CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left A-------GC-GGT---TGACTTTGATT-AGC----TAGATAATAAA----TATCCCCGAATGT-CCGGCAC-------TCACCTTTA-TA----GAGATATTGATGAT---G-ACATTT DroEre_CAF1_left T-------TG-ATTAGTCAGATGAAATATATC----CTCG-AATATA----CAGCTGATGATGATAC----A-------GATGAAATA-CATACCCAAACAAGAGGGTA---T-ACTACA DroMel_CAF1_left TCGTTGCGTC-AGT---TGACTTTGATT-AGT----CAGATGAAATA----TATTCTCGAGTGT-AT--------------ATCACCA-AACGATGAAATACTTACTAA---T-ACTATA DroMoj_CAF1_left A-------AG-TAC---TCACCAGTTAT-ACT----CT-ATG-TCTA----TCTCTAATATTGT-CT--GTC-------TCTTTATCA-CTCCCTCT--CTCACTCTGA---T-TATTAT DroPer_CAF1_left G-------TT--------GACTTTGATT-AGC----TAGATAAAATA----TGTCCCCAAGGGA-ACTTTGCA---AAGATAGAT-AT-GATGGG----GATGTACTCACC-TATTATTA DroPse_CAF1_left G-------A-----------CTTTGATT-AGC----TAGATAAAATA----TGTCCCCAAGGGA-ACTTTGCAAAAAAGATATAT-AT-GATGGG----GATGTACTCACC-TATTATTA DroSec_CAF1_left G-------TC-AGC---TGACTTTGATT-AGT----CAGATGAAATA----TATCCTCGAGTGT-ACAGTGT-------ACACCAGCA-GACGATGAAATACTTTCTAA---T-ACTATA DroSim_CAF1_left G-------TC-AGC---TGACTTTGATT-AGT----CAGATGAAATA----TATCCTCGAGTGT-ACAGTGT-------ACACCAGCA-AACGATGGAATACTTACTAA---T-ACTATA DroVir_CAF1_left T-------TAAGG-----GATGCACTTG-AGAATATAT-TTA-TAAA----GGGCTACTCACCA-GT--TGA-------TCTCTATTT-GTATGATT--AGCATTTCTT---T-TCATTG DroWil_CAF1_left T-------GG---------TCTTTGATT-AGC----ATTTGAGAAAG----ATCTTTTGTATTT-ACATATATA--TATAAATATAAC-TATATA---GGT-TTATACTTA-CTTAGT-T DroYak_CAF1_left T-------GA-GTCAGTTGACTTTGATT-AGT----CACATAAAATT----TATCCTAGAAATA-CT----T-------ACCCATACTTGGGGGTATACCACTACTACC---C-ATACTA DroGri_CAF1_left C-------GG-TTC---TG------ATT-AGC----GAGTTGCAAACATCTTTATAA--AAAAG-CAATATA-------AAAGGTATA-GAGGGTTA----CTCACCAGTTGT-TCTAGC DroAna_CAF1_left TTTAATTTAGACTTTGACGAAATGTTGACCAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGTTTGAATTAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTG DroEre_CAF1_left TACACCTTGATCACCTGCAAGTCGCTGGCCAAACTCATAGTGAATACGCCTTTTTCCCTTTCCTGTCGTTGTTGAAATGAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTG DroMel_CAF1_left TACACCTGGATCACCTGCAAATCGCTGAGCAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGTGGAATTGAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTG DroMoj_CAF1_left TTTAATA--GAAATTTTTATATCGTTGAAATAATTCATAGTAAATACGCCTTTTTCCCTTCCCTGCCGTTGTTC-AATAAAACGTCAGTAAGCGGAAAAAGACAAATCGACTAGAACTTT DroPer_CAF1_left -AGCTGAATTGGGTCGGTTGTTTGTTGGATAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGATCGAATAAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTT DroPse_CAF1_left -AGCTGAATTGGGTCGGTTGTTTGTTGGATAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGATCGAATAAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTT DroSec_CAF1_left CACACCTGGATCACCTGCAAGTCGCTGGGCAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGTGGAAATGAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTG DroSim_CAF1_left