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


DroAna_CAF1_left   GGGGTTGATCTT--CGACCCTTACTATCAGAATGTGATCA--A-AAGGGTT-CAA-AAG-GTAGTTTCAACCCCTGACTTCTGTTAAGTAA-GGCATTTGACAAGCT-CGGT-AA-TC-A
DroEre_CAF1_left   TGGTTCGTGTCCGTCTATGTGGTACGCCAT-CCCTGGCAA--G-TGTTTGA-TGA-GGG-GGTG-CTGAAATCTGGGCTTCATACCAACAT-GGAACTTTGCCACCG-GGCCGAC-TC-A
DroGri_CAF1_left   GC--TGCTACTTGGATAACAGATGGCGCTA-ACTTGCTTACAT-ATTAATA-TCA-TAG-ATGG-CGCTGCAGGGTACGCAATTTTAACCT-TCTCATTTGACAACA-GCCCAAC-ACGT
DroMel_CAF1_left   TGGTTCGTGTCTGTATAAATGGTGCGTCAT-ACCTGGCGA--A-GATAGGT-GAG-GGG-GGTG-CTGAAATCTATGCTTCATACCAAATA-GGAACTTTGCCACCG-GGGCGAC-AC-A
DroMoj_CAF1_left   AAGTATACGTGCAATAGATGGCGCTAAGTA-ATATTT-CG--AATTAGCAT-TCA-TAG-ATGG-CGCTGTGTGCAGTCTATTTTTAAATA-CATATTTTGACACCA-ACACAATGTA-T
DroPer_CAF1_left   TCCAGATATGTGCCTCGAGCTCGAGCTGAA-ACATCTGCA--A-GAATATC-CCA-CAG-GTAG-CGCGTTTGTGCACCCAGGCCCAAGAA-GCAATTCTGGCACGCGATTACATATC-A
DroPse_CAF1_left   TCCAGATATGTGCCTCGAGCTCGAGCTGAA-ACATCTGCA--A-GAATATC-CCA-CAG-GTAG-CGCGTTTGTGCACCCAGGCCCAAGAA-GCAATTCTGGCACGCGATTATATATC-A
DroSec_CAF1_left   TGGTTCGTGTCCGTATAAATGGTACGTCAT-CCCTGTG-C--A-TGATAGATGAG-GGG-GGTC-CGGAACCCTATGCCTTATAGCAAATG-GGAACTTTGCCACCG-AGGCAGA-AC-A
DroSim_CAF1_left   TGGTTCGTGTCCGTATAAATGGTTCGTCAT-CCCTGCGCA--T--GATAGA-TGAGGGG-GGTG-CGGAACCCTGTGCTTCATACCAAATG-GGAACTTTGCCACCG-GGGCAAA-AC-A
DroWil_CAF1_left   TCAAACTTGTCGGTTTTCGCTTTAATGAAA-CATGTTGCA--ACCGAAATG-TTG-TAAGCA-A-ACC-AAGACACTCATATAATCA-AATGAGTCATTTGACACGAGATCA-TCAAC-A
DroYak_CAF1_left   AGGTTCGCGTCCGAATATGTGGCGCGCCAT-CCCTGGCGA--G-TGTGGAA-GAG-GGG-AGGG-CTGAAATCTAGGCTTCATACCAACAT-GGAACTTTGCCACCG-GGGCGAC-AC-A
DroVir_CAF1_left   TTATTTTCTTACAGCAGATGGCGCT-TCAGGGCATTTCAC--A-TTTATTT-TCA-TAG-ATGG-CGGTGCAGACAGTCTATTTTTAACTA-CAATTTCTGGCAGTCTTTGG-CTATG-T

