CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GCGTTGAAGAAGTTCTC-ACCCCA-CAGACTGTA-A-AAT-GGATG--ATAAATG--GGA-TTAATTGT---TGAT--AC-TTGGATCGGACTAACT-GTAAG-CT-ATAACTAAAAG-A DroEre_CAF1_left ATTCTATCA-AATTCTA-TAAAA--TATACAGTAAC-AAT-TAATC--TTAAATA---TA-CGAACGAATTATGAG--GT-CAATAAAAGAT--TTATGTATA-CA-AGTTAAAAATT-A DroGri_CAF1_left TACTTATAT-CTCATTT-TTCAT--T-CTAAATATG-AAATAAATA--AATGAAC--TTA-TATGTGACAGAAAAT--TC-CATTTTAGAAT--CAA-AAATATGAAGCATT-ATTTATG DroMel_CAF1_left ATATCGATT-TGTATAA-TATGA--GGCCAAACAAC-AAT-TGATT--TCAGATA---TA-TGAAGAAATTATGTG--AA-CAATAAAAGAT-TTCT-GTATA-CA-ATTTAAAAATA-A DroMoj_CAF1_left AATAATAAT-TTTAAAA-TAGTT--TGCTATTAATT-CATGCATTT--A-TATTT---AG-TTTATTAGTCGCACTATTT-TCATGACCGTA--CCT-ATATA-TATAGATATATTGT-T DroSec_CAF1_left ATATCGATGTTGTATAA-TATGA--GGCCAAACAAC-AAT-TGATT--TCAAATA---TA-TAAGGAAATGATGAG--AA-AAATAAAAGAT--TCT-GTTTA-CA-AATTAAAAACA-A DroSim_CAF1_left ATATCGATGTTGTATAA-TATGA--GGCCAAACAAC-AAT-TGATT--TCAAATA---TA-TAAGGAAATGATGAG--AA-AAATAAAAGAT--TCT-GTTTA-CA-AATTAAAAACA-A DroVir_CAF1_left TATTTCTAA-TATAGCTGGAGCAATAGTAAATTAAT-CCAAAATGT--A-AA-CA---TG-GTAAACATATAGATT--AC-AGTTATCTGAA--TAT-GTCTA-AAATTATTTTGGGT-A DroWil_CAF1_left ATGAGTCAA-ACTCTTG-ACTAC--A-GGGTATACACTTTTAATG---AAAATAGAATCCATAT-GGA-A-TCTTA--GT-TTATGTTCTTA--AAT-AAACC-TTTCTAATTTATTA-T DroYak_CAF1_left TTTCGCTTT-TAAACAA-TTTAA--AGCCAACAACC-ATT-ATAGC--TTAAAAT---GT-ACTGTTGGTAACAAT--TAATTTCAAATGAA--TTT-GTATA-TAAGTAAAAAATTG-T DroPer_CAF1_left TGGCGTTGA-AGAAGTT-CTCAC--C-CCACAGACT-GTC--GGATAGAAATGGT---TT-TGAAGTTAGAAATAT--TG-AAGTAACGGTT--CCG-GCACG-CCCCAAGGTGTGGA-G DroPse_CAF1_left TGGCGTTGA-AGAAGTT-CTCAC--C-CCACAGACT-GTC--GGATAGAAATGGT---TT-TGAAGTTAGAAATAT--TG-AAGTAACGGTT--CCG-GCACG-CCCCAAGGTGTGGA-G DroAna_CAF1_left TAAGTGTGAGGGGACTGCCTTAGCA--TGACTCGTTGGGACATTAGGAAAGAGGTCCCGAGGCAGCGTTTCAACAGCTACCTG--CG---GTATGTTCTGCTTCTA-TTTTTG-TGGCAC DroEre_CAF1_left TTAGTGTAAGGTAACTGTTTTAACA--TGACTCATTGGAACATTAGGAAAGCGGTCCCCAGTCAGCGTTTAAACAGCATCCGA--AA---GTTTGATCTTCTTCTA-TTTATG-GTCCAC DroGri_CAF1_left GAATTGTCGAGTCGCTGCCTTAGCAAATGCACCGTTTGAACATTGGGAAAGCGGTTCCGATGCAGCGTTTCAGCAGCGTCTCC--AATGGTTTTGATCTGCTTTTATTGTTTG-TTGCAC DroMel_CAF1_left