CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TAAAGACCAGTTC---CGTAAA-CCA--GTTCCGTACT-AT-TCGTTA-TACCGTAAAC-CGTA--A-TTCGT--AAAACCG-TAAATCCGT-AAAA-AAAAACACACA---AAAAGAAA DroEre_CAF1_left AACCGTATAAACCGTAAACCGTACCATCCGTTATCCGT-AA-TTCGT-AACCCGTAATC----------CGTA-CAAAGAAAAAAACCAA-AGAAAAACATAAATAAAA---ACCAGTAC DroGri_CAF1_left ATATATATATATA-----TATATATA--TATATCCGTT-AA-ACCGTAAACCCGCTAAA-A-AA--A-AAGAA-GAAAAAAG-AAGAATATT-CAAC-AGCTTTCTCTA---TATTGTTG DroMel_CAF1_left CGTACCATCCGTT---ATCCGTA-ATT-CGTAACCCGT-AA-TCCGTACCAAAAGTAAA---AA--C-AAAAAAAAAACAAAGAAAAAAA--GTAACATGAATACAAAA---ACCAGTAC DroMoj_CAF1_left ATTTAAATGTATA---GATATATATGA-ATTTATATAT--A-TACAGA-TATATAAAT-GT-AT--ATCTAAC--GTATATATATATATT--TCTATATATGG---ATATATTCTATGTC DroPse_CAF1_left TTTCGTAAACCGT---AACCCGTAATC-CGTAATCCGT-AA-CCCGTA-ATGCGTAATCCG-TA--A-CAAAA-AACAGA-AGAAAAAAA--GAAACCGCTGAAGGCTT---TCAAAAGC DroSec_CAF1_left CGTATAAACCGTA---AACCGTACCATCCGTTATCCGT-AA-TTC-GTAACCCGTAATC-C-GT--A-CCAAA-AGTAAAAA-AAAAAAAACAAAGAA--AAAACGAAA---ACCAGTAC DroSim_CAF1_left TAAACCGTAAACC---GTACCATCTC--CGTTATCCGT-AA-TTCGTA-ACCCGTAATC-CGTA--C-CAAAA-GTAAAAAAAAAAAAAA--ACAAAGAAAAAACGAAA---ACCAGTAC DroVir_CAF1_left ATCGTAACCCGTA---TATCCGTATATCCGTAATACGTCAA-AAA-----TCAGAGAGA-G-AG--A-GAGAG-AGAGAGAAACAAAAAA--TATACAGCCTCCTCTAT---ATTGTTGT DroWil_CAF1_left TTTATATATTATT---ATTTTTTTTTT-GCTGTTCTGC-TA-TATACATATATATATAT---AT--C-TAAAT-ATATATATTATTATTT--TTATTATTATTATTATT---ATTTTTTT DroYak_CAF1_left TACTTTATATGGT---CGGAAA-CGCTTC--CTTCTGC-CTGTTA-CATACTTTTCAAC-G-AA--T-CTAGT-ATACCCTTTTACTCTA-CGAGTAACGGGTATAAAA---ACCAGTAC DroPer_CAF1_left TATGATGTGATGT---GATATGATAT----GATATGAT-AT-GCTG----TACAATAC-TG-TATAC-TATGACGTAACACA-CAGAGAG---AGAGAGAGAGAGAGAA---GATACAGA DroAna_CAF1_left AAA-ATCGATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATTTGA-GCCATTTGACGGACTCACTTTGCAACTGGAGATTGCTCGAGACTGCGGCATATGCCACAAAGTAT DroEre_CAF1_left CAA-TTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTTTGA-GCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACATT--AT DroGri_CAF1_left TTA-ACTTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATTATTAAGAATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCATATGCCACATT--AT DroMel_CAF1_left CAA-TTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTTTAA-GCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACATT--AT DroMoj_CAF1_left CAACTCTTATCTGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTTAACTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCAGCATATGCCACATT--TT DroPse_CAF1_left CGA-CTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATTT-GAGGCATTTGACACACTCACTTTGCAACTGGAGATTGCTCGAAACTGCGGCACATGCCACATT--AT DroSec_CAF1_left CAA-TTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTTTGA-GCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACATT--AT DroSim_CAF1_left CAA-TTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTTTGA-GCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACATT--AT DroVir_CAF1_left TAA-ACTTATCTGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTAAAGTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCTTATGCCACATA--AT DroWil_CAF1_left TTT-TTGTATCTGTAACATTGATTAATCTCAATTTGTAAATGTGAGCGATTTAAATCCATTCGATGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCATATGCCACATT--AT DroYak_CAF1_left CAA-TTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTTTGA-GCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACATT--AT DroPer_CAF1_left TAC-GTG-AAGCGTATCAGTC-GTAATCGTATATCGTNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NN DroAna_CAF1_left TATGTACACACCCTATAT-AG-GCA-C-ACTTGTATAT----ATATCTCGATATATGTATA-TAT-ATAATCCTATATAGACTGTCTACCTACCTATCTACCTATGT-ACCTC DroEre_CAF1_left TATGTACACACCTTATGTATA-GCC-T-ATATATCTAC----CGCCTCTATCTACTC-TGC-ATGTCTGCATTATGC-ATATATATAAATACATATATATATATCTG-TACGT DroGri_CAF1_left GTA---CAAACTATACATACA-TAC-ATACAAAGACAT----AT-ATATATTGTATTCCTA-TAT-AGAAATATATA-TATATGCTATATATATATATATATATATA-TATAT DroMel_CAF1_left TATGTACACACCTTATGTATA-GCC-T-ATATATATAT----TTATATATATCTACCGCCT-TTA-TCTACTCTGCA-TGTCTGCATAATGCGTATAAATAAATATA-TACAT DroMoj_CAF1_left GTACAAAAAAAAAAAAAAAAA-AAA-A-AACCAAAAAA----TAAATAAGCTAAACT-GAT-TTA-TGTATTGCTTA-CATATGTAGCCTACATT--ATATATTCCT-CTACC DroPse_CAF1_left GTACACCACACACCTAAACAA-CCAGT-AGCCCAAAGC----CCATGGGCTGTAGCA-TAC-CTT-TTCTGC-ATGT-CTGTATATAG-TACATA--TATACATATATATATA DroSec_CAF1_left TATGTACACACCTTATGTATA-GCC-T-ATATATATAT----CTACCGCCTTTATCTACTC-TGC-ATGTCTGCATA-ATGCATATATATAAATAATGATTTATATA-TACAT DroSim_CAF1_left TATGTACACACCTTATGTATA-GCC-T-ATATATATATATATCTACCGCTATTATCTACTC-TGC-ATGTC----TG-CATAATGCATATATATAAATAATGATTTA-TATAT DroVir_CAF1_left GTAAAA-ACTTAATTCTTGAATGCA-T-ACACAGACAC----CACATACATAAATATACCC-TAT-AAATA---TAT-ACATATATGTGCATATATATTTATATTTA-TGCCA DroWil_CAF1_left TTTTTATGTATGCTACCAATA--TG-T-ACATACATAT----ATACATATATATATATATATAGA-ATCACCTATAT-ATGTATCTATATATATGTATATATATATA-TGCAT DroYak_CAF1_left TATGTACACACCTTATGTATA-GCC-T-ATATATATAT----CTACCGCCTTTACCTAATC-TGC-ATGTCTGCATT-TTGCATATACATATATAAATATATATTTA-TATAT DroPer_CAF1_left NNNNNNNNNNNNNNNNNNNNN-NNN-N-NNNNNNNNNN----NNNNN--NNN-NNNNNNNN-NNN-NNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNN