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


DroAna_CAF1_left   ATGGG-CGGATGGGCGGATGGGTCTATTTTTAGTA-AC-ATAG-AAAGCTTTCGGCGGGAAGCTACGGACTCC---------ACTATATGACTGGGTTTTGGCCCGCACTCTTATCGTAA
DroEre_CAF1_left   CGGTGGGCGGTGGGCGGTG-TCACTATTTTTAGAG-CG-ATAG-AAAGCTCTGGGCGGCAAGCTCCGAACTCC---------ACCATATAGCAGTGTTTTGGCCCGCACTCTTATCGTAA
DroMel_CAF1_left   GGGAC--AGGTGGGCGTAG-TAACTATTTTTAGAA-TG-ATAG-AAAGCTCGGAGCGGCAAGCTCCGAACTCCGC-------ACCATATAGCAGTGTTTTGGCCCGCACTCTTATCGTAA
DroMoj_CAF1_left   TTGTT-GGTGTTGTAACTATTTATAGTCTGAAATG-GC-TGAA-AAAGCTTTTGGATGAAAGCACAGAGCTGC---------ACTATATGAAGGTGTTTTAGGTCGGGCTCTTATCGTAA
DroPer_CAF1_left   GTGGG-CGGT-GGGCGAAG-CTACTATTTTTAGTGGCGGGTAG-AGCTTTCGGGTGGGAAAGCACCATCCCAC---------ACGATATGGGGGCGTTCTGGTCCGCACTCTTATCGTAA
DroPse_CAF1_left   GTGGG-CGGT-GGGCGAAG-CTACTATTTTTAGTGGCGGGTAG-AGCTTTCGGGTGGGAAAGCACCATCCCAC---------ACGATATGGGGGCGTTCTGGTCCGCACTCTTATCGTAA
DroSec_CAF1_left   GTGGG-CGTAGT---------AACTATTTTTAGAA-TG-ATAG-AAAGCTCGGGGCGGCAAGCTCCGAACTCCGCACCATATAGCATATAGCAGTGTTTTGGCCCGCACTCTTATCGTAA
DroSim_CAF1_left   GTGGG-CGTAGT---------AACTATTTTTAGAA-TG-ATAG-AAAGCTCGGGGCGGCAAGCTCCGAACTCCGCACCATATAGCATATAGCAGTGTTTTGGCCCGCACTCTTATCGTAA
DroVir_CAF1_left   GC-ACTTGTTGGTGTTGTGACTATTTTTAGTGTTG-GG-TCGT-AGAGCTTTTGGTTGAAAGCACAGAGCTCC---------ACTATATATTGGCCTTTTGGTTCGTGCTCTTATCGTAA
DroWil_CAF1_left   CATATATGTATGTGTGTAG-GAAGGTGTGGGGGGG-TG-CGCC-GGGTTCTTGCCTAGACAGATCGGACCTCC---------ATCATATGTAGGCATTTTAGTTCGTACTCTTATCGTAA
DroYak_CAF1_left   GCGGGACAGGTGGGCGTTA-TCACTATTTTTAGAA-CG-ATAG-AAAGCTCTGGGCGGCAAGCTCCGAACTCC---------GGCATATAGCAGTGTTTTGGCCCGCACTCTTATCGTAA
DroGri_CAF1_left   TGCTA-TTATTTGTTGTTA-TCACTATTTTTAGTGGAG-GCAGTGGAGCTTTTGCTAGAAAGCACAGAGCTCT---------GCTATA-TGCACACCTTTATTTCCAGCTCTTATCGTAA

