CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GCTGCTG---TCTCGAGGAAGAAAC-A-AGGC-----TG---GGA---A-AAGC--TG-A-CATTACG--TATACAACGTGTGGGCGTGGCCAT-GCTCTATGGCCGTTCTAAT-TC--G DroEre_CAF1_left AAATGCT---TGCTTTTATCGTACC------------AA---CAG---A-TATCGCCGGAAAAAAATATACAAGTAAAATGAAAGCAAAGCTGC-GTTA--CTCAAGTCCAATC-GT-TC DroGri_CAF1_left ACGGTAA---ATGAAACAAGAAAGC------------GGCCAAAA---T-TTTT-TTT-TTTGTATCGAATGGACTGGAATGATAAATAGTAAAGACAG--A-CAAAAGCTGGC-AG-TC DroMel_CAF1_left GTGGCACAAATGCTTTGCTTTTATC------------GT---AGG---A-AATTCGCA-A--AAAATGTACAAATAAAACGAAAGAAAAGTTGCCACTA--T-CAAATCCCACC-GT-TC DroMoj_CAF1_left TTAGCCA---ATATTCGAGACCGAG------------AA---GAG---GAAAA-CGGA-AACAACATG-GAAAGCA--TTGAGAGCAAAGTCGTTATAATTTGTTTTATTAATTTTT-TT DroPer_CAF1_left TGGAAAT---CG-AGGGGAAAAGAA-A-GC-------AG---AGC---A-GAGCGGCG-G-CGTTACGTAGT--CACGTCTGATAAGTGGGCGTGGCCG--GTATAAGTGTGTT-TGTTC DroPse_CAF1_left CGGAAAT---CG-AGGGGAAAAGAA-A-GC-------AG---AGC---A-AAGCGGCG-G-CGTTACGTAGT--CACGTCTGATAAGTGGGCGTGGTCG--GTATAAGTGTGTT-TGTTC DroSec_CAF1_left GCACAAA---TGCTTTGCTTTTATC------------GT---AAA---A-AATTCGCA-AAAAAAATGTACAAGTAAAACGAAAGAAAAGCTGACACTA--TCCAAATCTCACC-GT-TC DroSim_CAF1_left GCACAAA---TGCTTTGCTTTTATC------------AT---AAA---A-AATTCGCA-AAAAAAATTTACAAATAAAACGAAAGAAAAGCTGCCACTA--TCCAAATCTCACC-GT-TC DroVir_CAF1_left CAATATC---CG-CCTTTGAGATTC-A-GTGAAAGAGAC---ATG---G-AAAGCATA-G--AAAAAAGTGTTGCCACGT------TATT--TTTATTA--TTTTTTTCAAGGG-GC-GG DroYak_CAF1_left CAAAGAA---AGTGGCACAAGCGCCTTGCTTTCATCGTT---AAA---A-ATTCGACAAA--AAAATATACGAATAAAAA----GGAAAT--GAAAGAA--ATGCAATCGTTCT-ATATC DroWil_CAF1_left TTGTTTT---TTTTTTTTTTTTGTT------------TA---AATGATG-AATCCGTC-C-GTTGACGTTCTTATTTGTTTTTTGTGTGGGCGT--GAT--TCCTTTTTTCCTT-TATGT DroAna_CAF1_left AAAATCGAAAATTTCCTTATAGATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCG--AAA-GTCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGACAAGACATCACAAA DroEre_CAF1_left TATCACCACAGTTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCA--AAA-GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAAGCAGCGAA-- DroGri_CAF1_left TCAAATG--GAATTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCACTTTTTCAA-TTCAATCAGACATAGCCTATGAGAGGTTAGGTGTACAAATGGATCAAAGCAACAAG-- DroMel_CAF1_left TTTAACTATAGTTTCCTTCTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCG--AAA-GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGCGAA-- DroMoj_CAF1_left T-TGCGGTGCATTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTG--ATA-TAAGATCAGACATAGCCTATGAGAGGTTAGGTGTAGCAAGG-GGTCAAACAGCAGA-- DroPer_CAF1_left -TAAAGCGAATGTGCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTG--AAAACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAAGAAATGCATCAAA-- DroPse_CAF1_left -TAAAGAGAATGTGCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTG--AAAACCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGAAGAAATGCATCAAA-- DroSec_CAF1_left TTAAAATAAAGTTTCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCG--AAA-GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTGAACAATCAGCGAA-- DroSim_CAF1_left TTAAACTAAAGTTTCCTTTTAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCG--AAA-GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGCGAACAATCAGCGAA-- DroVir_CAF1_left CGTCCGACAAATTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTCG--ATA-TACGGTCAGACATAGCCTATGAGAGGTTAGGTGTACCAAGG-GGACAAGCAGCGAG-- DroYak_CAF1_left CGTTATATCAGTTTCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATACG--AAA-GCCGATCAGACATAGCCTATAAGAGGTTAGGTGTACCAAGGTGAAAAATCAGCGAA-- DroWil_CAF1_left -AATATTAATATATCCTTATAAATCTAGCCTCTACTAGGCTTTGTCTGTGCATTTG--GA------TTCAGACATAGCCTATGAGAGGTTAGGTGTACCAAGGAGAAAATACAACAAT-- DroAna_CAF1_left AAC-GGATT-GAAGATTACAGTTACC-AAGT-CG-GAGGAGTACTCA-TAAT-AATT-TACCCATTTTT----CAGATTCCCAAATTTC-CCAATTTATA----GTAAATA--TTTCC DroEre_CAF1_left AAC-GGAAT-CG--ATTACAGTTTTGGGGACGT--GAGAAAGGTGGA-GAAG-GGGC-GACAGCCTGATAAAGCACGATCCC-C-C-GA-TCCCTTCAGC----ATTCCCC--AATCA DroGri_CAF1_left GCT-GCTGT-CG--GGGACTAAAAATGAATG-G--GCCGATTACCGT-AAGA-ACGA-GAGAGCGAGAAT---AACTTTAACGGAA-GC-GATCTCGTAG----AAACAGAGCGAACA DroMel_CAF1_left AAC-GGAAT-CG--ATTACAGTTTTGGAGAT-C--GTGAGAGGAGGA-GAAG-AGGC-GACTGCTTGATAA-GCCCGGACCCTCCA-GC-GATCTCCAAT----CAATATT--ACTTT DroMoj_CAF1_left GAGCACATA-T---TAAAATGAACTGCCGAT-T--ACCGTAATAGCGAAACA-TCGACCTGATAACTGTGA--CGACGAGCAGAAA-GA-GAAGGATATA----ATAAAAT--GTGGA DroPer_CAF1_left AGC-GGAAT-CCCGATTACAGTTACA-CTTA-C--GCG-AACGCCGG-GAAG-AGGA-GGAGGAGGAGGAG-GTGGCAACCG-ACT-GATAAGCAATATA----TTCTCCC--CCCAC DroPse_CAF1_left AGC-GGAAT-CCCGATTACAGTTACA-CTTA-C--GCG-AACGCCGG-GAGG-AGGA-GGAAGAGGAGGAG-GTGGCAACCG-ACT-GATAAGCAAAATA----TTCTCCC--CCCCA DroSec_CAF1_left AAC-GGAAT-CG--ATTACAGTTTTGGAGAT-C--GAGAAAGGTGGA-GAAG-AGGC-GACTGCCTGATAA-GCACTGACCCTCCA-GC-GATCGCCAAT----CAATATT--ACTTT DroSim_CAF1_left AAC-GGAAT-CG--ATTACAGTTTTGGAGAT-C--GAGAAAGGTGGA-GAAG-AGGC-GACTGCCTGATAA-GCACTGACCCTCCA-GC-GATCGCCAAT----CAATATT--ACTTT DroVir_CAF1_left GGC-GTCGT-TG--GGGTCCATCGAAATGAA-C--TGCCGATTACCG-TAATAGCGA-AACATGCTGCTGA-TAACTGTAACGACA-GC-GTCATGGAAA-----ACGGAG--AGGAG DroYak_CAF1_left AAC-GGAAT-CG--ATTACAGTTTTGGGGCT-C--GCGAAAGGAGGA-GGAGGACGC-GACTGCCTGATAA-GCACGATCCCTCCA-GC-ATTTCCCCCC-----CAAATC--AATAA DroWil_CAF1_left CAA-TTACAGT---T-GCCATTTCTATCTAC-CTACATATAGTTAGT-T-----ACG-AACGAACA-A-AA-GAACCAGCTTTTTG-TT-TATTTGTTTTATTAATCAAAT--ATTAA