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


DroAna_CAF1_left   CCACAATCCT-CCACAC----TAACATGGGCTTGGGAATCGGTTCGGTTGTGTGT-----TAAAAGTGCTTTATTTGTAACTTCATTTGAATTA-AAACCAACTAACCTGGGAGTC-CT-
DroEre_CAF1_left   ACGCGTGATT-AATTTG----GAAAGTGGTGTCTGCATTGTGTCCCAAGTGTTAA-----ATTAAGTGCTTGA-TCGTAACCCCATCCAAACTCGTTATTAACTAACCGATTGGTC-CTC
DroMel_CAF1_left   TTAATTTGGA-AGGAAA----GGTGTCTGCTGTGCGTCCCGGTCCCGAGTGTTAA-----AATATGTGCTTGA-TCGTAACTCCATCCAAACTCGATATTAACTAACCGATTGGTC-CTC
DroMoj_CAF1_left   ACC-GACACA-CACAC--------GTACAGAAACACACACAGAGACACACCTATA-----ATCATATCAGTTT-CGTTTACTCAAGTGCTTTGCATCATTAACAAACCTAACCGTT-CGT
DroPer_CAF1_left   GTGCCTCAAG-TCGTGGGTCCTCAGTGTGCTAAGTGCTTGATCGTATGTCGTCTA-----TTTTAACTCGCAA-ATCAAATCGCT-CC---ATCCAAACTAACTAACCGATTGGCCTCTC
DroPse_CAF1_left   GTGCCTCAAG-TCGTGGGTCCTCAGTGTGCTAAGTGATTGATCGTATGTCGTCTA-----TTTTAACTCGCAA-ATCAAATCGCT-CC---ATCCAAACTAACTAACCGATTGGCCTCTC
DroSec_CAF1_left   TGGCAACGCG-TGATTA----ATTTGGAAAGTGGTGTCCCGGTCCCGAGTGTTAA-----ATTATGTGCTTGA-TCGTAACTCCATCCAAACTCGATATTAACTAACCGATTGGTC-CTC
DroSim_CAF1_left   TGGCAACGCG-TGATTA----ATTTGGAAAGTGGTGTCCCGGTCCCGAGTGTTAA-----ATTATGTGCTTGA-TCGTAACTCCATCCAAACTCGATATTAACTAACCGATTGGTC-CTC
DroVir_CAF1_left   AATCAATTCC-CGCCTA----GTGCCCAAACG--TGCCTCTAAATCGAATCGAAT-----CGAATCGTATCAA-TCAATCAGCCAATCAATCAGCCAATGCCTCAAACTAACCGTC-GT-
DroWil_CAF1_left   CCATCG--CG-TGTGCT----TGCTAAAATCTGTTTTCTCTTA-CCAACTGCTAACTAACTCTTAACTCTCTA-ACTTAACTCTGGGTTAACAAAATAAAATCAAAAATT----GTGTGT
DroYak_CAF1_left   ACGCGTGATT-AATTTG----GAAAGTGGTGTCTGCGCTGTGTTCCAAGTGTTAA-----ATTAAGTGCTTGA-TCGTAACTCCATACAAACTCGTTATTAACTAACCGACTGGTC-CTC
DroGri_CAF1_left   TAACCCAAAAGTGCAAA----TCGTTTAGCGTATCTG-TCGCATGTCAAAT-CAA-----ATCAAACTTTTCT-GCAAATCATCA-TCAATCAA-TCAATGCCTGAAACTAAC-TA-TCG

