CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroAna_CAF1_left   T--TC--CCAGCT-GGTTGGCTTATTGATAC-AGCCATGGC-C-ATGGCC-------C-C--AAGAGAGAATAAAGAGGTGAGT-GTAGTGGCTCCAAGA--TGAGTGCAGTGAAGCATT
DroEre_CAF1_left   C--CA--AGATGG-CCAAGACCCACGGAGCG--CGAAGGTGAGTAGTGTG-------G-G--GAGTGGAGTG---GAGTGGACT-GGAGTGCATCCGAGACGAGAGTGCAGTGGTACATT
DroGri_CAF1_left   T--TG--GCTGCT--CTTGGCTTATTGATAT-TTCAATGGG---AATGTT-------TGT--CCGAGTCTCTCTCTCTATCTGC-GTG-TGTGTGTGTGTAAGTGATGTGGTGCAACATT
DroMoj_CAF1_left   G--CTGACGTCCC-GCTTGGCTTATTGATAT-TGTTATGGG---AATGTG-------T-A--GCTGCCATCTCTGCGAGTATGT-G---TGTGTGTGTGTTTAAAGTGCTGTGCAACATT
DroVir_CAF1_left   A--CA--GT-----GTTTAAGCCAAGCTAGAAAAGCCGACGACTCGCTTG-------G-CTTATTGATATTG----TTAGAGGCATTTGTGTACGTGTGTGCTAAGTGGTGTGCAACATT
DroWil_CAF1_left   G--CT--AAGTGCAGTGATGCAT--TAAAAC-GTCACCGTCAACTGTGCT-------G-T--TGATGTAAAT---GTAATTTGT-GTATCTTAACTGTGTGCGGAAATTGTATCTTTAAA
DroYak_CAF1_left   TATTG--ATATGG-CCAAGGCCCACGGAGCG--CGAAAG--GTGAGTGCT-------G-T--GTGGAGTAGG---GAGTGGAGT-GGAGTGCATCCGAGATGAGAGTGCAGTGGTACATT
DroMel_CAF1_left   C--AG--GCCCAC-AAAAGGAACGCGAAAGG--TGAGTGGTATGGGGATT-------G-G--GCAGTTTGGA---GTTTGGAGC-GGATTGCATCCGAGATGTGAGTGCAGTGGTACATT
DroSec_CAF1_left   C--AG--GCCTAC-GAAAGAAGCCCGAAAGG--TGAGTGGGGTGGGGATT-------G-G--GCAGTTGGAA---GTTTGGAGC-GGACTGCATCCGAGATGAGAGTGCAGTGGTACATT
DroSim_CAF1_left   A--CG--AAAGGA--------GCGCGAAAGG--TGAGTGGTGTGGGGATTGGGCAGTT-G--GGAGTTTGGA---GTTTGGAGC-GGAGTGCATCCGAGATGAGAGTGCAGTGGTACATT

DroAna_CAF1_left   AAAACGTCACCTGATGTAGGCCGTGCCCGGTGCTTATTTGTTACTT-TTGGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCAAAGGCAGCTATCTTCACTGGAAA-AA-TA
DroEre_CAF1_left   AAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCAGCGATCTACACAGTGCA-AA-AT
DroGri_CAF1_left   AAAACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAAACAACAAACAACAA-CAGCA-AAAAA
DroMoj_CAF1_left   AAAACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGCGAAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAAACAACGTC----TGTGTGTG-TC-TC
DroVir_CAF1_left   AAAACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGCGAAAATCCAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGCCAACGTTCCTTGTTTATCA-CC-GG
DroWil_CAF1_left   AATACGTCACATGATGTAGACCGTGCCTGGTGCTTATTTGTTGCTATTTAAATATACAAATTGCACTAGTCCCGGCCTGCAGTAAGTGTCGCAAACAACTTTACTTTTAACGTTTTA-GT
DroYak_CAF1_left   AAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCAGCGATCTGCACAGTGCG-AA-AT
DroMel_CAF1_left   AAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCATTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAATGAGTGTCGCAGTCGACGATCTACACAGTGCA-AA-AT
DroSec_CAF1_left   AAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCGACGATCTACACAGTGCA-AA-AT
DroSim_CAF1_left   AAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCGACGATCTACACAGTGCA-AA-AT

DroAna_CAF1_left   ATTAATAT-CGAAT-ATTGTGGTTAC-AAA--ATTTTACTTAAAATAAAATGTTAAATTATTATGAA-CTATTTCTAAACTTTCTAG-ATTTATTTAATA
DroEre_CAF1_left   AATT-GGTGCAA-CGAATCGAAACGT-ACAAGTCCATAGC-TGTACTCTAAATTGT-ATTTTAAAGTTTGTCA-TTTTTTAAATATA-ATCAATAGCATG
DroGri_CAF1_left   AGC--ATC-GCTTTCCCTGCAGCTGCCCCA-AAAGGTGGT-GCCACTTGGCTTATT-CGTGTTACCGACGGCC-TCTCATCTTCGCC-AACCTATAATTA
DroMoj_CAF1_left   ATCTGGGC-AGGCA-TCCG-CCTCTC-TGT--TGCCTGTTGCCCTGTAATTATATAATTTAATCAAA-TTACTTGCATATGTTA------CCAAAAAAAG
DroVir_CAF1_left   TCGG-TCAGCCA---AAA--T-GTGG-TGGCATGCCTCCG-TCACTG-TGTGGCAG-AACAGTCGCTTC-TCT-GCCTGCTGTGAAG-CC---CTGTAAT
DroWil_CAF1_left   ATTA--A-------GATTGTTTTTGT-T-TTGT-TGTTG--TTAACAATAATGTTTGTTGCTGCTGC-TGCTG-CTGATGCC-TCGC-CGGGTGCGTGTT
DroYak_CAF1_left   AATT-AGTGCGA-AGAATTAAAAGGT-ATAGGTTCATAAT-TGTACTATAATTAGT-AGTGGTTATTACTTTG-ATGTT-TATTACTTTTGATTATATTA
DroMel_CAF1_left   AATT-TGTAAAA-ATAATTAAAAATA-ATAACTTCATAG--ATTTTTTTATTAAATTAGTTTTTGTG-TGGGATCTAATCACTAATC-TTGCAACAAATT
DroSec_CAF1_left   AATT-AGTACAA-TGAAATAAAAATA-AGAAGTTCATAG--TTAAGAATACATACAATTATAGATAA-TGATGATTATGTTATACTC-GTTACTCGTTAC
DroSim_CAF1_left   AATT-AGTACAA-TGAAATAAAAATA-AGAAGTTCATAG--TTAAGAATACATACAATTATAGATAA-TGATGATTATATTATACTC-GTTACTCGCTGC