CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AGGC--ATGTGTCTAG-ATATTTTTATTTTTGTATT-------TATTTATTTTTAT-AAA--TATTACATAATAATATTTATTGTAAAGAAAATAAAAGAATAAAAATAAATAAATAAAA DroEre_CAF1_left TCAA--CGAAG-G--G-AATCTGATATTTCCCAAA-------TTGTAT---TGTAAAATT--GATTTTAATA-AGTTTATATAG------AAAC--AATTTTTCAAGAATACCAATAGCA DroYak_CAF1_left TAGTC-AGAAA-T--T-AAGATATGGCTATTGTATTGCTTAAATCAGT---TATATTTAT--TTAGACATAT-ATAAAAAAAGT------TTTA--AAGAAT--AAAAATACCATTGACC DroMel_CAF1_left ATTA--TGT-T-A--TGATTGAACAACCGCAAT----------TCTGT---ATTTCTTAAATTTTATTGTTA-AATATATTTTT------ATAC--GTTA-TAT---AGAAA-AAACTTA DroPer_CAF1_left GCAC--AATAG-C--T-AGTTCATAACGTTGATAAA-------TTTCC---ACTGCTCAA--ATACTTAATA-ATGCCACAGAC------A-AA--AATAATTTAATCTATT-AATTTAT DroPse_CAF1_left GCAC--AATAT-C--T-AGTTCATAACGGTGAAACA-------TTTCC---AACGCTCAA--ATACTAAATA-ATGCCAGAGAC------A-AA--AATAATTGAATCCATT-AATTTAT DroSec_CAF1_left TTGA--AGAAG-C--ACAATTCGGTATATCATAAAT-------TTTAT---TTTGTAAAT--TTATTTTTAT-ATGTTATAAAG------CAAC--AATTTCTCCGCCATAA-AATCGCA DroSim_CAF1_left GATTGAAGAAG-C--GAAATTCAGTATATCTTAAAT-------ATT-----ATTGTAAAA--TTATTTTTAT-ATGTTATAAAG------AAAC--AATTTCTCCACCATAA-AATCGCA DroAna_CAF1_left TATAATAAT-C-ATTGTAAA-------ATAGAACAAAAAATTTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCAC-ACACTTTCGTTCAGAAAGCAAGAT DroEre_CAF1_left TTGATTACA-A-AAACAA---------TAAACAAAAAAAGTTTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCAT-ACACTTTCGTTCAGAAAGCAAGAT DroYak_CAF1_left ACAAAAAAG-T-AATAAT---------ATATGAAAAAAAGATTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCCCAT-ACACTTTCATTCAGAAAGTAAGAT DroMel_CAF1_left TCAACCATTCAAAAACAAAA-------CCACTAAAAAAAATTTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCAT-ACGCTTTCGTTCAGAAAGTAAGAT DroPer_CAF1_left GGAATGTAA-A-AAAAAACA-------ACAGCA-AAAAAGGTTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCA--ACACTTTCGTTCAGAAAGCAAGAT DroPse_CAF1_left AGAATGTAA-A-AAAAAACATCAAAAAACAGAAAAAAAAAGTTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCA--ACACTTTCGTTCAGAAAGCAAGAT DroSec_CAF1_left TTTACTAAACA-AAACAAGA-------GCAT-AAAAAAAGTTTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCAT-ACACTTTCGTTCGGAAAGTAAGAT DroSim_CAF1_left TTTACTAAACA-AAACAAGA-------GCAT-AAAAAAAATTTTGTCAGAAGTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCATAACACTTTCGTTCGGAAAGTAAGAT DroAna_CAF1_left TCTATA--TCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACATATGTTAGTTGTGCGTCCGAAGCGCTAGTT--GTG-TGAGCG-CA-ACAGAATGT--ATAACAGTATTAA-C DroEre_CAF1_left TTGACA--TCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACACATGGCATGCTTGTGTCAGATTCGCTTGTT--CTC-TGCGCG-AATACTGCGCGT--ATGTCAGTTCT-A-C DroYak_CAF1_left TTTAAA--TCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACACATGATATACTAGTGTCCGATTCGCTTGTT--GTC-TGCACG-AATACAGCGCGT--ATATCAGTTCT-A-A DroMel_CAF1_left TTTAAA--TCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACATATGCCAAACTCGTGTCCGATTCCGTAGTT--GTC-TG-CGCGAGCACA-GCG-CATGTGCCAGTACT-AGA DroPer_CAF1_left TTCAAACACCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACACATGCTAATTCCGTGTCACAAACCGTATTTGTGCCAGC-AAC-GTTAAATGTT-GT-ATAACAGAAAA-T-A DroPse_CAF1_left TTCA-ACACCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACACATGCTGATTCCGTGTCACAAACCGCATTTCTGCCAGC-AAC-GTTAAATGTT-GT-ATAACAGAAAA-T-A DroSec_CAF1_left TTTCAA--TCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACATATGCCAAACCAGTGTCCGATTCCGTAGTT--GTC-TGCGCG-AACACAGCGTGTA--TGACAGTACC-AGA DroSim_CAF1_left TTACAA--TCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTGACATATGCCAAACCAGTGTCCGATTCCGTACTT--GTC-TG-CGCGAGCGCT-GTG-TA--TGACAGTACC-AGA DroAna_CAF1_left AGAGAAC-ACTTCTGTTAT-ACCA-CTGTTAA-ACATAACATAGAAGAGAAATGTTATAAAT-AACAT-- DroEre_CAF1_left TCGTAAT-ATAACAGTCAA-ACGA-ACATGGA-ACATTTCTCTGTAGCTCGGTTATCTT-CGCTGTTC-- DroYak_CAF1_left TCGTAAT-ATAACAGTTGCCAATA-TCGAATG-GTGTTTCTTCGAATTTCTGCTAGCTT-CG-CTATT-- DroMel_CAF1_left ACAATTCTATTCGTAATAT-AACAGTT-GCAG-TCAAACCAACATGGAAGGTA-T-TGTTAG-CTTCG-- DroPer_CAF1_left CC-ATCGAACAGTTCTC-G-CTCTGAG-AAAGTTTCGTGCTACAGAATTTACT-G-AGCAAG-CAGTC-- DroPse_CAF1_left CC-ATCGAACAGTTCTC-G-CTCTGAG-AAAATTTCGTGCTACAGAATTTACT-G-AGCAAG-CAGTC-- DroSec_CAF1_left ACAATTCTACTCGTAATAT-AACAGTT-GCAG-TGGAATGGAAGGTATTTATC-T-GTAGCT-CTGTT-- DroSim_CAF1_left ACAATTCTACTCGCAATAT-AACAGTT-GCAG-TGGAATGGAAGGTATTTATC-T-GTAGCT-CTGTTAG