DroAna_CAF1_left   --GTGGAAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTTTATGGTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTCG--GCTCATCACTCTATCGAT-G
DroEre_CAF1_left   --CTGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCTATCGAT-G
DroMel_CAF1_left   --CTGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCTATCGAT-G
DroMoj_CAF1_left   CGTATCGAGTGCTTGCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTA---ATAACAATAAATCCCTTGTCTTCTTATGGCTCGCATT-G-AGCTCTTCATTTCAAATCT-C
DroPer_CAF1_left   --CTGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCTG-TGCTCTTCATTCTATCGAT-G
DroPse_CAF1_left   --CTGGGAGTGTATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATCTG-TGCTCTTCATTCTATCGAT-G
DroSec_CAF1_left   --CTGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCTATCGAT-G
DroSim_CAF1_left   --CTGGGAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCTATCGAT-G
DroVir_CAF1_left   --CTCCAAATGCTTTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTCTGCTA---ATAACAATAAATCCCTTGTCTTCTTATGGCGCGCATTC--TGCTCTTCATTTATAATAA-T
DroWil_CAF1_left   --GGTGGAATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTAATAAAATTAACAATAAATCCCTTGTCTTCTTATGGCGTGTATTTAAAGCTCTTCA--TTTGTTGT-T
DroYak_CAF1_left   --CTGGGAGTGCATTTCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTA---ATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTTG-TGCTCTTCATTCTATCGAT-G
DroGri_CAF1_left   --GTTTAAATGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGTTA---ATAACAATAAATCCCTTGTCTCCTAACGGCGCGCATT-G-TGCTCTTCATTATTTCTTAAC

DroAna_CAF1_left   GATTAA---CCA-ATTAAACTGAACTATTTTTCACTAA-AAGTGTCACTC-CAAGCTTCATCATTAAA-AGAGGAAAGAAAAC-A-AAAT-AAAAA--AAAGGAG
DroEre_CAF1_left   GT-TAA---CCA-ATAAAACTAAACCCGGCATTGGAAA-CTCCTCAACTA-AATGCGTTCCGTCACAA-AGAAAAAGCATCCATC-GCGT-ATAAC--TATTTCA
DroMel_CAF1_left   GT-TAA---CCA-ATAAAACTAAACACGGCATTGGAAA-CTACCTAACTA-AACGTGTCACAATTCAT-CCTTGTCCCAGCTCGC-AAAA-AAAAA--AAAAATA
DroMoj_CAF1_left   GT-TAA---CGG-TGGTGCCACAACTAACTAAACTAAA-TAATACTAAAT-GTCGTGTTCATTCATAA-TCAATCCCACACACAT-ACAC-ACACA--ACACACA
DroPer_CAF1_left   GT-TAA---CCAAATTAAACGGAACTCGACATTCAACA-AA--AAACCAA-CAAAATACTTGTTTATT-AATTTACTAATTGTG--TCAT-GGCTTATCCCAATC
DroPse_CAF1_left   GT-TAA---CCAAATTAAACGGAACTCGACATTCAAAA-AAAAAAACCAA-CAAAATACTTGTTTATT-AATTTACTAATTGTG--TCAT-GGCTT--ATCCCAA
DroSec_CAF1_left   GT-TAA---CCA-ATAAAACTAAACACGGCATTGGAAA-CTCCTTAACTA-AACGTGTCACGATTCAT-CCTCGTCCTAGCTCGC-AAAT-AAATA--AACATCC
DroSim_CAF1_left   GT-TAA---CCA-ATAAAACTAAACACGGCATTGGAAA-CTCCTTAACTA-AACGTGTCACGATTCAT-CCTCGTCCCAGCTCAC-AAAT-AAATA--AACATCC
DroVir_CAF1_left   TT-CGG---TGG--TGCCACAAAACAATAAATAATAAT-AACAATAACAG-CAACAATATATAACAAT-AAAATACATTTGTTCA-ACTTGTACTA--AACGTGT
DroWil_CAF1_left   TG-TTTGTTTGTTTTTTTTCTCCACAGTGCGCATA-----TTAACAAATC-GAAGTACTAAAAAAAATGTGTCTACTATTATATTTACAT-TCCAT--ATTCATC
DroYak_CAF1_left   GT-TAA---CCA-GTAAAACTAAACACGGCATTGGAAA-CTCCTCACAAA-GAAAGAACATCCATCGC-GATTAACTATTTCACC-CAAA-AAAGA--AATCCCC
DroGri_CAF1_left   GG-TGG---TGCCA-CTAAC--AACAATGATAACAACAGCTCTACAACATTGGAAATACTCT-TGTAC-TAAACTCGTGTCTCGG-TTCA-TTCAA--CATCCCA