DroAna_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-AAATC--AGTT-TGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATTTTATCTTTTGCAT
DroEre_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-GAATCCCATGT-CGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATTTTATCTTTTGAAT
DroMel_CAF1_left   CTTGTGTGGCTTCGAACTTACCTAGTTGAGG----A-A-AACTCCCATGT-CGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATTTTATCTTTTGCAT
DroMoj_CAF1_left   CTTGTGTGGCTTCGAATGTACCTCGTCGAGCGAAAAGC-GAATTCATTGT-TGGATTTTG-TTGCTCTTGGTATTCGAGCCAATAAGTTCGGCAACCAGTTCGCATTTTATCTTTTGCAG
DroPer_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-AACTCC-GAAA-TGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAAATCGCATTTTATCTTTTGCAT
DroPse_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-AACTCC-GAAA-TGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAAATCGCATTTTATCTTTTGCAT
DroSec_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-AAGTCCCGTGT-CGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATTTTATCTTTTTTTG
DroSim_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-AAGTCCCGTGT-CGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATTTTATCTTTTTTTG
DroVir_CAF1_left   CTTGTGTGGCT-TGAATGTACCTGGTTGAGG----A-ACGAATTCAACGTTTGGATTTTGTTGCCTT-TGGTATTCGAGCCAATAAGTTCGGCCACCGGTTCACATTTTATCTTTTGCAT
DroWil_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-AAATTCAATGT-TGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATTTTATCTTTTGAAT
DroYak_CAF1_left   CTTGTGTGGCTTCGAATGTACCTAGTTGAGG----A-A-AAACCCCATGT-CGGATTTTGTTACCTC-TGGTATTCGAGCCAATAAGTTCGGCCACGAATTCGCATTTTATCTTTTGCAT
DroGri_CAF1_left   CTTGTGTGGCTTCGAATGTACCTGGCTA-----------AGGAAAGTTGG-ATTTCCT----------AGGTATTCGAGCCAATAAGTTCGGCAGCGGGTTCGCATTTTATCTTTTGCAT

DroAna_CAF1_left   TTTTTTTTATTAT-T-ATATTT-TC--AATTTTTCTTTTTTTTT---TCTTTTGTCTTAAAT--TGATATTTG--AATTACT-TGCAACAATT--TTTTGGCCAGT-GCAC
DroEre_CAF1_left   ATTTATTATTTTC---GATTTT-TTT-TTTTTTTGTTT-CTTTT---TTTTATTCATTTTTA-AATTGCCTGC--AGCGTAT-GTTTTTGGCCAGTGCACGGGGTC-A--C
DroMel_CAF1_left   TTTTATTATTTTC---GATTTT-TTG-GTTTTTTTTTT-TTTAA---TAATTTGTAAATCAC---CTGCAGCG--TATCATT-TTTTTTGGCCAGTGCACGGGGTC-ACCT
DroMoj_CAF1_left   TTTTTATTATTTT-T-GATTTT-TC--GATTTTTTTTTTTTTTT---TTTTTTTTTTTTATA--ATTTTGCACAAAATTTTT-GGCAACCGGT--CAGCTGC--AC-TTGC
DroPer_CAF1_left   TTTTTATTATTTT-TCGATTTT-TT--G-TTTTTTTTT--TCAGCTGTTTTTTTTGGATTTT---TGAACTAT--TTGCAGCATTTTTCGGCCAGTGCACGGGGTC----A
DroPse_CAF1_left   TTTTTATTATTTT-TCGATTTT-TT--G-TTTT-TTTT--TCAGCTGTTTTTTTTGGATTTT---TGAACTAT--TTGCAGCATTTTTCGGCCAGTGCACGGGGTC---AC
DroSec_CAF1_left   CATTTTTATTATTTTCGATTTT-TT----GGGTTTTTT--TTTTTAATAATTTTTAAATCAC---CTGCAGCG--TATCATTTTTTTTTGGCCAATGCACGGGGTCA----
DroSim_CAF1_left   CATTTTTATTATTTTCGATTTT-TT----GGTTTTTTT--TTAA---TAATTTCTAAATCAC---CTGCAGCG--TATCATT-TTTTTTGGCCAGTGCACGGGGTCACCTG
DroVir_CAF1_left   TTCTTTTTTAT-T---ATATTT-CGATTTTTATTTTTT--ATTT---TTCATTTTTTCATTTTTTTTTTTTTC--AATTTTT-TGCACAAAAT--TTTTGGCAAGT-CAAC
DroWil_CAF1_left   TTTTTTATTAT-T---ATTATT-ATAATTTTTTTTTTT--TTTT---TTTTATTATTATTTTTGAATTTTTAT--TTGCAAC-AACTGCAGAG--GTCATCAGTAA-ACAT
DroYak_CAF1_left   TTTTATTATTTTC---GATTTT-TCG-GTTTTATTTTT-TTTTT---CTTTTTTGTATTAAT---TTTTAAAT--AACCTGC-AGCGTATTTTTTTTGGCCAGTGC-ACGG
DroGri_CAF1_left   TTTTATTATTTTT-G-AT-TTTTAT--TTTGAGTTTTT-TTTTT---TTAA-TTTTTTGCAGCACTTTTTGTT--ATTTTTT-GGCAGCCAAC--GGGTCACCTGC-ACTT