAAGG-----GGGCGAA-TGACT---ATTAATAGCAATC-TGTGC-TC DroSec_CAF1_left CGCAAGCC-C--AC-ACAC--AAT---ACAAC-CATA-TTAAATATGGT-TGGAAAAGGAGAGGTTACTGCAGTACG-----AG--GTA-CGCCAT--CGCCTTCGGATAT-TATTA-GC DroSim_CAF1_left CGCA--AG-CCCAC-ACAC--AAT---ACAAC-CATA-TTAAATATGGT-TGAAAGAGGAGAGGTTGCTGCAGTACG-----AG--GTA-CGCCTT--CGCCTTCGGATAT-TATTA-GC DroWil_CAF1_left GTTTTAAA-T--AT-ATGT--TTT---TTTTG---CA-TTTGTTGGTTC-TCTCC-TGCGCAGGTCCACACAAACACGCACACA--CAT-TGAGTT--TTGTG----TGTA-TCGCA-TC DroYak_CAF1_left CA--AGCC-C--AC-ACAC--AACACAACAAC-CATA-CTAAATATGGT-TAAAA-AGGGGAGGTGGCTGCAGTACG-----AG--GTA-CGCCTT--CGCCTTCGGATAT-TATTA-GC DroAna_CAF1_left ACTGC-GC-A--AGCCCACGCCAG---CCAGC-CAGG-GGGCATATGGG-AGGATGGGGCGTTGGGGCCGCCTTC-G-----TC--TGT-TGCTAT--TTTTAGGTCTCGGTTGTGCTAG DroVir_CAF1_left TTCCA-TT-T--AT-GGAC----C---TCGGC-TATA-CGAATAAGCGCATGCAAGTGTTTCAGTTTTTGCTGGGGG-----GT--TGC-CTTGTG--CTTATTTTAAAATTGCGTTGTG DroEre_CAF1_left T--GGCG-AGGCATTAGTTGCCGCTTGGTCGCGCGGAGTGCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGG DroGri_CAF1_left T--TGCG-CTGTTCTAGTGCTGGTTAAGTCGTCGCAGTTGTATCTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGG DroMel_CAF1_left T--AGCG-AGGAATTAGTTGCTGCTTGGTCACTCGAATCCCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGG DroMoj_CAF1_left T--CTAG-TGGTTCTAGTGGCAGTTAAGTCGCTGGCAACGTATCTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGG DroPer_CAF1_left G--CTGTGCGGCTGTACTTGCTGTTCGGCCGGTCGAAGCCCATCTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGA DroPse_CAF1_left G--CTGTGCGGCTGTACTTGCTGTTCGGCCGGTCGAAGCCCATCTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGA DroSec_CAF1_left T--AGCG-AGGAATTAGTTGCCGCTTGGTCGCGCGAACTCCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGG DroSim_CAF1_left T--AGCG-AGGAATTAGTTGCCGCTTGGTCGCGCGAACTCCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGG DroWil_CAF1_left GACTGTG-TGTCTTAAATGGCTATTTGGTCAGGCAACTTCCAATTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGA DroYak_CAF1_left T--GGCG-AGGCATTAGTTGCCGCTTGGTCGCGCGAACTCCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGG DroAna_CAF1_left C--AACG-CGCCTCAAGTGGCTGTTTAGCCGCGCTTGCTCCAACTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGG DroVir_CAF1_left G--CTTG-TGGCTCTAGTGCCAGCTAAGTCGCTCGGTTTGCATCTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGG DroEre_CAF1_left TAAACCTTTTTGCTCCCCAGT-------TTTACTA--AAATTTAT-ATATT---TTTGTCTGATCAG-TTGTTATC-TTTTGTTTTTCT--AGG-AG-GGGTCTG-GT-TTATTATCA-G DroGri_CAF1_left