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


DroAna_CAF1_left   CCAGCGG-CAAGATCACCGACTACATCAAGTTCGATTCCGGTAAGAATTCAATCTGATC--TGT---ACTTGTATTGGCTGGTTCGAAGACCACAAAACGATTA----CTT-AAGTTGCG
DroEre_CAF1_left   CCTCTGG-CAAGATCACCGACTACATCAAGTTCGATTCCGGTAAGGATCCCCAC-CGTTG-ATC---GCTTTCATTGGCTGGTTCGAAGACCACAAAACGCTCA----TCA-AAGTTGCG
DroGri_CAF1_left   CC---GG-AAAGATCACCGACTACATCAAGTTCGATTCGGGTAGGTGCTAAAGAGACTTT-ATG---AATATTCTTGGCTGGTTCGAAGACCACAAAACGCATTCAAATTC-AAGTTGCG
DroMel_CAF1_left   -----GG-CAAGATCACCGACTACATTAAGTTCGATTCTGGTAAGCATCCGCTATCGTAGATCATC-GTGTTCATTGGCTGGTTCGAAGACCACAAAACGCTCC-T--CGA-AAGTTGCG
DroMoj_CAF1_left   --------CAAGATCACCGACTACATCAAGTTCGATTCGGGTATGTTCTGGTCATGAAATGTTACTTCTTTGTCTTGGCTGGTTCGAAGACCACAAAACGCTTT-C--CAACAAGTTGCG
DroPer_CAF1_left   ------G-CAAGATCACCGACTACATCAAGTTCGATTCCGGTAAGCACCCTTTGATGGAGCAGAA--ATCCTCCCTGGCTGGTTCGAAGACCACAAAGCGCTAA-AATTCC-AAGTTGCG
DroPse_CAF1_left   ------G-CAAGATCACCGACTACATCAAGTTCGATTCCGGTAAGCACCCTTTGATGGAGCAGAA--ATCCTCCCTGGCTGGTTCGAAGACCACAAAGCGCTAA-AATTCC-AAGTTGCG
DroSec_CAF1_left   -----GG-CAAGATCACCGACTACATCAAGTTCGATTCCGGTAAGCATCCCCCATCGTAGATCATC-GTGTTCATTGGCTGGTTCGAAGACCACAAAACGCTCC-T--CGA-AAGTTGCG
DroSim_CAF1_left   -----GG-CAAGATCACCGACTACATCAAGTTCGATTCCGGTAAGCATCCCCCATCGTAGATCATC-GTGTTCATTGGCTGGTTCGAAGACCACAAAACGCTCC-T--CGA-AAGTTGCG
DroWil_CAF1_left   -----CTACATCAAGTTCGATTCGGGTAAATATGATTCAAGATTTC-CCTAAATTTATTGATTGGC-TGGTTCGAAGACCACAAAATGTATGGAGAAGCAATTC-T--CTC-AAGTTGCG
DroYak_CAF1_left   CCTCTGG-CAAGATCACCGACTACATCAAGTTCGATTCCGGTAAGGATCCCATCGTTGA--TCG---CCTTTCATTGGCTGGTTCGAAGACCACAAAACGCTCA----TCA-AAGTTGCG
DroVir_CAF1_left   CC---GG-CAAGATCACCGACTACATCAAGTTCGATTCGGGTAGGTGCAT-C-AATTAAACAAAC--TTTAAACTTGGCTGGTTCGAAGACCACAAAACGCTTT-C-TATT-AAGTTGCG

