CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TTCAGAAACACTCT-TTAAT-GATTGTCACATATTA-GA-T-TGT-CCAGTTTTGATTTGTTGAAAAACACACAC--AAAACACTTTATCTGTTGAGTGGTTCTTATCAAAAGCACTGAT DroGri_CAF1_left GATTAGAGTCAATTGACTGT-GATCGTGG-CAATAT-CA-T-GAA-TCACTTTTGATAAATCACTTGAAACACTT--TGTGCTAATGCGCCGCTGATCGGTTCCAATACAAAGCACTGAT DroMel_CAF1_left GTTTTTGCTTAAAATTTGTA-TTTCG--AGTGTTCCGAT-T-GAG-TTATTTAACAGCACATTTGAAGTTCGCTT--CGATTTGACACTTCGCTGATTGTTTCTTATCAAAAGCACTGAT DroMoj_CAF1_left TTATTAACATTTATATAGAC-AGTTC-AATTCTTTCTTT-C-GC--AACATATTCAT-AGATCACTGTTA-GACACTTGTTCCCATACACCGTTGATCGGTTCCAATAAAAAGCACTGAT DroPse_CAF1_left TTAAACTTTTTGTATGGAAA-CCTTT--GGATTT-TAAC-A-TGAATTGTCATGCACTGAAAAAAAATCACTTTG--GAGAAACACTTTCTGTTGAATGGTTCTCATCAAAAGCACTGAT DroSec_CAF1_left GTTTTTGCTTTAAATTCGAT-TTTCG--AATGTTCCCAT-T-GAG-TTATTTAACAGCACATTTGAAGTTCGCTT--CGATTTGACACTTCGCTGATTGTTTCTTATCAAAAGCACTGAT DroSim_CAF1_left GTTTTTGCTTTAAATTCGAT-TTTCG--AGTGTTCCCAT-T-GAG-TTATTTAACAGCACATTTGAAGTTCGCTT--TGATTTGACACTTCGCTGATTGTTTCTTATCAAAAGCACTGAT DroVir_CAF1_left GTGTGCTGCAATAA-TTTTGTATTGA-TTCAGGTTTGTT-T-TCA-ATATTTGCTGTAATACACGCGAAACACT---TGTTTTGATGCGCCGCTGATCGGTTCGAATAAAAAGCACTGAT DroWil_CAF1_left AAAACACACACACACACAGC-TTTCG--TAGTCAGACAC-A-TTT-ACTTAGTATTTACTGTAGCAATTGTAATT--TAATGCCATCTCTTGTTGATTGGTTCTAATCAAAAGCACTGAT DroYak_CAF1_left AATTC-GTTTAAAATTCGTA-TTTAG--AGTGTTCCGAT-TTGAG-TTATTTAACAGCACATGTGAAGTTCGCTT--CGATTTGACACTTCGCTGATTGTTTCTTATCAAAAGCACTGAT DroEre_CAF1_left TTTTTCTTTAAAAT-TTGTA-TGTAG--AGTGTTCCGATTT-GAG-TTATTCAACAGCACATTTGAAGTTCGCTC--CGATTTGACACTCCGCTGATTGTTTCTTATCAAAAGCACTGAT DroAna_CAF1_left TTCGAATGGTGCTAGAATTGAAAT-GATCG----GA-----TCTCCTTGATATCTATGCACCAATCGATCTCAGTTCTTTGATTCGAATTATCCTGGCTAG-----CTAATCCTGTCAA- DroGri_CAF1_left TTCGAATGGTGCTAGAATTGAAAT-TAAAT----TATT---CTTGGACGATATCTATGCACCAATCGATCTCAGTTCTTCAATTTGAACTGGCTGCTACAT-----AGGTTATT--AGT- DroMel_CAF1_left TTCGAATGGTGCTAGAGTTAAATT-GAGTG----GG-----TTCTCCTGATATCTATGCACCAATCGATCTCAGTTCTTCGATTCGAAGTGGCAGGGCAAG-----TAGGTAGC--TCC- DroMoj_CAF1_left TTCGAATGGTGCTAGAATTGAAAT-AAAAT----GACT--TTTTGGGCGTTATCTATGCACCAATCGATCTCAGTTCTTCAATTTGAACTGGTGTGGTGTT-----T-GATGTC--TGC- DroPse_CAF1_left