TAAACTTTTTTGTACACAATGCT-----TTTTTTA--GAATAAGGAATATTATTTTCTGTTGAAGTA-AATTACTC-A----TATT-----GCTATC-TGTTTTT-AG-TCTATTTATAT DroMel_CAF1_left TAAACCTTTTTGTTGCTCCCCCC-----AGTCCGA--ATACAAAGTATATT---TTTTTCTGATCAC-TCGTTATT-ATTGGTTTTTCT--AGG-AG-TGGTCAG-GT-TTATTATCA-G DroMoj_CAF1_left TAAACTTTTTTCACATTATTTGT-----TTATTTA--AAATGAAT-GTATT---TTTATCAGCACTTTAATTAAACTCTTTACTTAGTA--ATA-TA-TGTTCTT-GC-TG-GTTCTA-T DroPer_CAF1_left GTAACCTTTTTTCCTCTTTTTTT------TTACTTATCTCAACATTTCAGC--GTTCTTTTGATCAA-TTCTCATC-TGCTTTTCTTTT--T-T-TCGCCCACGA-TAGCAGGCAACT-G DroPse_CAF1_left GTAACCTTTTTTCCTCTTTTTTT-----TTTACTTAACTCAACATTTCAGC--TTTCTTTTGATCAA-TTCTCATC-TGCTTTTCTTTT--T-T-TCGCCCACGA-TAGCAGGCAACT-G DroSec_CAF1_left TAAACCTTTTTGCTGCTCCCA--------GTTCAA--ATATAAAGTATATT---TTTTTCTGATCAG-CCCTTATC-ATTGGTTTTTCT--ATT-AG-CGGTCTT-GT-TCATATCTG-G DroSim_CAF1_left TAAACCTTTTTGCTGCTCCCC-------AGTTCAA--ATATAAAGTATATT---TTTTTCTGATCAG-TCCTTATC-ATTGGTTTTTCT--ATT-CT-TCT-GCA-TC-TTCCTAATG-T DroWil_CAF1_left GATAACTTTTTTGTTCTTTGC-------AGTCAAA--TAATTTTTTTTTGT---TTTTTTTTTTTAA-ATTAGTTT-CTTTTCTTCTTC--TAT-AT-TGTTGTTCGT-TAAATGCCT-C DroYak_CAF1_left TAAACCTTTTTGTTGCTGCCTGCTCCCCAGTTCTA--AAATGTAT-ATAAT---TTTCTCTGATCAG-TTCTTATT-GTTTGTTTTTCTAGAAT-AG-GGGTCTG-GC-TTATTATCA-G DroAna_CAF1_left TAAACTTTTTTGTTCTTTTTC--------CAACCT--TTCTTTATTTTT-C---CTGATCAATCCTT-ATCATTCG-TTCGGCTAT-CA--AGG-AG-AATGAAG-CT-ATTTTAG-A-G DroVir_CAF1_left TAAACTTTTTATTATATACAA--------CTTTTT--ATCAGCGCTTGA-A---TTTATTAGTTGTT-ATCTGTTT-GTTCTATTT-AT--AAT-TC-AAAAC-A-CG-AACTTGT-T-G DroEre_CAF1_left GCT--CTTTGT--GCTCT-----TACTTTA-AGTAATAACAGCG--ATAATTAGCT-CAT--TGGGCCT DroGri_CAF1_left T---TAGGAGC--ATTAAATTGGTGTTGCT---TGGCGACTGTA--GCTCCATGTG-GTGGAGATCA-- DroMel_CAF1_left CCC--CTTAAT--GTTCT-----TATTTTA-GGCAGTAACAAAG--ATAATTAGCT-CAT--GGAACCT DroMoj_CAF1_left TTA--TAGTTTT-AATCG-----ATGAAATGGTGTTGTTTGGGGGTTTTAGGTGCA-CTA--CTCGC-- DroPer_CAF1_left AGT--CGAAAA--ATAGC-----AACCAGC-TGCAGTTACTTCA--TTAGCGCTCA-TTT-GGACGG-- DroPse_CAF1_left AGT--CGAAAA--ATAGG-----AACCAAC-TGCAGTTACTTCA--TTACCGCTCA-TTT-GGACGG-- DroSec_CAF1_left ATCTTCCTAAT--GTTCT-----TATTTTA-AGCAGTAACAAAA--ATAATTAGCT-CAT--GGGGC-- DroSim_CAF1_left TCT--TATTTTAAGCAGT-----AACAAAA-ATAATTAGCTCAT--GGGGCCTTTGTTGG--AGCT--C DroWil_CAF1_left AAACTTTGTCT--AATTG-----TTAGTGT-AGCCTTCTCAATT--GGAACTTTAG-AAA--GATTT-- DroYak_CAF1_left GCT--CTTCGT--GTTCT-----TGTTTAA-AGCAGTAACGGAG--ATAATTAGCT-CAT--GGGGC-- DroAna_CAF1_left ACG--AAAACG--GAGCT-----GGTTAGC-TCTTGGGA-GCTC--CGTTGGAGCC-CGC--ACCAA-- DroVir_CAF1_left TTG--CTTGGG--GATTG-----TAGCTCC-A-TTGGTT-GGAG--C--TGCAAGT-GTG--G------