CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left GAAATTTTATTTGTTAGCGTGAAGAAGAACAA-TTCTGAAAGAGTGGGGC--C------T-TTAACTATT-CAAA---------T-ATAAATGATAAAAACATGTG-CAAT--------- DroMel_CAF1_left CAATTATGTATGAGT--GAAGA--AATTTAAC-GTT-----TAATTATAA--A------A-C-GGTTGCTGTTTC----ATTTTT-CTAAA-ATAAATATTTAGTT-CTGT--------- DroMoj_CAF1_left ATTATGCCTCACATAATCATAT--A--AATTAATAA-----TTGATCAAA--T------T-A-TTTTGTG-ACGC----AAAATA-ATTAT-GAAAACATTAAA---CATG--------- DroSec_CAF1_left AAGAGCGAGGAATTA--TATAT--CATTTCAT-GAA-----TTATATATC--A------T-T-TATTATA-TTTC----ATTTTT-CCAAA-ATAAATATTCAGTTTTTGT--------- DroSim_CAF1_left AAAAGCGAGGAATTA--TATAT--CATTTCAT-TAA-----TTATATATC--A------T-T-TATTATA-TTTC----ATTTTT-CCAAA-ATAAATATTCAGTTTTTGT--------- DroYak_CAF1_left TTGAAGAAGTCCAAA--TTAGA--TAGTGTGG-GGC-----TATTTAACTTTCAAATAAA-A-ATTGTAAAATAAAAATGTTAACTTTTTA-AT----ATATGTAC-ATTTTTAATGTTA DroPer_CAF1_left CTCTTTTAGTGCATA--AATAA--TGCATAAA-TAG-----TTGTCACAA--A------ACA-TGTATTAATATC----ATAATA-ACAAT-GCAAATTTCTGT---ATAG--------- DroPse_CAF1_left TTTGAAACCCTTATA--AAGAA--TGCTTAAA-TAG-----TTGTCACAA--A------ATG-TGTATTAATACC----ATATTA-ATAAT-GCAAATTTCTGT---ATAG--------- DroEre_CAF1_left TTTTTG--AATGTTAATTATT-TCAATAAAAAATAT-AGAAAAAAAAATAATGAAAAAATAATCATAAACGATCCTGCCAGGAGTCGAA--CCTGGAATC-TTCTGATCCGTAGT-CAGA DroMel_CAF1_left ATTTTT--CTAAA---------TA-ATCCG-TTGATTTCA--ATAAAGAAACAATAAAAAATTTAATTCCGATCCTGCCAGGAGTCGAA--CCTGGAATC-TTCTGATCCGTAGT-CAGA DroMoj_CAF1_left AAAATGC-TTTAC-TA----TAT-TTAGTA-AACTGAATT--AATAAAA-A--AA-CTTTCAAAAAATTCGATCCTGCCAGGAGTCGAA--CCTGGAATC-TTCTGATCCGTAGT-CAGA DroSec_CAF1_left ATTTTT--CTAAA---------TA-GTCTG-TTGATTTTA--ATAAAAG-A--AA-AAAAATCTATCTCCGATCCTGCCAGGAGTCGAA--CCTGGAATC-TTCTGATCCGTAGT-CAGA DroSim_CAF1_left ATTTTT--CTAAA---------TA-GTCTG-TTGATTTTA--TTAAGAG-A--AAAAAAAATCTATCTCCGATCCTGCCAGGAGTCGAA--CCTGGAATC-TTCTGATCCGTAGT-CAGA DroYak_CAF1_left AGGATT--TCGGT---------AA-AAGAA-AATAAAGGT--CAAAATA-A--TAAAATAAAATATGTTCGATCCTGCCAGGAGTCGAA--CCTGGAATC-TTCTGATCCGTAGT-CAGA DroPer_CAF1_left TAATATTCACAAAA------AGC-TTTAAA-AATAAA-----TCCAAGTGAAAATAAAAGTATTAGTCACGATCCTGCCAGAAATCGAAACTCTGGAAACTTCTGCATCCGTAGTCGCAG DroPse_CAF1_left TAATATTTACAAAA------AGC-TTTAAA-AATAAA-----TCCAAGTGAAACTAAAAGTATTAGTCACGATCCTGCCAGAAATCGAAACTCTGGAAACTTCTGCATCTGTAGTCCCAG DroEre_CAF1_left CGCGTTATCCATTGCGCCACAGGACCGATGAAATCTTCTGCGCCAAACACCTGTTCTTAAT-AAG--GTAAGTTAATGATGTGTATTGATATGAACGATACATAAAACTACA DroMel_CAF1_left CGCGTTATCCATTGCGCCACAGGACCGATGAAACCTTCTGTGCCAAACACCTGTTGTTAAT-AGG--GTAATTAGGTATTATGATATGCATGATTTGAAAAAAATAACATTA DroMoj_CAF1_left CGCGTTATCCATTGCGCCACAGGACCGCTTAATAACACCGGAGCTTTCTTCTCTACAAAAATATT--G-CTATAAATAACATGAAATGCTTATTCATGATTTTTCGTTGTTG DroSec_CAF1_left CGCGTTATCCATTGCGCCACAGGACCGATAGAAGTTTGCGTGCCAAACACCTGTTGTTAAT-TAG--GTATTATGAATGGTATCATAAAAATAAAATTAGTCTAATGCTATT DroSim_CAF1_left CGCGTTATCCATTGCGCCACAGGACCGATAGAAACTTGCGTGCCAAACACCTGTTCTTAAT-TAG--GTATTATGCGGGGTATCATAAAAATAAAATTAGTCTAATGCTATT DroYak_CAF1_left CGCGTTATCCATTGCGCCACAGGACCGGTAGAATCTCTTGCGCTAAACACCTGTTCTTTAT-TAT--GTAAGATAATAATATGTTATGATATGAATGATAAATATAATAACA DroPer_CAF1_left CACTGGATCTTTCACTCTAATTTTAATATCAAAGCAAAACTAGTTATA--ATCGATACTC--GAT----GAGTATAGTAGTGTATTCGA--TTT-GTTATCTGGAAGATTCA DroPse_CAF1_left GACAGGATCTTTCCCACTAATTTTAATATCAAAGCAAAACTAGTTATA--ATCGATTTGT--TTTTTCTACAAATATAACTGGTAGATT--CAT-GTTTTGGTTGTGG----