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


DroAna_CAF1_left   GAAGGTCTCGAACCCAGAACC--------CAG------AATCCAGA-TCGCGTCGCG-ATGGATG-TTC-C----C-CTC-CGATAAAAAAAAATGA---AAATATCCTGGAAACA----
DroEre_CAF1_left   GAGTCGAGCAGAGTCGGAGTCGG--AGTCGGAGT-C-GGAGTCGGA-GCAGAGCAGT-CCGAC-----G-A----G-TAG-GGCAT-CATTCCC-GCG--ACGCAGTGAAGGATCG----
DroGri_CAF1_left   CCCACCCACACACACACAG--AG-----AGAGAC-C-AACTGACTG-AGCAG-CTGCACCTTGAG-CAAACAGCTA-AAC-TTAAT-CGCAGCA-TCAGCATCAGCATCAGCATCC----
DroMel_CAF1_left   ATCACC-ACTGACCAGTAGATTC-----CAGTCG-A-GCCATCGGA-GCAAAGCAAT-CCGATTG-GGC-A----A-TAG-GAACC-CATTGCC-GCG--ACGCACTGAAGGATCG----
DroMoj_CAF1_left   AAGCAGCTGCTTTATTTAGC-CA-----CAAGCC-G-CAGCATCTGCATCTG-CATCTCCAACAA-CAA-C----A-ACA-GTAAC-AACAGCA-ACAACAACAACAGCAACTGCA----
DroPer_CAF1_left   AGCCAG-CCAGCCAGCCAGCCAG-----CCAGCC-A-GCCAGACAG-CCAGA-CAGC-ACCAAAGCCAC-T----C-GCA-GCCGC-CAACTCC-GCT--AACCATTCGCGACGCG----
DroPse_CAF1_left   CTATGT-CAACCCATCAATACAG-----CCAGCC-A-GCCAGCCAG-CCAGA-CAGC-ACCAAAGCCAC-T----C-GCA-GCCGC-CAACTCC-GCT--AACCATTCGCGACGCG----
DroSec_CAF1_left   ACAACC-ACTGACCAGTAGATTC-----CCGTCG-A-GCCATCGGA-GCAAAGCAAT-CCGATTG-GGC-C----A-TAG-GGAAA-CATTGCC-GCG--ACGCACTGAAGGATCG----
DroSim_CAF1_left   ACAACC-GCTGACCAGTAGATTC-----CAGTCG-A-GCCATCGGA-GCAAAGCAAT-CCGATTG-GGC-C----A-TAG-GGAAC-CATTGCC-GCG--ACGCACTGAAGGATCG----
DroVir_CAF1_left   GCCAA--CCAGCCAACCAGCCACTCAGCCAACAG-A-GAAGCTGCC-TCTTAGCCAA-ATGCCAG-CCG-C----A-TCA-ACATT-AATAGCA-GCC--GCA-TCAACAGCCGCA----
DroWil_CAF1_left   CAGTCAGTCAGTCAGTCAGTCAG-----TCAGTC-A-GTTAGTCAG-TTTAACCAAT-CAACTAT-AAC-C----AATCTACAAAT-CTCATTG-GAG--ATTCTCTCGAGCGGCTCCAT
DroYak_CAF1_left   AATCAC-CAACTCT--GAACCAT-----AGACTCTACGCGAACCGT-GAGAACCGAG-CACTCCA-GAG-A----C-TAA-GGAAC-CTTTTTC-GGG--GCTCAGTGAACGATCG----

DroAna_CAF1_left   --CACTC--G-AC-AACTGGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACCGATCGCACTAACCGCA
DroEre_CAF1_left   --GCTGTACGAAG-GAGCAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAAACCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAACCGCA
DroGri_CAF1_left   --GAAGCA-GCAT-CACAAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACCAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAACCGCA
DroMel_CAF1_left   --TCTGTACGAAG-GAGCAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAACCGCA
DroMoj_CAF1_left   --TCAGCA-TCAG-CATCAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCAATTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAACCGCA
DroPer_CAF1_left   --TTTCCAGGATC-CAGCAGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATCGCACTAACCGCA
DroPse_CAF1_left   --TTTCCAGGATC-CAGCAGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATCGCACTAACCGCA
DroSec_CAF1_left   --TCTGTACGATG-GAGCAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATCGCACTAACCGCA
DroSim_CAF1_left   --TCTGTACGATG-GAGCAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATCGCACTAACCGCA
DroVir_CAF1_left   --TCAGCA-TCCG-CATCAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAACCGCA
DroWil_CAF1_left   CGAACAC-AGCCGCTGGCAGCGCCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAACTGCA
DroYak_CAF1_left   --CATGTACGAAG-GAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