TTAGTGTAAGGTAACTGCCTTAACA--TGACTCGTTTGAACATTAGGAAAGCGGTCCCGAGTCAGCGTTTAAACAGCATCCGA--AA---GTTTATTCTTCTTCTA-TTTAAG-GTCCAC DroMoj_CAF1_left AATTTGTCGAATCGCTGCCTTAGCAAATGCACCGTTAGAACATTAGGAAAGAGGTTCCGGTGTAGCGTTTCAGCAGCGTCTAC-TTA---ATTTGATCTGCTTTTA-TTTTCGATTGCAC DroSec_CAF1_left TAAGTGTAAGGTAACTGCCTTAACA--TGACTCGTTAGAACATTAGGAAAGCGGTCCCAAGTCAGCGTTTAAACAGCATCCAA--AA---GTTTAATCTTCTTCTA-TTTATG-GTCCAC DroSim_CAF1_left TTAGTGTAAGGTAACTGCCTTAACA--TGACTCGTTAGAACATTAGGAAAGCGGTCCCAAGTCAGCGTTTAAACAGCATCCAA--AA---GTTTAATCTTCTTCTA-TTTATG-GTCCAC DroVir_CAF1_left AATTTGTCGAGTCGCTGCCTTAGCAAATGCACCGTTGGAACATTAGGAAAGCGGTTCCGGTGCAGCGTTTCGGCCGCGTCTTC--AA---TTTTAATCTGCTTTTA-TTATTG-TTGCAC DroWil_CAF1_left AAATTGTAAAATAACTGCCTTAGCA--TGCAACGTTTAGACATTAGGAAAGAGGTCTCGATGCAGCGTTTCAACAGTTTTTTT--TAAAATATTTGATCTACTTTTATTTTTA-TGGCAC DroYak_CAF1_left TTAGTGTATGGTAACTGCCTTAACA--TGACTCGTTAGAACATTAAAAAAGCGGTTCCCAGTCAGCGTTTAAACAGTATCCGAGAAA---GTTTGATCTCCTTCTA-TTTATG-GTCCAC DroPer_CAF1_left TGAATGTAGGGTCGCTGCCTTGGCA--TGCCTCGTTTGGACATTAGGAAAGCGGTCCCAAGGCAGCGTTTCAACAGCTTCCCAAGTA---ATTTTCTCTACTTCTA-TATTTA-TAGCAC DroPse_CAF1_left TGAATGTAGGGTCGCTGCCTTGGCA--TGCCTCGTTTGGACATTAGGAAAGCGGTCCCAAGGCAGCGTTTCAACAGCTTCCCAAGTA---ATTTTCTCTACTTCTA-TATTTA-TAGCAC DroAna_CAF1_left TTGTGGCGCCCTCAGCACGCGCGACTCTA----A--AGAC--AATTA-GTC-----------------C-----AAGATGCCGCACGCTCAGCGTCACACGTTTTGTGCTAGAAGCGTTA DroEre_CAF1_left TTGTGGCGCCCTCAGCACGAGCGACACTA----A--AAAGA-CTGC--CCCTGGGG-AGAAG-TCTTTC-----AAGAAGCCGCCCGCTCAGCGCCACACGTTATGTGGTAGAAGTTTGA DroGri_CAF1_left TTGTGGCGCTTTCAGCACGCGCGGCTCTT----G--AGAT--TCGAGAATCG----------------G-----AAGAGTTCGCACGCTCAGCGTCACACGTTTTGTGCTAAAAGCAAAG DroMel_CAF1_left TTGTGGCGCCGTCAGCACGAGAGACTCTA----A--AAGG--ACTTT-CCTTGCGGAGATGT--CTTTC-----AAGAAGCCGCCCGCTAAGCGCCACACGTTTTGTGGTAGAAGTTTGA DroMoj_CAF1_left TTGTGGCGCTATCAGCACGCGCGGTTCTAGCTGA--ACAGCCACGCC-CCTTGCAGGTTTGTGACTGTC-CAAAAAGAAGTCGCACGCTCAGCGTCACACGTTTTGTGCTAAAAGCGTAT DroSec_CAF1_left TTGTGGCGCCCTCAGCACGAGAGACTCTT----A--AAGG--ACTTT-CCTTGCGGAGATGT--CTTTC-----AAGAAGCCGACCGCTCAGCGCCACACGTTTTGTGGTAGAAGTTTGA DroSim_CAF1_left TTGTGGCGCCCTCAGCACGAGAGACTCTT----A--AAGG--ACTTT-CCTTGCGGAGATGT--CTTTC-----AAGAAGCCGACCGCTCAGCGCCACACGTTTTGTGGTAGAAGTTTGA