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


DroEre_CAF1_left   TATCCTTATT-CCGTTTTCCGAC-TTTCAGATGGTTATTGGGC-GTATTGGGCGTCGAC-AAAT--GCAAGATGGCA-AAGTGGATCTGCAAGT-AACTCATAA-GTGGCGC-TCATTGT
DroGri_CAF1_left   ACATCTAAAT-AA-TTTGTGTAT-TTATTACC-GTTCATGATACGAATCAATCCAAA---GGATCTATAATT--GATTGAAATGTACATTTGTAAATGCATTTTTTTTCTGT-TTTCTGT
DroMel_CAF1_left   AAAAACAAAA-AA-AAACAAAAT-CTAAAACT-TATGTGTATCCTTATTCCTTCTCCG--ATTT--TCAGATGGTTA-TTGGGCGTCGTCGACGAGTGCAGGATAGATCCGT-TCAATGT
DroMoj_CAF1_left   CATGTGTATTTAT-TACCGTTTAGTCGCGAGG-A-CTTGGCCTGACTTCATTCCAAG---GGATCTGGAATAT-AAT-TAGTACAACATACATGTCGGACGCGT-AACGCGA-GCTCTGT
DroPer_CAF1_left   CCTTATTTCCGGT-TATCTTGAG-CTGGCGGG-CAGC-CCGTCATCATTTTTCTCCCG--GGGA--ATGGATCGGAT-CGGATCTGAAAAGAATGGATTGTTAAGGGGGCAT-TTCATGT
DroPse_CAF1_left   CCTTATTTCCGGT-AATCTTGAG-CTGACGGG-CAGC-CCGTCATCATTTTTCTCCCG--GGGA--ATGGATCGGAT-CGGATCTGAAAAGAATGGATTGTTAAGGGGGCAT-TTTATGT
DroSec_CAF1_left   ACAA-CAAAA-AA-ACCAAAAAT-CTAAAACC-TTTGTGTATTCTTATTCCTTCTCCAA-ATTT--TCAGATGGTTA-TTGGGCGTCGTCGACAACTGCAGGATGCATCCGC-TTAATGT
DroSim_CAF1_left   ACAA-CAAAA-AA-ACAAAAAAT-CTAAAACC-TTTGTGTATCCTTATTCCTTCTCCAA-ATTT--TCAGATGGTTA-TTGGGCGTCGTCGACAACTGCAGGATGCATCCGC-TTAATGT
DroVir_CAF1_left   AATATCTTGT-GT-ATTTATTAG-CGTTCAAC-GCAAAGGCATGACATCCAGCCGCA---GGATCTGCAAGAGATAA-GAGGAGCATGTACACGTCGCACACAT-TATGTGT-GCTCTGT
DroWil_CAF1_left   GTATGCATTT--C-TTTTATTTC-AAGCAATC-TCTGAAGGTCATCTTGCATCAAGTGG-A-TG-AGGA-TGGTTAT-CCGGTTGACTGGCTGGTTGGTCGTAAATAGGAACTACAATGT
DroYak_CAF1_left   TTAT-AAA-T-TT-AAATAAAAA-CAAAAACT-ACAAAAAAACAACAAAACAAAAAAA--AAAA--ACAAAACATCT-AAA-ACTTTTGTG-TATCCTTATTACTTTTCCG--AAATTGT
DroAna_CAF1_left   TTATAAATTT-AA-ATAAAACAA-AAAACTAC-AAAAAAAAAAAACAAAAAACAAAAAAAAAAT--CCAAAAATTAT-GTG-TATCCTTATTTT-TGGGGGGGGAGGGGCGT-CGAATGG

