CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left -ACCAGT--TA---TCAGTT-GACAACT--GTTTAAA---CACAACTCAC----TTGTGTCATGTA---TC-TCGAAGAT-ATTT----TTCGTTC--TGG-GGGC-ACGGCAA-AGG-T DroEre_CAF1_left -CAACT--GTT---TAAAC--ACGTGTT--TATTGTT---CTCTCATGTT----TCGCCG-AGATACTATC-TTTCGGTG-GCAG----AACCA-A--AAG-AATA-GCCAAAT-GGG-C DroGri_CAF1_left -TGCGAC--ATTTTTCAAC--TTATCAT--TTGCTAT---CTACGAGCAC----CTAAGT-AATTA---ATATTTACACA-GATG----ACTGAGA--ACTATTTAACTAATGA-TACTT DroMel_CAF1_left ACAACT--GTT---TAAAC--ACGTGTT--TATTGTT---CTTTTATGTT----TCGACG-AGATA---TC-TTTCGGTG-GCAG----AACGAAA--AAG-AGTA-CCCAAATGGGG-C DroPer_CAF1_left -TGCTGA--CA---ACTGT--TTGAACA--GTTGTTT---ATGATTGCTA----TTCATC-AGAAA---CT-TTCTATGG-GTTG----AACTCTCTTTCT-CTCT-CTCTCTA-TAG-A DroPse_CAF1_left -----GA--CA---ACTGT--TTGAACA--GTTGTTT---ATGATTGCTA----TTCATC-AGAAA---CT-TTCTATGG-GTTGAACTCTCTTTCTCTCT-CTCT-CTATCTA-TAG-A DroSec_CAF1_left -CAACT--GTT---TAAACACACGTGTT--TATTGTT---CTTTTATGTT----TCGCCG-AGATA---TC-TTTCGGTG-GCAG----AACGAGA--AAG-AGTA-CCCATGG-GGG-C DroSim_CAF1_left -GGCAACTGTT---TAAAC--ACGTGTT--TATTGTT---CTTTTATGTT----TCGCCG-AGATA---TC-TTTCGGTG-GCAG----AACGAGA--AAG-AGTA-CCCATGG-GGG-C DroWil_CAF1_left -TGAAGT--AT---TCAAT--TTA-ATTAGTTTCGTAAAATCAGTAAAAG----ATAATG-ATAGA---TA---ACATTT-CCAC-----AGATGC--TGA-AGAT-ATCATTT-GCT-A DroYak_CAF1_left -GTT----------TAAAC--ACGTGTT--TATTGTT---CTTTTATGTTTCGCCGACCAGATATA---TC-TTTCGGTT-GCAG----AACCCAAAACCC-AGTA-CCCAAAT-GGG-A DroMoj_CAF1_left -ATTCGA-CGC---TCTGTACTCTTATC--AAGAAGT---TTCACTTAAC----TAATTA-ATATC---TG-CTTTGATGATCTG----TGCCAGC-ACTT-AGCT-AATGATG-CGT-T DroAna_CAF1_left AGTTTAAATTGACTTT-TGGGCCGCC-CTCGATATGTGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAAGAGGCAACTG--GG- DroEre_CAF1_left CGCTTAAATTGGCTTC-TTTGCCGCC-CTCGAAACGTGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAGGAGGCATA---GGTC DroGri_CAF1_left TAATTTTATTCTCGAG-TTCTTTGG--CCCAAAATGTGCGCCTCTTTAGCTCAGAGGCAGAGCACTGGTCTTGTAAACCAGCGGTCGTGAGTTCAATTCTCACAGGAGGCATAT---AAT DroMel_CAF1_left CACTAAAATTGGCTTT-TTTGCCGCC-ATCAAAATGTGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAAGAGGCATATAAGGTC DroPer_CAF1_left TGCTTTTGTTGCCTTT-GGGGTCAGG-TGAGATATGTGGGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAAGAGGCATGA---CT- DroPse_CAF1_left TGCTTTTGTTGCCTAT-GGGGTCAGG-TGAGACATGTGGGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAAGAGGCATGA---CT- DroSec_CAF1_left CACTTAAATTGGCTTT-TTTGCCGCC-AACAAAACGTGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAAGAGGCATAG---GAC DroSim_CAF1_left CACTTAAATTGGCTTT-TTTGCCGCC-ATCAAAACGTGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCATTT---GT- DroWil_CAF1_left