DroAna_CAF1_left   GCTGCGGTGTCCGAGCGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCACAGGTTCGAATCCTGTCCGCAGCGAGA--GTCTT-TTTTTAAT-TT---C-TTTATTTTTAC
DroEre_CAF1_left   GTTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCGCAGGTTCGAATCCTGTCCGCAGCGGA--TGATCT-TTTAATTT-TT---TTTTTTTTGGCAC
DroGri_CAF1_left   GCTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCACAGGTTCGAATCCTGTCCGCAGCGAAATTCG--A-TTTTTTAT-TTTTCAACTTGTAAATAT
DroMel_CAF1_left   GTTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCGCAGGTTCGAATCCTGTCCGCAGCGCA--GAACTT-TTTTTATT-TT--TTATTTATTGTGAA
DroMoj_CAF1_left   GCTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCACAGGTTCGAATCCTGTCCGCAGCGAA--GATGATATTTTTGTT-AA---A-ATAGTTTTTAT
DroPer_CAF1_left   GCTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCACAGGTTCGAATCCTGTCCGCAGCGGC--AGTTCC-CTGACGTT-CT---T-TTTTTGTCCAC
DroPse_CAF1_left   GCTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCACAGGTTCGAATCCTGTCCGCAGCGGC--AGTTCC-CTGACGTT-CT---T-TTTTTCTCCAC
DroSec_CAF1_left   GCTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCGCAGGTTCGAATCCTGTCCGCAGCGCA--GGTATC-TTTTTATT-TT---T-TTCTTTATCTT
DroSim_CAF1_left   GTTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCGCAGGTTCGAATCCTGTCCGCAGCGCA--GGAGTC-TTTTTTTT-TT---T--CTTTATTTTT
DroWil_CAF1_left   GCAGTTGTGGCCGAGTGGTTAAGGCGTCTGACTTGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCAGCTGCGAA--CGATTA-GAGTTTCT-TT---T-TTGTACTACTT
DroYak_CAF1_left   GTTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCGCAGGTTCGAATCCTGTCCGCAGCGGG--ATCGGA-TGATCTTC-TTTTTTTTTCTTTGGCAC
DroVir_CAF1_left   GCTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCACAGGTTCGAATCCTGTCCGCAGCGAGA--GTGAT-CTTTTTATTTT---C-CTTTTCCATAT

DroAna_CAF1_left   TTTTTTATTTTACT-TTATT--TT--TATTTGAA-TT-TTTCATC-ATATG----CAGTTCATATATCCTTTAAACCCAA-AGGCTTAC-A-ATTATATG
DroEre_CAF1_left   TTATTTTATTTGTT-GTGTA--TTTTGATGCTCG-TACTA-ATGA-CTGGA---TTTTATAAAATTCGT-----TACACA-TTTGATGA-T-TGGGTCTT
DroGri_CAF1_left   TATTTTGACTGCTT-TTTCTTAATATTAATAATA-TACAA-ATA----------AGTTTTTTCTGGTCTCC---AAAATG-ATTTGTATTG-AAAGGCAT
DroMel_CAF1_left   T----TTGCAGAGG-GTACT--AATAGCTGACCT-TAATA-TTTC-TTTGA---CATTTCATTGTTAAGCAT--TATACTTTC-TGTGATG-AAGATGAA
DroMoj_CAF1_left   TTTTTATTTTCCTT-GTTTC--AATGTTTACTCA-TT-TC-ACTT-TTTAT---CCACATATGTATATATTTG-TTATT--AAAAACAT-G-TTTTGTTT
DroPer_CAF1_left   TTTTCCTTTATTTT-TTAAT--AA--CATTTTCT-AC-TT-TTAT-TATAA---CTTTAAACGACCTCAATTA-AATCAT-TCTGTGGC-C-TTGAAACG
DroPse_CAF1_left   TTTTCCTTTATTTT-TTAAT--AA--CATTTTCT-TC-TT-TTAT-TATAA---CTTTAAGCGACCTCAATTA-AATCAT-TCTGTGGC-C-TTGAAACG
DroSec_CAF1_left   CG-GCACTTGTTTT-ATTTT--ATTTATTGTGCA-TT-TG-CTGC-ATTAG---CTGACCTTAATAATATTTG-TTTGAC-ATTTCTTT-G-TTAAGCAT
DroSim_CAF1_left   GGCACTTGATTTAT-TTTAT--TT--ATTGTGCA-TT-TG-CTGC-AGCGT-G-TACTAATAGCTGACCTTAA-TATTTG-TTTGACAT-T-TCTTTGTT
DroWil_CAF1_left   TTTTATATATTTCT-TCTTC--TT--TTTATATT-T-----TGTT-GAACAAAAATCATATCATAAACTT----ATTTAG-AACTTAAG-ACTTT-CTAA
DroYak_CAF1_left   TTATTTTATTTATT-GTGTA--TCGTTCTTAAGA-CAGGC-TTTC-ATAAT---ATTTGTTATACATTG-----GATGAT-TGGGTCTT-A-AGAAAGAT
DroVir_CAF1_left   GAAAA--ATATATTAAATAT--GT--TTATAGTTTTT-AT-CCAAATCAAA---GTTATTTCTAATTTAAAAG-CATTTG-ATTGTTGT-T-ATTTTGTG