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


DroAna_CAF1_left   TATATTTA-AAAAATT--CAGTGA----GTTTTAGTTTTTC-TGT-TTTATTCAAAGCAG-TTATAAAGTATTT-ATAAGATGGT-ATCTT-ATGA-ATT-TAGC--AAAATATTT---C
DroEre_CAF1_left   ATTTA--TGATTAGTT--ATTTCA----TTAACAGT-TTTATTGA-A-AATATATAATATAATACATT--T-TTTCCGTTTTCTACG-GATTCACTAAACATATTTTTTGTCGTTG----
DroGri_CAF1_left   TTTAATA-TAAGTTGG--AAATGA----TTTATTGA-CTGAGTAA-T-TCATGATTTTTTTTTATATA--A-ATAACAA-TGTTGCG-TTA-AGAC-AAAAAGT-ACGATTTGTAG---T
DroMel_CAF1_left   ACGTTGTGGTAAATGT--GTAGAA----AATATATA-TATATGTT-A-TATATACTTATGTTAAATAT--C-CGTTCTTTATGACTG-ATA-AACT-ATACCTT-AATTTGTTATG---A
DroMoj_CAF1_left   ATTAAAGT-AAAGTTA--ACA-TT----GTAACTAAATT-ATATA-T-ATAGTTATACT-GTAACTAT--A-ATGAAAAGTGAAGCA---AATCTAAAGTTGTGTTCTTGGAAATA----
DroSim_CAF1_left   ACTGTTAA-ATATCCT--CTTTTT----CCACCTGATTAGA-ATC-TTTGCACTATACCT-TAATTCA--AAGA-CTCTAAAAAATGATAT-TGTC-TTT-GCTTA-ATTTTATAT---T
DroWil_CAF1_left   CGAGACT-CCATATGGAATTATAATTTGAAATGTGA-ATGAAGTAAA-AATTGTTAGCATTTTCTTAT--T-CAAC---AAAGTTT--TTA-AAAT-AGAC----TCAATATGGTGTCCT
DroYak_CAF1_left   AAATTTAGTAACATTT--TTATTT----TTTAAGT-TATTTTATT-A-ATGTTTTTATTGAAGAATAT--T-ACTGTAATGAATTTT---TTTTTTGATTGGTACGAATTTTTTAA----
DroVir_CAF1_left   TAAAAAAA-AAAAAAA--AAAATT----GTTTCAAA-T-TAAATC-A-ATNNNNNNNNNNNNNNNNNN--N-NNNNNNNNNNNNNNN-NNN-NNNN-NNNNNNNNN-NNNNNNNNN---N

DroAna_CAF1_left   C-CTTGTAATAAAATCGA--TTTTTGACACCT-CA-GTAACCATATCCCATATGGTCTAGTGGCTAGGATATCTGGCTTTCACCCAGAAGGCCCGGGTTCGATT-CCCGGTATGGGAAGT
DroEre_CAF1_left   --TTGGTATCTGAAATATGATTTT--GTGTGATAC-CCATTCATATCCCATATTGTCTAGTGGTTAGGATACCCGGCTCTCACCCGGGAGGCCCGGGTTCAATT-CCCGGTATGGGAAAT
DroGri_CAF1_left   GAATAT--AACATAACTGA-TTTC-TGGTGGACAT-TACTCTGTATCCCATATGGTCTAGTGGCTAGGATATCTGGCTTTCACCCAGAAGGCCCGGGTTCGATT-CCCGGTATGGGAAGT
DroMel_CAF1_left   ATGGTA--TCCAAAAATTT-ATTT-TATGTGGTCC-CGCGATATATCCCATATTGTCTAGTGGTTAGGCTACCCGGCTCTCACCCGGGAGGCCCAGGTTCAGTTCCCTGTATAGGAAATG
DroMoj_CAF1_left   --TAAATATAACAAAACCGGCAAT--GGCTACTCTTCTAGAAGTGTCCCATATGGTCTAGTGGCTAGGATATCTGGCTTTCACCCAGAAGGCCCGGGTTCGATT-CCCGGTATGGGAAGT
DroSim_CAF1_left   A-ATGGTATCAAAAATTT--CATTTTGTGCGATTA-GATAACATATCCCATATTGTCTAGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNN
DroWil_CAF1_left   GATAAC--A-AAAA--TAA-TTTT-TGGCAACGGC-AAGAACATATCCCATATGGTCTAGTGGCTAGGATATCTGGCTTTCACCCAGAAGGCCCGGGTTCGATT-CCCGGTATGGGAAGT
DroYak_CAF1_left   --TTGGTATCGGAAATTTGATATT--GAGCGTTTG-ACCATTATATCCCATATTGTCTAGTGGTTAGGATACCCGGCTCTCACCCGGGAGGCCCGGGTTCAATT-CCCGGTATGGGAAAT
DroVir_CAF1_left   N-NNNNNNNNNNNN-NNNN-NNNN-NNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNN

DroAna_CAF1_left   AATTTTTTTGGCCATTTTTAATCATTATAGACTTAA-TT-TTTTA-TTTGTTTATTATTTTTAAATTTAAATATTCACTAC--GG-TT-TCTCTTAAAGTAGTGTGTCTAGA
DroEre_CAF1_left   GTTAAGAACATTTCAATTCTTT--TTTACTT-TGCA-ACAAC-AA-ATGTAAAAAGTTGGAACACGCAAAAAGTTGACGACGAGG-CC-AACAACACACGGTGTTCCCAAGC
DroGri_CAF1_left   AATTTTTTTACATTTTATTTCTATTTGACTTAATAT-TT-AATTA-ATTTATATATTTAAAATACATGCATATATATAATT--AA-CA-TGTCTCGTTTAATTTAGAAAATG
DroMel_CAF1_left   TGC-AAGTACATTTTCGAAAAAATTGTTTTGTTATT-AT-TTTAG-TTTGCAATCGAATAATGAAGATTATGTAAAAATCC--AA-AAACTT-CATTACGAAACGCTCAAAG
DroMoj_CAF1_left   AAATTTTTTGTTTTTGTTTTTGTTAATAATA-TTTA-ATATTCAT-ATTCATTCATTAAATACAGAAAATATCTTTAAAGG--GT-CT-GCAAAAATACTTGATCATATGTA
DroSim_CAF1_left   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NN-NNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NN-NN-NNNNNNNNNNNNNNNNNNNNNNN
DroWil_CAF1_left   AACTTTTTTGCTATTTATTATTAATTTTTTTTGTTA-TT-ATTATATATTCTGGAATAGGGCTTATTGTT-TTTTGTTGTT--GTAGCAAT--CATATGTTTTTTTTTTTAC
DroYak_CAF1_left   GACAAGGTGGGTG-GGTACACTTCATCTACT-TTTTCTTATTTGC-AGAAATAAAATTTTAAGAGCGCAAAATGT-AGATG--AG-CG-ATACGGACACCGTTATGCACAAG
DroVir_CAF1_left   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NN-NNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NN-NN-NNNNNNNNNNNNNNNNNNNNNNN