TCAGTCAAATTTAGTTATGGAACTCA-CATTAAATGTGAGCCTCTTTAGCTCAGTGGTAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCATCC---TTT DroYak_CAF1_left CGCTTAAATTGGCTTT-TTTGCCGCC-CTCAAAACGTGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAAGAGGCAAAG---GTC DroMoj_CAF1_left TTCTCTCTTATGCCAG-AGCTGTGCGATCCCAATCGCCGGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGCCGTGAGTTCAATTCTCACAGGAGGCAATA---GGG DroAna_CAF1_left G-CCAAGCCCCTTATTTTTGT------------CAAT--TT-TTTTTGGATCCCCCG-AA--AGTATTTGCTGATTGCCG---CATAT-TTCAAG-CT-TGA-----TTGAACTGC-TG- DroEre_CAF1_left AACCGCATTT-TTGCATGCATTTTTTTTTGTCACCCCAGCT--ATTTTTT--GATTT-CT-GCATATTTCAAGCTTGATT---GAAGTGCAGCAG-TC-TG------GCTTTC-GG-GG- DroGri_CAF1_left T--TTTATTT-ATCATTATAA------------ATAA--TT--TTATATA-CCTTTG-AA--CCTTACACATTT----GG---TGAAAAAATTTT-AT-TTT-----ATGGTATTT-TT- DroMel_CAF1_left AACAGCATTT-TTTGTTCTGTCTGTCACCGTCACCCTAACT--ATTTTTT--GATTT-CT-GCATATCTCAAGCTTGATT---GAACTGCTGCAG-CC-TG------GCTTTC-GG-GG- DroPer_CAF1_left TTTTTTTTGG-TATTTCTCCC------------CTAG--CA--ATTTGAT-GTGTTG-CA--CAAATTTCAAGCATGATT---GAGCTGCTGCAG-CG-CG------GCATTTTCT-AG- DroPse_CAF1_left TT-TTTTTGG-TATTCCTCCC------------CTAG--CA--ATTTGAT-GTGTTG-CA--CAAATTTCAAGCATGATT---GAGCTGCTGCAG-CG-CG------GCATTTTCT-AG- DroSec_CAF1_left AACTGCACTT-TTTGTTCTGT------------CAAC--CT-AACTATTTTTTGATT-TC--TGCATTTCAAGCTTGATT---GAACTGCTGCAG-CC-TG------GCTTTCGGCAATC DroSim_CAF1_left AACGAAATTA-TATTTTTATT------------TTAT--TT--TCGTATT-TCATAC-GA--CAAGGTTGAAACAATTAT---CAAAATTAACTT-AA-TTC-----AGTTTCACT-AA- DroWil_CAF1_left T--TGCTT-C-TATTAAAATC------------AGAT--TG--AATCTTT-TTCGTCAAA-CTGATTTTTGACTTTTGTC---AGAGAGAGAGAGAGA-G-A-----GAGAGACGT-AT- DroYak_CAF1_left AATCGCACTT-TT-TGCATGC------------ATTT--CTTCATTTTTTGTTCTGT-CACCCTAGCTATTTTTTGATTTCTGCATAT-TTCAAG-CT-TGA-----TTGAACTGC-TG- DroMoj_CAF1_left A-CGACTTTT-TTATAGAAAT------------AAAT--AA--AAAGGGAGCTTGGG-CA-------CTGAT-T-GGAGT---CAGTAAATTCAG-GGAAAACTTCAGC-AATATG-AG- DroAna_CAF1_left CG--TGGCTTTGCCTG----GTCT---TCAATCAGGAGT-TGA DroEre_CAF1_left G---T-CTTCAA--------TCAG----CGTCTGACGTT-TTC DroGri_CAF1_left C----AAAATATTTGA----TAGT---TTTTAA-AATGA-AAA DroMel_CAF1_left ----G-CTTCAA--------TCAG----CTGCTGACGTTTTCG DroPer_CAF1_left G---T-CTTCAA--------TCAG----GCAATGACATT-TCC DroPse_CAF1_left G---T-CTTCAA--------TCAG----GCAATGACATT-TCC DroSec_CAF1_left A---G-CTGCTGACGT----TTTC---GATATTTGACTT-ATG DroSim_CAF1_left C---A-TTTTGGCGTT----ATAA----TTACCTTTATG-AAT DroWil_CAF1_left GA--ATTTTCAACCATTTAGATAG----AGGATGGCATC-TTA DroYak_CAF1_left CAGTC-TGGCTT--------TCGGGGGTCTTCAATCAGC-GTC DroMoj_CAF1_left A---T-GAATAG--------ACGG---CGCATTCTTTCA-TTT