TTCGAATGGTGCTAGAGTTGAAAATTAGCG----AG-----TCCTCTTGATATCTATGCACCAATCGATCTCAGTTCTTCGATTCGAACTGTAATTGTAAG-----AAGTGTCC--TGCT DroSec_CAF1_left TTCGAATGGTGCTAGAGTTGAATT-GAGTG----GG-----TTTTCCTGATATCTATGCACCAATCGATCTCAGTTCTTCGATTTGAAGTGGATGGGCAAG-----TTGGTAGC--TCC- DroSim_CAF1_left TTCGAATGGTGCTAGAGTTGAATT-GAGTG----GG-----TTTTCCTGATATCTATGCACCAATCGATCTCAGTTCTTCGATTCGAAGTGGCTGGGCAAG-----CTGGTAGC--TCC- DroVir_CAF1_left TTCGAATGGTGCTAGAATTGAAAT-GAATT----ACTT---TTTGGGCGATATCTATGCACCAATCGATCTCAGTTCTTCAATTTGAACTGGCTGGTGCAT-----AGTTGGGT--GTC- DroWil_CAF1_left TTCGAATGGTGCTAGAATTGAATG-AAATCAAATGATAGAATTCGCATATTATCTATGCACCAATCGATCTCAGTTCTTTAATTCGAACAATTTGTATGTG-----GTCCGTAT--GTC- DroYak_CAF1_left TTCGAATGGTGCTAGAGTTGAATT-GAGTG----GG-----TTGTCTTGATATCTATGCACCAATCGATCTCAGTTCTTCGATTCGAAGTGGTAGGGCAAG-----AAGGTAGC--TCC- DroEre_CAF1_left TTCGAATGGTGCTAGAGTTGAATT-GAGTG----GG-----GCTTCTTGATATCTATGCACCAATCGATCTCAGTTCTTCGACTCGAAGTGGGAGTGCAGCTCCTGAAGGTAGC--TCC- DroAna_CAF1_left TGATGATCCTGTTGC-CTTCAAGCTGCCGG--CTGAAAGCCGCTTTTACGATCA-GTTCCGAGG-CG--AGTGC-CGTTGAT--GACTGTAT-A-CCCC DroGri_CAF1_left GATTGACTGCTCCTT-CATTGTACTGTACG--C-GATTGCGATTGCGATTGCGA-TCACGATGA-CG--AGTGA-TAACGAGGCGAGCGAGA-G-TCAC DroMel_CAF1_left TGT-TTCCGATCCTG--AACCCTTTGGACTAAA-GTTACCGACTAAAAGCCGCCGTACTAACAA-CG--ATCGC-TTGCGAGGCGAGTCGAG-T-CGAC DroMoj_CAF1_left TGG-GTGTGTGGCAT--AATAGATAATATTATC-TAGGCACTACTTCATTTTTTTTATTTATAT-AA--TTTTT-TTTTGAGCGAACGCGATCA-CGAC DroPse_CAF1_left GCT-CGGCTGCTCCTGGTCTCCT--GCCGGCGC-TGACTGGAAGCGCAGTCTTTGATCGGTCGGGCC--CGAGA-TCACGATCGAT-TCC-G-T-GGCG DroSec_CAF1_left TGT-TTCCGATCCTG--AACCCTTTGCACTGAA-GATACCGACTGAGAGCCGCCGTACTAACAA-CG--ATCGC-TTGCGAGTCAAGTCGAG-T-GTCT DroSim_CAF1_left TGT-TTCCGATCCTG--AACCCTTTGGACTGAA-GATACCGACTGAGAGCCGCCGTACTAACAA-CG--ATCGC-TTGCGAGTCAAGTCGAG-T-GCCT DroVir_CAF1_left GTATTAGTCTATATA-TATATATATATATT--G-AAGCACTTC-TTGTCACATT-CATTCAATC-CCATCGCGA-TCACGACTGAT-AACGA-G-GCGA DroWil_CAF1_left C-T-TAATGTCATAG--GGATCCCCATTGAGGT-GTACTG-AAGGCTCCTTCCTTCTCCTTCTT-CT--GCTTC-TCACGATCAATTACGTA-G-CGAG DroYak_CAF1_left TGA-TTCCGATCCTG--CACCCTTTGGACTGAT-GAAACCGACTGAAAGCCGTA-CTA-ACGAT-CG--CTTGCGAGGCGAGTTGATTCGAT-TCGAGT DroEre_CAF1_left TGC-TACCGATCCTG--CACCCCTTGGACTGAA-GATACCGACTGATCGC--TT-G-CGA--GG-CG--AGGCG-ACTCGAGTGCCTCTGATGA-CTGT