CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TGAGT---GACAGC---GAAGGATGGATATCGATTC--GAGGAGTTACGGAT-AACAATTCTACTACT-TACT-ACAATAATACTACA-TCTAAGATCTACTTT--GAAG-C-GTTAA-T DroEre_CAF1_left ATTGA-----ACAC---GTGT-----GCCCGCATGAGGCAGCGAAGGATTCGACTCG-ACTCGACTTG-GTTC-GGATTGGACACATGCCCTAT-GACTATGTTCTACAGTTGGTGTACA DroGri_CAF1_left CACAA---GTTGCG---TCGGGTCACAATGAAAGGA--CAATCATTGAGCGT-ATAATACCGATAAGC-GATATCTAC-GAGAAATGG-AGACGGA-TTCCTAG--TTGGAA-TCTAG-A DroMel_CAF1_left GGAAG---AAACGC---GTGT-----GCCCGCATGAGGCAGCGAAAGATTCGACTTG-GTTTAAAACG-GAAC-GGACACCTACCTAC-CCTTCCTATGACTATCATC-TAC-ATTTAGC DroMoj_CAF1_left AGGTT---TTCACAAGTGAAGAAATGAATAACAAAAGCCATTCTG-GAGAGATCATTGATCATC-GAT-AATT-GATAAGCGAATTA-TCAATTAGAAGATTAA-----AAT-ACG---A DroPer_CAF1_left CACTT---TATACA---GAGACGCGTGCCGCCATGA--TAGGCGAATCGAAG-ATTG-ATCGACAGAG-TAGT-GTTTGAAGACGATT-TTCTATTTTGTCTAA--ACTGAT-TGTGA-A DroPse_CAF1_left CACTT---TATACA---GAGACGCGTGCCGCCATGA--TAGGCGAATCGAAG-ATTG-AACGACAGAG-TAGT-GTTTGAAGACGATT-TTCTATTTTGTCTAA--TCTGAT-TGTGA-A DroSec_CAF1_left CGAAG---AAACGC---GTGT-----GCCCGCATGAGGCAGCGAAAAATTCGATTTG-GTTTAAAACG-GAAC-GGACACCTACCTAC-CCTTCCTATGACTATCTTC-TAC-ATTTAGC DroWil_CAF1_left CCCCT---TTTCAG---AAAATTCAAATCGAAAATG--CCGCCAAAATGATA-GACGGAACGA-AAGC-AATT-AGAC-GAGAGATTG-TGATTGT-GGTTTGT--TTGGAG-GGAGT-C DroYak_CAF1_left CTGCGGAGAAACAC---GTGT-----GCCCGCATGGGGCATCGAAGAATTCGGTT------CGGAACGGACAC-ATGACACACCCTATGACTAC-GAATTTGCTCTAGAGTA-GCTTACT DroVir_CAF1_left NNNNN---NNNNNN---NNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNN---NNNN-NNNNNNNNNN--NNN-NNNNNNNNNNNNNN-NNNNN-NNNNNNNNNNNNN-NNN-NNNNNNN DroAna_CAF1_left CTTG-TTC-CAGAAGTTGTTAACCGCCAGCAGCACG-GC-AGATGG-TC-TGCTGGCAGT---AATCGCAAATGGAG-A-G---GCTTCGCT-ATAACCACAACTTTTTATCCAAAGCCC DroEre_CAF1_left GTTG-TTC-CAGAAGTTGTTAACCGCCTGCGGCACGGGA-AA--AG-TC-CGCTGGCAGTT-TATCGCCAAA--TGGAGTG---ACCTCACT-GTAACCACAACTTTTTATCCAGAGCCC DroGri_CAF1_left CTTGT-TTCAG-CAGTTGTTAACCGCAAATGGCTGGCAT-AATTTT-GC-CAAGTGCAGTT-TAATCGCTAC--CGAAA-T---TATTTGCT-GTAACCACAACTTTTTATCCAGAGCCT DroMel_CAF1_left GTTG-TTC-CAGAAGTTGTTAACCGCCGGCGGCACGGGA--A--AG-TC-CGCTGGCAGTT-TATCGCAAAA--TGGAGTG---AACTCACT-ATAACCACAACTTTTTATCCAGAGCCC DroMoj_CAF1_left AGTG-TTC-CAGAAGTTGTTAACCGTAGTTGCCATT--C--A--GG-AC-CAACTGCAGTT-TAATCGCTAG--TG-GAAT---AGTTTACT-ATAACCACA-CTTTTTATCCAGTGCCT DroPer_CAF1_left CATG-TTC-CAAGAGTTGTTAACCGCTAGCGGAACGGAT-ATTGAA-TC-CGCAAGCAGTT-TAATCGCAAA--TGAAA-G---TT--CGCT-ATAACCACAACTTTTTATCCAAAGCCC DroPse_CAF1_left CATG-TTC-CAAGAGTTGTTAACCGCTAGCGGAACGGAT-ATTGAA-TC-CGCAAGCAGTT-TAATCGCAAA--TGAAA-G---TT--CGCT-ATAACCACAACTTTTTATCCAAAGCCC DroSec_CAF1_left CTTG-TTC-CAGAAGTTGTTAACCGCCGGCGGCACGGGA--A--AG-TC-CGCTGGCAGTT-TATCGCCAAA--TGGAGTC---AATTCACT-ATAACCACA-CTTTTTATCCAGAGCCC DroWil_CAF1_left ATTTGTCC-CAGAAGTTGTTAACAATCAACGGTGAGAGCAATTTTACTCACTCATCCGGATGAAAGTTTAAT--CGCAA-CTGGATTTCTAT-ATAACCACAACTTTTTATCCAAAGCCT DroYak_CAF1_left