CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TAAAC--CTTGTT-GATCTTTT-AAGA--CCTGCTGACCAGTAGAGTATATATCGTACTCCCCATATATACA-TATAGTATATTTTTTGGTTAACCTTCTCTCCTCACGCA-CTC----- DroEre_CAF1_left ACAGC--ATCGCC-ACCGAAAA-GCCTC-GCATTTACGG---A--AATCAATCAGTTCATGCAT--TATGTA-CTCGCCCT-TTTTTT--CGGTTCTTTGCTCACATTTCTCCTATTGCA DroGri_CAF1_left CTAGT--TGATAAGCTACTCGG-ATATGTCATG---T----GT--TTTTGCTCACCATGCT--ATGTTTCAC-CATGTTTTTTGTCTTAACTATATAGTTAGTACCACACA-CAATTGCA DroMel_CAF1_left GATGT--AGCCTC-GCATTTAC-GGAAA-TCAATCAGT----T--CAGCTCTTCATGCATTATG--TACTCG-CCCACATTTTTTTTT--CGGTTCTTTGCTCACATTTCTCCTCTTGCA DroPer_CAF1_left TATGTACATATAC-GCACATGC-ATAT--GTATTATCGTTATT--TTTTTTTGTGTTTGTGTTTCACTTCTC-TATCTCTCTCCCATTCGCTGTCTGCCGCCTTCCATGCA-CTTTTTGT DroPse_CAF1_left C--ATACATATAC-GCACATGC-ATAT--GTATTATCGTTATTTTTTTTTTTGTGTTTGTGTTTCACTTCTC-TATCTCTCTCCCATTCGCTGTCTGTCGACTTCCATGCA-CTTTTTGT DroSec_CAF1_left GATGT--AGCCTC-GCATTTAC-GGAAA-TCAATCA-GC---T--CATCATGCATTATGTACTC--GACCAC-ATTTTTTTTTTTTTT--CGGTTCTTTGCTCACATTTCTCCTCTTGCA DroVir_CAF1_left GTTAC--ACGTTC-AATGTCAT-TCGGA-TTTGTCATGT---G--TT---TTGTGTTTG--TTTTATCTCAC-AATTCCATGTTTTGT--CTCACCCACACACACACACACACACACACA DroWil_CAF1_left ATATT--TCGTAT-TTTTTTTC-CTTTT-TTTTAAT-TC---T--ATTATGTCAACTTTTTTTA--TATTTT-TTCCACATTTTCTTC--CTCCCCTCTTCACCATCTTTTCCTCTCCCT DroYak_CAF1_left G-AGC--ATCGCC-ATCGATATAGCCTC-GCATTTACGG---A---ATCAATCAGTTCATGCAT--TATGTA-CTCGCCCACTTTTTT--CGGTTCTTTGCTCACATTTCTCCTCTTGCA DroMoj_CAF1_left TTACG--ATTTGT-CTATGTGA-T--TT-TTGTGTT-GT---T--TTTTATACATATA-TACAA---TATATAACTCACTGTTCTATA--TGTTTTTTGTCTCAC-CCACA-CAATTGCC DroAna_CAF1_left CCTTTCATTATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAAC DroEre_CAF1_left CCTTTTATCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAAC DroGri_CAF1_left ATTTCTTTCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCTA---TATCTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCACCGCCTGCAC DroMel_CAF1_left CTATTTATCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACATGATATTTCA DroPer_CAF1_left TCTCCTTTAATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAAC DroPse_CAF1_left TCTCCTTTAATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAAC DroSec_CAF1_left CTATTTATCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAAC DroVir_CAF1_left CAA-TTTTCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTT-ACAGTTTGT--ATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCACCGCCCGCAC DroWil_CAF1_left CCATCATCATTTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCAACGCACCCCA DroYak_CAF1_left CTATTTATCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAGCGCACCAAC DroMoj_CAF1_left ACT-CTTTCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT-CACATATTGT--ATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGACACCGCCCAACC DroAna_CAF1_left AA---CAACAACAAC---AA-CAACAGGAA-TGATAC-AAC-A-ACA---A-TAAATCCAAAA-AAA-AAAATAATTAAATATTA-TTG-GATGCACGTTTTCTG---AAAA DroEre_CAF1_left CA-AAAAACAGCCAC---AA-ATACAGGAA-TGATTT-CTA-A-TA----TATCACCTGCTTG-CCAATGTCAATTTGTTC---A-TGT-GCCTTCC-GTGTAATT--CGTA DroGri_CAF1_left CC---CGCCACCAAC---AG-CAACAGCAA-CAAAAACAAC-A-AAA---CTAGCTGCAATGG-ATA-ACGTAACAGCAACAA-C-AGC-AACAACA-ACAACAG---TCAA DroMel_CAF1_left CC---CGCTTGCCAA---AT-CAATTTATT-CATGTG-TCT-T-TCGT----GTAATTCTTCGTCTG-TGCTTGCAAATAA-TCCATTC-AAATAAT-ATGGCAT---ATGT DroPer_CAF1_left AA---CAACAACAGT---AA-CTACAGTAA-TCAGAA-AAC-G-AAC---CCCGAATCGAATG-ATA-GTACAGTTATAACATGC-AAA-AAATAAAACAAACA----TCAT DroPse_CAF1_left AA---CAACAACAACAGTAA-CTACAGTAA-TCAGAA-AAC-G-AAC---CCCGAATCGAATG-ATA-GTACAGTTATAACATGC-AAA-AAATAAAACAAA-------CAT DroSec_CAF1_left CC-A-AAACAGCCAC---AA-ATACAGGAA-TGATTA-ATG-A-TA----TTTCACCCGCTTG-CCA-AGTCAATTTATTG---A-TGT-GTCTTTC-GTGTAATTCGTCTA DroVir_CAF1_left CCGC-CAACATCAGC---AT-CAACAAAAA-CAAAGA-CAACA-ACA---ACAAAAATGAACT-GTA-ATATGGCC-GAAC---T-ATTACATGAGT-TGAACAA---CGAC DroWil_CAF1_left AA----AACAAAATA---AA-ATGCAACAAAATAATA-ACT-G-TA----CACAATATTAAGG-TAT-TATATACATAAATATACATAT-TTACATC-GGAAATG---TAAC DroYak_CAF1_left CA-A-AAACAGCCAC---AA-ATACAGGAA-TGATTA-AAA-A-TATCTTTATCACCAGCTTG-C-AAAGTCAATATATT----C-TGT-GTTTTTC-GTGTAAT---TCGC DroMoj_CAF1_left GC---TCGCACAATC---CGCCAACATCAG-TAAAAC-AAA-ATAAT---AAATAAATAAG---AGA-ACAAAAAAAAA-CAAAAAAAA-AAAAACA-GTTCCTT---AAAC