DroAna_CAF1_left   TGCCTCC-AAAAAAA--AAAACAAAACAGAAAACTAAATAAAAG-CCTTAAAATAAATC-CTAAACAGACACTA-AATAAATC----CCTAA-AATA-TTCA---TA-----ATTTTTTT
DroEre_CAF1_left   TGACCA--AA-AACC--A-CGCGCGCGCTTCTCCCACACGGATG-TG-CCA------TGAGT-TTCACTCACAT-GCCCATGC----CTCTA-ATTGAACTC---CCTTTGCCCCATTCC
DroGri_CAF1_left   TGCCAC--GCCTACAAAACAAATAAT-TACCCGCGCGCCCGCGT-TT-CGTGTAA-ACTATT-ATCTATCCCTAAGTTAG-TA----TCCGC-CTGA-ATTG---TG-----CACTGATT
DroMel_CAF1_left   TGACCA--AC-AACC--AACGCGCGCGCTTCACCCAAACGGATG-TG-CCTCCCT-TCGAGT-TCCACTCACAT-GATCATGC----CTCTA-ATTTAAACG---CC-----CATTCAAC
DroMoj_CAF1_left   TGCCAC--GCCTTAAACAAAAATATATAAAAAAAAAAAAAAAAC-TA-TTTACGC-GCGCGC-GTCTTTGTGTAAGCCTT-AG----ATTTAAGAAC-TGTG---AG-----AAAGCGAA
DroPer_CAF1_left   TGCCAAGACCAAGCC--AAAGCCAAAGCCAAAGACAAA-------GC-CCA--AG-CCATC--TCCAGATCCAG-GCGCGCGCGCTTTATCA-ACGGATTTGTAGCC---CTAAGATTCA
DroPse_CAF1_left   TGCCAAGACCAAGCC--AAAGCCAAAGACAAAGCCAAAGACAAA-GC-CCA--AG-CCATC--TCCAGATCCAG-GCGCGCGCGCTTTATCA-ACGGATTTGTAGCC---C------TAA
DroSec_CAF1_left   TGACCA--ACAAACC--AACGCGCGCGCTTCACCCACACGGATG-TG-CCTCCCT-CCGAGT-TCCACTCACAT-GCCCATGC----CTCTA-ATTC-AACG---CC-----CATTCAAC
DroSim_CAF1_left   TGACCA--ACAAACC--AACGCGCGCGCTTCACCCACACGGATG-TG-CCTCCCT-CCGAGT-TCCACTCACAT-GCCCATGC----CTCTA-ATTC-AACG---CC-----CATTCAAC
DroVir_CAF1_left   TGCCAC--GCCTTTC--AAAAATGTTTATGTTCGCACACGCGCG-CG-CCCTCCT-CGTCTC-CCCGT-GTCAATGTGTT-AC---GCTTTA-AATT-ATGA---TC-----TTGGCATA
DroWil_CAF1_left   TGTCCAC-ACCATCC--TGATCATCATCATCGTGAACGTGAAATGTA-ACGGCGC-GCGCGT-TATTTTCAGCT-AGTATTTG----ATTTA-ATCC-TTG----TC-----ACATTTCA
DroYak_CAF1_left   -NNNNN--NNNNNNN--NNN-NNNNNNNNNNNNNNNNNNNNNNN-NN-NNNNNNN-NNNNNN-NNNNNNNNNNN-NNNNNNNN----NNNNN-NNNNNNNNN---NN-----NNNNNNNN

DroAna_CAF1_left   AATTCAATACTT-ATACG
DroEre_CAF1_left   GGTTACTAATCA-CCGGT
DroGri_CAF1_left   AGTCGTATCCAT-ATATC
DroMel_CAF1_left   TTTCAATTCCGG-TTACT
DroMoj_CAF1_left   AGAGAGAGTGTG-AGAGA
DroPer_CAF1_left   ATAATTAACCGA-AAACC
DroPse_CAF1_left   GATTCAATAATT-AACCG
DroSec_CAF1_left   TTCCAATTCCGGTTACTA
DroSim_CAF1_left   TTCCAATTCCGCTTACTA
DroVir_CAF1_left   CTTCTTAGGCTAAGAGTT
DroWil_CAF1_left   TTTCTTATTCTA-ATTGA
DroYak_CAF1_left   NNNNNNNNNNNN-NNNNN