GTTG-TTC-CAGAAGTTGTTAACCGCCGGCGGCACGGGA-AA--AG-TC-CGCCAGCAGTT-TATCGCCAAA--TGGAGTG---AACTTACT-TTAACCACAACTTTTTATCCAGAGCCC DroVir_CAF1_left NNNN-NNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNTGT--T--TG-AC-AACGTTCAGTT-TAATCGCTAT--GGAAATA---CTTTG-ATATAAGCCACAACTTTTTATCCAGAGCCT DroAna_CAF1_left CT--GGGATGAGTT--GGCGGGCAATGAAAAGCTTGGTGCGGTAGCAACTGATTCTGATTCTGAT-AT-----------GAGGCAGC--AGGCTGGATGCTGGAGG-CTTCGGTGGGCAT DroEre_CAF1_left CT--AGTTA-ACTT--GGAGGGCAATGGAAAGCTTGGTGCGGTAAGACTATA-CTGATTTGGTTGGT------TA-TTCTGCTTATT--GCTTTCA-------GA--TGTTTTGGGAGA- DroGri_CAF1_left CT--GTGTT-TTGC------GGCAATGAAAAGCTTGGTGTGGTAGCACTGGA-CTGACGTCACTGTTGCG---CT-GTTTTTGTCGC--TATCTTT-------GAGGTTATGG--TTAGT DroMel_CAF1_left CT--GGTTA-ACTT--GGAGGGCAGTGGAAAGCTTGGTGCGGTAAGACTATA-CAGATTTCGATCTGGTT---AATGCTTTCAAATG--TTTTGGG-------AGA-ACAATTTATAGTT DroMoj_CAF1_left CG--GGCA---GTT--TGC-GGCAATGGAAAGCTTGGTGTGGTAAGACAGGC-GTCGCTGCGTTG-CC--------AATTGCCAAAT--GAGATCA-------TGT-TCACCAGCTCCAT DroPer_CAF1_left CA--GGCTA-TGAT--TGGGGGCAATGGAAAGCTTGGTGCGGTAGCCAGAGTTCAGCTGATGGCG-GT--------TCTTGGGCAGA--TGGCTCG-------GGG-TACTTACGAAGTC DroPse_CAF1_left CA--GGCTA-TGAT--TGGGGGCAATGGAAAGCTTGGTGCGGTAGCCAGAGTTCAGCTGATGGCG-GT--------TCTTGGGCAGA--TGGCTCG-------GGG-TACTTACGAAGTC DroSec_CAF1_left CT--GGTTA-ACTT--GCAGGGCAGTGGAAAGCTTGGTGCGGTAAGACTATA-CTGATTTCGATCGATGG---TC-ATCTGGTTAAT--GCGTTCA-------GA--TGTTTTGGGAGAA DroWil_CAF1_left CTGGCATTA-ATTGTTTGAAGGCAATGAAAAGCTTGGTGTGGTAAAACAATG-TTCTCAATGTGGGGCAA---TA-GTAGGAGGTGA--CGGCACT-------TACTCTCCTC--ATCCT DroYak_CAF1_left CT--GGTTA-ACTT--GGAGGGCAGTGGAAAGCTTGGTGCGGTAAGACTATA-CTGATTTAGGTGGTTATGGATA-TTCTGGTTATT--GCTTTCA-------GG--CGTTTTGAGAGA- DroVir_CAF1_left CT--GGCTG-TTT-----GCGGCAATGAAAAGCTTGGTGTGGTATCATAGAC-GCTCTGACGTCA-CTGTT--GC-CCATTGTCATTGAGGTTATG-------TT--GTATGCTCTGC-T DroAna_CAF1_left CCA--GAG---TCCATGCTGGTACTTAC------AAAGTCGGCCACATCCATGATG-CT---G-TC-CTCAGCAATG DroEre_CAF1_left --CT-ATCCTTCGTTATAAACTGGTTGAGATCCACTTTTACCATAGATTCTGAA-C-AA---T-ATCC-----GAAG DroGri_CAF1_left AGCC-GCTGCTGCTGCTTCTTCTTGGTT------TGGAT---GCAACATGAATG-T-GTTGTG-GGAA-----ACTT DroMel_CAF1_left ATAG-ACGGCACACTACTACTT-TTACC------ATAGACAGTGAAAGATACTA-A-TG---G-GC-A-----ATAC DroMoj_CAF1_left GGTG-ATTGGGGATTTGGAGTTAATCAC------GTCGGCGTGAG-GGGTACTT-A-CG---A-AA-T-C---GGCC DroPer_CAF1_left AGCA-ACATCCATGATGCTATCCTCA---------GCGATGTTGGTGCAGTCGA-T-GG---T-GA-AGC----GCA DroPse_CAF1_left GGCA-ACATCCATGATGCTATCCTCA---------GCGATGTTGGTGCAGTCGA-T-GG---T-GA-AGC----GCA DroSec_CAF1_left ATAT-ATTGTTCTTATGGACGGCACAGA------CGTGTCTTGGATGTTTTCAA-ATGG---T-GG-A-----GATC DroWil_CAF1_left ATTG-GTGGTACTTACGAAATCGGCAAC------ATCCA---TGATGCTGTCTT-C-AG---C-AATG-----TTGG DroYak_CAF1_left -ACT-ACCGTTGGTTATAAACTGGTTGA------CATACAAAAGAAGCTTCGGG-C-AA---T-TG-A-----ACGA DroVir_CAF1_left TCTGGTGATGCGTGAAGCATGTTGTTGT------TTTGGGTTAGAAACATTCGA-T-CG---CGGA-AG----TGAT