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


DroAna_CAF1_left   CCA-------AAATCCTCAATCACAAA--TGGTGCAACATGCAATTCGTG---GAT-----AATGGTAAGGATTAA---ATGGAAATCTA-TTCC--GATTGGA-T-GTGAAAGTGCCA-
DroEre_CAF1_left   TCA-------CAAATG-GTGCAACATG--CAGTTTGCAGACAATGGTAAG---TAC-----TTTGTACTGCACGGTTC-GCTTAAATCTG-T-GT--ACAAGTC-A-GTGAATAGTTTA-
DroGri_CAF1_left   GAGAGATAAA-AAAGC-GAAAGATTCG--TTCGTCGATTGGTTCTTATTC---TTG-----TGTT-AAT-----CATT-ATCAGT-GTTA-A--ATGTGGAAAA-A-CCAATCCAATCC-
DroMel_CAF1_left   CCCTGGATCACAAATG-GTGCAACATG--CAGTTTGCAGACAATGGTATG---TGT-----TATTTAG------TGGT-GTTTCT-TGTG-T-GT--TTAAATC-A-GTGAATAGTTTA-
DroMoj_CAF1_left   TCCTCGATCACAAATG-GTGCAACATG--CAGTTCGCCGAGCATGGTAAG---AAC-----TCAG-GCT-----CCAT-CAATAT-AGCT-A-GAGAGTGCCCG-A-TTC--ATGATGT-
DroPer_CAF1_left   CG----ATCACAAATG-GTCCAACATG--CAGTTCGCCGAGCATGGTAAG---GGT-----GTTAATTTG----ATGCGGGCGCC-TTCG-A-GT--GTTTATCGA-GTGATTTATCTA-
DroPse_CAF1_left   CG----ATCACAAATG-GTCCAACATG--CAGTTCGCCGAGCATGGTAAG---GGT-----GTTAATTTG----ATGTGGGCGCC-TTCG-A-GT--GTTTATCGA-GTGATTTATCTA-
DroSec_CAF1_left   CCCTGGATCACAAATG-GTGCAACATG--CAGTTTGCAGACAATGGTATG---TTT-----TATTTAG------TGGT-GACTTT-AGTG-T-GT--TTAAATC-A-GTGAACAGTTTA-
DroVir_CAF1_left   CA----------AATG-GTGCAACATG--CAGTTTGCTGAGCATGGTAAG---AAACGTCGGCCACCAGTG---CCGT-GTCAGT-TGTGCT-TT--TCCGTGC-TGAACTCCTCCCGC-
DroYak_CAF1_left   TCA-------CAAATG-GTGCAACATG--CAGTTTGCTGACAATGGTACG---TAC-----TTTGTAGTGCACGATTC-GATTAAATCTG-T-GT--ATAAATC-A-GTGAAAAGTTTT-
DroWil_CAF1_left   AATGGTGTAATATG------CAGTTTGCCGAGCACGGTGAGCAAATACCTATTAAA-----TACTTATCC-ATAAGGT-GACAAA-AAAG-T-GA--CTATACA-A-AGTGATACGAGTT