DroVir_CAF1_left TTGTGGCGCCGTCAGCACGCGCGGTTCTAGCGAA--GCT--GTCGCC-CTTTGAAGGGGAGGC--AGCGATCAAAAGAAGTCGCACGCTCAGCGTCACACGTTTTGTGCTAAAAGCAAGC DroWil_CAF1_left TTGTGACGTCTTCATCGCGCATAGTTCTC----T--CTCT--T-AAA-AGAG----------------A-----GAGAAACTGCACGCTCAACGTCACACGTTTTGTGCTAAAAGCATGG DroYak_CAF1_left TTGTGGCGCTTTCAGCACGAGCGACTTTA----A--AAAGA-ATGCC-CCCCTTGGGGAGATGTCTTTC-----AAGAAGCCGCCCGCTCAGTGCCACACGTTTTGTGGTAGAAGTTTAA DroPer_CAF1_left TTGTAGCGCCCTCAGCACGCGCGACTCTA----AAAAAGG--GGCCC-CCGTACGGAGGAA---CTTTC-----AAGATGTCGCACGCTCAGCGTCACACGTTTTGTGCTAGAAGCGTGT DroPse_CAF1_left TTGTAGCGCCCTCAGCACGCGCGACTCTA----AAAAAGG--GGCCC-CCGTACGGGGGAA---CTTTC-----AAGATGTCGCACGCTCAGCGTCACACGTTTTGTGCTAGAAGCGTGT DroAna_CAF1_left ACTGCA--AACTAACTAACC-TTA-AGT-ATATGATAACTTACCGGTTCATTAGCTTGACCACATCGATCTTGAACTTCTCGGAGTACATCTC------- DroEre_CAF1_left ATATAT--TTAAAA-----A-ACA-AT--GAGA-ACGACTTACCGGTTCATTAGCTTGACAACATCGATCTTGAACTTCTCGGAGTACATCTCGGAGAAC DroGri_CAF1_left GGATGC--GGAGCG-GAGTG-GCGGAT--TGGTTAAAACTTACCGGTTCATTAGCTTGACGACATCGATCTTGAACTTCTCCGAGTACATTTC------G DroMel_CAF1_left AAACAT--TTACAA--ACAA-ACT--T--GAGACATGACTCACCGGTTCATTAGCTTGACAACATCAATCTTGAATTTCTCGGAGTACATCTCAGA---G DroMoj_CAF1_left AGATTG--ATATAGATATAT-ACA-AGTATTAGTTTAGCTTACCGGTTCATTAGCTTGACAACGTCAATCTTGAACTTCTCAGAGTACATC--------T DroSec_CAF1_left ATACAT--TTAAAA-AAAAA-ACT-TT--GAAATATAACTCACCGGTTCATTAGCTTGACAACATCAATCTTAAACTTCTCGGAGTACATCTCA-----G DroSim_CAF1_left ATACAT--TTAAAA-AAAAA-ACT-TT--GAAATATAACTCACCGGTTCATTAGCTTGACAACATCAATCTTAAACTTCTCGGAGTACATCTCA-----G DroVir_CAF1_left AAATGG--GTTGCAGTTATG-TTA-ATACGCGGCGATTCTTACCGGTTCATTAGCTTGACAACATCAATCTTGAACTTCTCGGAGTACATC--------T DroWil_CAF1_left AAATAC--TATACG-TATTA-GGGAGG--GAAGTGGGACTTACCGGTTCATTAGCTTGACCACATCGATCTTGAATTTCTCAGAGTACATTTC------A DroYak_CAF1_left ATAGAT--TTAAAA-CATTC-CCT-AT--AAGACACGACTCACCTGTTCATTAGCTTGACAACATCGATCTTGAACTTCTCGGAGTACATCTCG-----G DroPer_CAF1_left TAGTGTAAGGAATG-GAGTG-GCG-ACACGAGGGATGACTCACCGGTTCATTAGCTTGACAACATCGATCTTGAACTTCTCGGAGTACAT---------C DroPse_CAF1_left TAGTGTAAGGAATG-GAGTGGGCG-ACACGAGGGATGACTCACCGGTTCATTAGCTTGACAACATCGATCTTGAACTTCTCGGAGTACA----------T