CACACCTGGATCACCTGCAAGTCGCTGGGCAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGTGGAAATGAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTG DroVir_CAF1_left AATAGGT--GTTTAAACAGATTGGTTGAACAAATTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGCTC-AATAAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAACTTT DroWil_CAF1_left -GTAGAGATTTTGTGGAGAATTTGTTGATTAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTAGTTAAATAAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTA DroYak_CAF1_left TGCACCTTGATCACCTGCAAATCGCTGGTCAAACTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGTTGAAATGAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAATTTG DroGri_CAF1_left TTTATAGATATTTGAATAGGTTTGTTGATTACATTCATAGTAAATACGCCTTTTTCCCTTTCCTGTCGTTGCTC-AATAAAACGCCAGTAAGCGGAAAAAGACAAATCGACTAGAACTCT DroAna_CAF1_left AATATATGT--TCTT-G-------AAGAAAAGC---ACTATCGTTTTATACTTA---GACTTGGCCCCGAACACATGGCACCCG-ATGA--GATATGTTAGCTT----CTCGTG--TATT DroEre_CAF1_left TGTAT--CC--ACTT-TGTGTATTTCACATACC-----GATCCGCACACATGGC---ACCGCGATGAGATTGGTTCTTGTTTGG-GA----ATTGAATTAATTT----AATTTGATTCGA DroMel_CAF1_left TGTAT--CC--ACTT-T-------TCACATACC-----GATCCGCACACATGGA---GCCGTGATGAGATTGGTTCTTGTTTGG-GATTTGGAT-TGGAATTGA----ATTGAATTAATT DroMoj_CAF1_left ATATA--AA--AATC-G-------ATTCAGTTA-----GATCAAATATTATTTT---GACAATTAAGT-ATGTATATTTCTATA-GCTGCTTCTGCTGCTGGGTCTGCTGCTGC--CACA DroPer_CAF1_left GATCT--TT--GTAT-A-------TTTTACAATATATTTAGCTGCGAAAACCTC---GGAC-TTTTTTGAACACATGGCACCAC-GAGGCGGACGGTTTTTTGC----TTC--A--GCGT DroPse_CAF1_left GATCT--TT--GTAT-A-------TTTTACAATATATTTAGCTGCGAAAACCTC---GGAC-TTTTTTGAACACATGGCACCAC-GAGGCGGACGGTTTTTTGC----TTC--A--GCGT DroSec_CAF1_left TGTAT--CC--ACTT-T-------TCACATACC-----GATCCGCACACATGGC---GCCTTGATGAGATTGGTTCTTGTTCGG-TATTCGGATTTGGTTTTGA----ATTGAATTGAAT DroSim_CAF1_left TGTAT--CC--ACTT-T-------TCACATACC-----GATCCGCACACATGGC---GCCGTGATGAGATTGGTTCTTGTTCGG-TATTCGGATTTGGTTTTGA----ATTGAATTGAAT DroVir_CAF1_left ATAGA--TC--AAAG-A-------TATACAATC-----AAGTTAAGTATACTTT---CATATAGACCC-TGACAAGACACATTGCGTTGGGTTGTTAGATTAGAAAAAAGCTTT---AAT DroWil_CAF1_left TACAT--ACATTATA-T-------ATATATCTATATGATGATATATATGTATA-----------TGTGCATGTGTATGTATGT---ATATCTTAAGATTAGGAT----AGA--A--AACA DroYak_CAF1_left TGTAT--CC--ACTT-T-------TCACATACC-----GATCCGCACACATGGC---ACCGTGATGAGATTGGTTCTTGTTTGG-GA----ATTGAATTAATTT----AATTTGGTTCGA DroGri_CAF1_left GAAGA--TT--GCTTAA-------TCATACAAT--AC--TTATACACAAAATGTTTAGTCTCTGGTAAAAACACATTGCTCTCG-GACATATAGATATAAAAAG----AGA--T--TTAA DroAna_CAF1_left T---GC-TT-------GT DroEre_CAF1_left TT--------------GA DroMel_CAF1_left T---AATTT-------GG DroMoj_CAF1_left T---TG-CT-------TT DroPer_CAF1_left G---TT-TA-------GA DroPse_CAF1_left G---TT-TA-------GA DroSec_CAF1_left T---AA-TT-------TA DroSim_CAF1_left T---AA-TT-------TA DroVir_CAF1_left T---TC-GT-------AT DroWil_CAF1_left C---AT-GCCACATTTTG DroYak_CAF1_left TTGATTTAT-------GG DroGri_CAF1_left T---TT-CG-------TA