DroAna_CAF1_left   GAAGTCCACT-TGGTAGCTCAGGTACTTAGTGACTCTCAA-----TGC---AT-TTGACA-TTTTGGGAGCCACTTTGTGCCTGGGCCATCAGTGC---GACTATATCTTCTATTAAAAA
DroEre_CAF1_left   AGTGTCCACT-CGGTGGCTCAGGTACTTAGTGACTCTCAA-----TGC---TT-TTGACA-TTTTGGGGGTCACTCTGTGCCTGTGCTGCCAGTGG---GACGCAATCAACAAAATAAAG
DroGri_CAF1_left   GCTGCACACG-TTGCTGCTCAGGTACTTAGTGACTCTCAATTCAACATTGTAT-TGCACGCCTTTGAGGGTCGCTCTGTGCCTGTGTTGCACGTGT---TGCATTCACACCATCCGAGTG
DroMel_CAF1_left   AAAGTCCACT-CGATGGCTCAGGTACTTAGTGACTCTCAA-----TGC---TT-TTGACA-TTTTGGGGGTCACTCTGTGCCTGTGCTGCCAGTGG---GACATAATCTACAAATAAAGT
DroMoj_CAF1_left   CCAGCACACG-CTGCAGCTCAGGTACTTAGTGACTCTCAATCACATATTGCTT-TGCAT-ACTTTGAGGGTCGCTCTGTGCCTGTGCCGCCCGTGT---TGCACACAGCCACACAATTGT
DroPer_CAF1_left   CAAGCACACTTTGCCGGCTCAGGTACTTAGTGACTCTCAA-----TGC---TT-TCGACA-TCTTGAGAGTCTCTCTGTGCCTGCACTGGCGGTGG---TGCAACTGCAACGATTAAGGG
DroPse_CAF1_left   CAAGCACACTTTGCCGGCTCAGGTACTTAGTGACTCTCAA-----TGC---TT-TCGACA-TCTTGAGAGTCTCTCTGTGCCTGCACTGGCGGTGG---TGCAACTGCAACGATTAAGGG
DroSec_CAF1_left   AAATTCCACT-CGATGGCTCAGGTACTTAGTGACTCTCAA-----TGC---CT-TTGACA-TTTTGGGGGTCACTCTGTGCCTGTGCTGCCAGTGG---GACATAATCTACAAATAAAGG
DroVir_CAF1_left   CCTGCACACC-CCGCTGCTCAGGTACTTAGTGACTCTCAATCATCTATTGCTT-TGCATA-CCTTGAGGGTCGCTCTGTGCCTGTGCCGCCTGTGC---TGCACAACCAACGACGAGATG
DroYak_CAF1_left   AAAGTCCACT-CGGTGGCTCAGGTACTTAGTGACTCTCAA-----TGC---TT-TTGACA-TTTTGGGGGTCACTCTGTGCCTGTGCTGCCAGTAG---GACATAATCCACAAATA----
DroWil_CAF1_left   ATCTCTGCCT-AAACAGCTCAGGTACTTAGTGACTCTCAA-----AGA---ATATATATAGACTTGAGAGACGCTCTGTACCTAGACTGTTGTGTCTGCGGA-ATGTCAACATCATGTGT

DroAna_CAF1_left   AATTGTT-----TAAAATA--TATGGTATATAGTGTTCTATA-GCTGCTTAACCGATGCTTTGGCGCTTTAGCTGTATGATAGATTTAA-------------ATACT-TCATAAAG
DroEre_CAF1_left   TGATAAG-----TACAAGT-GAATTGCATTGGAATAAGT-GA-CTTAGAGTGCAGCTGCCTTGCCATTGCTTTGGCGCTTTAGCTGTAT-------------GATAG-ATTTAAAC
DroGri_CAF1_left   ATTTGT------GTCCTTT-GAGTGTCGATTTGTGTTAC-AT-CTATACGGTTATTTAAAGTGCTTCTTC-TTGGTGCCACATTGCCGT--------------CGCT-T--T-GGC
DroMel_CAF1_left   GATAATCAGTGATATCAGT-GAAATACATTGCAATGAGT-GC-CTTAGAGTGAAGCTGACTTGCCATTGCTTTGGCGCTTTAGCTGTAT-------------GA------TAGATT
DroMoj_CAF1_left   GAATTC------GAGTTCG-AACTCCCCGGACTAGAGAA-TA-CAAGTGCAAGTGTCTTGTAATGTAAAC-GTGTTTTTAAATATTCGC-------------CCCAT-TGCCGTTG
DroPer_CAF1_left   TGTTCCT-----AATAAGT-GTTATATTTAGAGTGTTATATC-GAAAGTGTTTAAAAGTACGACAATCTAATCTGTGCTTAAGCCCT-G-------------CTCTG-CTTCTGCT
DroPse_CAF1_left   TGTTCCT-----AATAAGT-GTTATAATAAAAGTGTTTTATC-GAAAGTGTTTAAAAGTACAACAATCTAATCTGTGCTTAAGCCCT-G-------------CTCTG-CTTCTGCT
DroSec_CAF1_left   GATAAG------TACCAGT-GAATAACATTGAAATGAGT-GC-CTCAGAGTGTAGCTGACTTGCCATTGCTTTGGCGCTTTAGCTGTAT-------------GATAGATTTAAACT
DroVir_CAF1_left   CATACGT-----GACCCTGACCGTGACCGGGAGTGAAGT-GT-AATAGCCAGGATTAGATGA-ACGCCGCACTGCCGTTGCTTTGGCGC-------------TTTAG-CTGTATGA
DroYak_CAF1_left   ---------------AAGT-GATTTACATTGGAATAAGT-GAATTGAGAGTGTAGCTGCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTATACTACTT-CATAAAGC
DroWil_CAF1_left   GTGTGTG-----TGTGTGA-TATATAGTGACATATTATT-AT-AGTAATGGATAATGGTCTTGCCTATGCTTTGGCGCTTTAGCTGT-A-------------TGATA-GATTTGAC