DroAna_CAF1_left   TGGTTCAAAAACA-CAAGCCAAGAGCAATTTTTGTCACGACGGTCTCTGATT-CG-GCACACC-A-CAGTCGTCTCAGTAACTTTTACGTGCAATTACAATCTTAACTACTATTTAGCTA
DroEre_CAF1_left   TGGTTCAAAAACAATAAGCCAAAAGCAATTTTTGTCACGACGGTCTCTGATT-CG-GCATTCC-A-CAGTCGTTTCAGTAACTTTTACGTGCAATGACAGTCGCACAATCTGAGC---TA
DroGri_CAF1_left   TGGTTCAAAAACA--AAGCCCAAAGCAATTTTTGATACGACGGTCTCTGATT-TGTGCATTTT-ATCAGCCATTTCAGTAACTTTTACGTGCAATTACATTTGAAGCAAAACAAAA--AT
DroMel_CAF1_left   TGGTTCAAAAACAATAAGCCAAAAGCAATTTTTGTCACGACGGTCTCTGATG-CG-GCATTCC-A-AAGTCGCTTCAGTAACTTTTACGTGCAATGACAGTCGCCCAATATTATTAACCA
DroMoj_CAF1_left   TGGTTCAAATACA--AAGCCAAAAGCAATTTTTGATACGACGGTCTCTGATCTTGAGCATTCT-C-CAGCCATTTCAGTAACTTTTACGTGCAATTACAAAGTTCTTAAAACTAT---T-
DroPer_CAF1_left   TGGTTCAAATACT--AAGCCAAAAGCAATTTTTGTCACGACGGTCTCTGATC-TGAGCATTCC-A-CAGCCGTTTCAGTAACTT-TACGTGCAATTACAACTCAACTCGCGTATTACGTA
DroPse_CAF1_left   TGGTTCAAATACT--AAGCCAAAAGCAATTTTTGTCACGACGGTCTCTGATC-TGAGCATTCC-A-CAGCCGTTTCAGTAACTT-TACGTGCAATTACAACTCAACACACGCATTACGTA
DroSec_CAF1_left   TGGTTCAAAAACAATAAGCCAAAAGCAATTTTTGTCACGACGGTCTCTGATG-CG-GCATTCC-A-AAGTCGCTTCAGTAACTTTTACGTGCAATGACAGTCGCCCAATATTATTAACCA
DroSim_CAF1_left   TGGTTCAAAAACAATAAGCCAAAAGCAATTTTTGTCACGACGGTCTCTGATG-CG-GCATTCC-A-AAGTCGCTTCAGTAACTTTTACGTGCAATGACAGTCGCCCAATAATATTAACCA
DroWil_CAF1_left   TGGTTCAAATACA--AAGCCAAAAGCAATTTTTGTTACGACGGTCACTGATTTTG-GTAAACT-C-TAGCCATTTCAGTAACTTTTACGTGCAATTACATCTGAAAAATATTTTTATCTA
DroYak_CAF1_left   TGGTTCAAAAACAATAAGCCAAAAGCAATTTTTGTCACGACGGTCTCTGATT-CG-GCACTCC-A-CAGTCGTTCCAGTAACTT-TACGTGCAATTACAGTCGCTCAATCTACGT---CA
DroVir_CAF1_left   TGGTTCAAATACG--AAGCCAATAGCAATTTTTGATACGACGGTCTCTGATT-TGTGCATTTAGC-CAGCAATTTCAGTAACTTTAACGTGCAATTACATTTACAATATTTAAGGGAATA

DroAna_CAF1_left   TATTTT-TGGTGA-AAACTAATTGATT-----TTT--GTTGATCGG--CAGGCAACCTGTGCATGATCACCGGAGGCAGGAATTTGGGACGT----------G
DroEre_CAF1_left   AGTATT-GCGATTTCA-ACTAATTGGA-----TGC--TTCTCGATTCACAGGCAATCTCTGCATGATCACCGGAGGCAGGAATTTGGGACGTG---------T
DroGri_CAF1_left   AGATTG-ACCATAATA-ATAAACATTA-----TA----TTTAAATTCGCAGGCAATCTGTGCATGATCACCGGAGGCAGGAATTTGGGACGTG--------TT
DroMel_CAF1_left   AGTCGT-ATGATTCCAACTAACTGGTA-----TATTTCTCCGTCTCCACAGGCAACCTCTGCATGATCACCGGAGGCAGGAATTTGGG---------------
DroMoj_CAF1_left   --TTTT-ATCA-TCGATAGACAATAAT-----ATA--CATCTTCTTCGCAGGCAACCTTTGCATGATCACTGGAGGTAGGAATTTGGGACGTGTCGGCTCTGT
DroPer_CAF1_left   TTTCGT-TGAAAACTAATCGAGGTATT-----TTC--AATTCCATCCATAGGCAATCTGTGCATGATCACCGGAGGCAGGAATTTGGGA--------------
DroPse_CAF1_left   TTTCGT-TGAAAACTAATCGAGGTATT-----TTC--AATTCCATCCATAGGCAATCTGTGCATGATCACCGGAGGCAGGAATTTGGGA--------------
DroSec_CAF1_left   AGTCGT-ATGATTCCACTA-ACTGGTA-----TGCTTCTCCGTCTCCACAGGCAACCTCTGCATGATCACCGGAGGCAGGAATTTGGGA--------------
DroSim_CAF1_left   AGTCGT-ATGATTCCAACTAACTGGTA-----TGCTTCTCCGTCTCCACAGGCAACCTCTGCATGATCACCGGAGGCAGGAATTTGGG---------------
DroWil_CAF1_left   GTTTTA-ACTGACTAA-TGTGTAATTT-----ATCA-ATGTATCGTTGTAGGCAACCTCTGCATGATCACTGGAGGCAGGAATTTGGGAC-------------
DroYak_CAF1_left   ATTAGT-TTGATCCTA-ACTAACTGGA-----TGC--TTTTTGATTCACAGGCAACCTCTGCATGATCACCGGAGGCAGGAATTTGGGACGTG---------T
DroVir_CAF1_left   TCAAGCTATG-AGTGTAACAACAAAAAAATGTCTT--ATTTCGATTCACAGGCAACCTCTGCATGATCACTGGAGGCAGGAATT------------------T