DroEre_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TG-CG-AATACATAAGTTCACAAACATTTTAACGACATGGTATAAGAAAGACGTTGTTC----AA-TCGCTTT
DroGri_CAF1_left   TGACATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---AT-AA-AATACATAAGGTCACAAGCATTTTAACGACATGGTATAAGAAAGAAAGAAAGA----AACACACAAA
DroMel_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TG-TG-AATACATAAGTTCACAAACATTTTAACGACATGGTATAAGAAAGACGTGGTTCAGTCAG-TCGGTTA
DroMoj_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---AG-TG-AATACATACGGTCACAGACATTTTAACGACATGGTATAAGAAAATTGCAATTC----GA-ATGCAAA
DroPer_CAF1_left   TGAAATTTCTGTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TCAAG-AGTACATAAGGTCACAAACATTTTAACGACATGGTATAAGAAAGATGCTTTCC----GT-CCACTCT
DroPse_CAF1_left   TGAAATTTCTGTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TCAAG-AGTACATAAGGTCACAAACATTTTAACGACATGGTATAAGAAAGATGCTTTCC----GT-CCACTCT
DroSec_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TG-CG-AATACATAAGTTCACAAACATTTTAACGACATGGTATAAGAAAGACGCGGTTC----AG-TCGGTTA
DroSim_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TG-CG-AATACATAAGTTCACAAACATTTTAACGACATGGTATAAGAAAGACGCGGTTC----AG-TCGGTTA
DroVir_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---AT-AA-AATACATAAGGTCACAGGCATTTTAACGACATGGTATAAGAAAATTGCAATGC----AA-AAACGAT
DroWil_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAATAGAG-AC-ACAACATAAAGTCACAAACATTTTAACGACATGGTATAAGAAAGTTGCAGTCA----AT-TCACATA
DroYak_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TG-CG-AATACATAAGTTCACAAACATTTTAACGACATGGTATAAGAAAGACGTGGGTC----AA-TCGATTA
DroAna_CAF1_left   TGAGATTTCTTTACCCAAACTCGTCAAAATGGCTGTGATATGAT---TG-CGAAATACATAAGGTCACAAGCCTTTTAACGACATGGTATAAGAAAGATGAACA-C----AA-TCGGTTA

DroEre_CAF1_left   -----TGAAATAT-GTTTTCTTAA-CCCGCTTTTTAAATTCGC-A-CG-AAACTC-ATCA-AAAT---GGC--TGTGATATGAGTAGATAATAGTCGACATT-TCA
DroGri_CAF1_left   -G--GAGAAGGAG-GAGGAAC-AG--GAGGAGGCGGCGACTGC-ACGA-ACCGGC-CCCG-GCGA---GGGACAATGATCACTGTGATGAAAGCAATTCGCACGAA
DroMel_CAF1_left   -----TGAAATAT-GTTTTTTGAT--CCGCTGCCGCGATTCGC-A-CG-AAACTC-ATCA-AAAT---GGC--TGTGATATGAGTAGATAATAGTCGACA----TT
DroMoj_CAF1_left   -----TGAA-GAT-GGAGATTGAG-GTGGA-TAATCCAGTGAC-A-CAAAACGGA-TGGG-ACAA---TGC--TGAAAGCAATTCACACGAAACTCATCAAAATGG
DroPer_CAF1_left   -----GTGCTCCA-TCCTGCCCTG--CCCCGATCGATGATGGATT-GC-TGGCCA-TTCC-ACAC---GAA--ACTCATCAAAATGGCTGTGATATGATTTG-ATA
DroPse_CAF1_left   -----GTGCTCCA-TCCTGCCCTG--CCCCGATCGATGATGGATT-GC-TGGCCA-TTCC-ACAC---GAA--ACTCATCAAAATGGCTGTGATATGATTTG-ATA
DroSec_CAF1_left   -----TGAAATAT-GTTTTTCGAT--CCGCTGACCAGATTCGC-A-CG-AAACTC-ATCA-AAAT---GGC--TGTGATATGAGTAGATAATAGTCGACATTTCAC
DroSim_CAF1_left   -----TGAAATAT-GTTTTTCGAT--CCGCTGCCGAGATTCGC-A-CG-AAACTC-ATCA-AAAT---GGC--TGTGATATGAGTAGATAATAGTCGACATTTCAC
DroVir_CAF1_left   -----AATC-GTC-CTTGCCAGCC-CATTCTGCCGACGAGGGC-A-ATGAATTTA-AGCA-ATTC---GCA--CGAAACTCA-TCAAAATGGCTGTGATATGACTT
DroWil_CAF1_left   -----TTCT-AAG-G-ATACCATC-CATTTCGAATACTGTTGC-A-GGAATACTC-GCACGAAAC---TCA--TCAAAATGGCTGTGATATGAGTTG-AATAAAAT
DroYak_CAF1_left   TGAAATATGTTTGAAATACATGAAATAAGTTGCCGAGATTCGC-A-CG-AAACTC-ATCA-AAAT---GGC--TGTGATATGAGTAGATAATAGGC--------GA
DroAna_CAF1_left   -----TGACATCC-TGCCGCCGCG--CCCCTTTCT-GACGGTT-T-TC-TGACGATTCCC-ACGAAACTCA--TCAAAATGGC--TGTGATATGAGTAGATA-ATG