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


DroAna_CAF1_left   GTT-TTGAATT-CTGTT--CACG-AAACTCGGTTCGAGTTGTCGTAGGCCAA---AA-------AGCTTTCCAAAAGCTCTTTTCTG--TTCGTCTTTCTGCTCCGAAGCTTATGGAGCA
DroEre_CAF1_left   ACCCAT-GACTTCCGACTGAGGGAAGTAAATGAAATTTACTTTGCGTTGCCC---TAGGCTGAAAGCTCTTGAAAGCTCTAC-TTTGAGCTCATCGAAATATGATGCTTGTA-TGGGGAT
DroMel_CAF1_left   CTCATG-ACTTCCGGACTGAGAGCAGTGAATGAAATTTACTTTGACTTGCCC---TAGGCTGAAAGCTCTTGAAAGCTCTAC-TTTTGTCTCATCGAAATATGACGTAAATA-CTGGGGC
DroSec_CAF1_left   ACTCATGACTT-CCGACTGAGCGTATTAAATGAAATTTACTTTGACTTGCCC---TAGGTTGAAAGCTCTTAAAAGCTCTAC-TTTGAGCTCATCGAAATATGACGTAAATA-CTGGGGC
DroSim_CAF1_left   ACTCATGACTT-CCGACTGAGCGTATTAAATGAAATTTACTTTGACTTGCCC---TAGGCTGAAAGCTCTCGAAAGCTCTAC-TTTGAGCTCATCGAAATATGACGTAAATA-GTGGGGC
DroYak_CAF1_left   ACCCATGACTT-CCAAATGGGGGAAGTAAATGAAATTTACTTTGCGTTGCCC---TAGGCTGAAAGCTCTTAAAAGCTCTAC-TTTGAGCTCATCGAAATATGATGTTCGTA-TTGGGAT
DroPer_CAF1_left   AAGTAAAGCTG-TGTGGAGTGGGGTTCGAACTCGCGTCTTTTATATGTTATTGAAAAGTGGCTTTGAAAGCTTTTCCATGAC-ATAGATTTTAGCTTACGCCGACTGGAGCT-TCGAGAT
DroPse_CAF1_left   AATTAAAGCTG-TGTGGAGTGGGATTCGAACTCGCGTCATTTATATGTTATTGAAAAGTGGCTTTGAAAGCTTTTCCATGAC-ACAGATTTTAGCTTACGCCGACTGGAGCT-TCCACAT

DroAna_CAF1_left   TGTT---GGGAGTT-GTAACGGTACGAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCAAAATAA-CTTTTTTTTAATTT
DroEre_CAF1_left   -TTT---CTGTAAG-CG-AAGACAACAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCA-AAATAATTTTTTATT-TTTA
DroMel_CAF1_left   -TTT---GAGTGTG-TG-TAGACATCAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCA-AAATAACTATTTT----TTT
DroSec_CAF1_left   -TTT---GAGTGTA-TG-AAGTCATCAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCAAAATAATTTTTTTATT-TTTA
DroSim_CAF1_left   -TTT---GAGTATA-TG-AAGTCAACAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCAAAATAA-CTTTTTATT-TTTA
DroYak_CAF1_left   -TTT---CAGTGCA-TT-AAGTCACCAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCAAAAATAATTTTTATTT-TCTT
DroPer_CAF1_left   -GCAAATCTGAGCTCTT-CAGTTATCAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCAGAATTA-ACTTTTTTTTCCTT
DroPse_CAF1_left   -GCAAATCTGAGCCCTT-CAATTATCAAGCATCGGTGGTTCAGTGGTAGAATGCTCGCCTGCCACGCGGGCGGCCCGGGTTCGATTCCCGGCCGATGCAGAATTA-ACTTTTTTTTGGT-

DroAna_CAF1_left   TAATATTATT-------------TTTATTTATTTACTTT-T----GCATTAT---ACGAT-TGAGTTAACTATAGCATTCCAATTTTAGCAGCTTTTTTTGTTGGAATTTATCAAA----
DroEre_CAF1_left   AAT--TGTTTTT-----------TACAATTCAACATATTTTCCTTTGTTTGCATATTCTC-TGACTAAACTGAAGCATTCATATTTTAGCAACTC-TGTTGTTGTAATTTA---------
DroMel_CAF1_left   AAT--TATTTTT-----------CTA-AGTTTTTTCTATTGTTTGCATACACT------C-TGACTTAACTGAAGCATTCCAATTTTAGCAACTC-TATTGTTGAAATTTATCAAA----
DroSec_CAF1_left   AAA--TTATTTT-----------TCT-AAATCTTTTTTTTTTTTG--TATA----AACTC-TGACTTAACTGAAGTATTCCAATTTTAGCAACTC-TATTGTTGGAATTTATCGAA----
DroSim_CAF1_left   AAA--TTATTTC-----------TTTTTGCATACACTCT-G----------------------ACTTAACTGAAGCATTCCAATTTTAGCAACTC-TATTGTTGGAATTTATCAAACAGT
DroYak_CAF1_left   TTA--AT--TTA-----------TTT-TTTGTACAAATTTGTTTG--AATA----ATCTA-TGACTAAACTGAAGCATTCATATTTTAGCAACAC-TGTTGTTGAGATTTATCAAA----
DroPer_CAF1_left   TT---TTTTTTGGTTTTTTTTTCTTT-TTCTCTTGAACTTGAATT--ATTT----GCTTTAAATATTAACAAAATCGTTTCTTTTGCAGCAGTC--TAATGCT-TGG-------------
DroPse_CAF1_left   -T---TTT------------TTCTTT-TTCTCTTGAACTTGAATT--ATTT----GCTTTAAATATTAACAAAATCGTTTCTTTTGCAGCAGTC--TAATGCT-TGGCTTATATAC----

DroAna_CAF1_left   ------ATGTCAA---TAAT
DroEre_CAF1_left   --------TC------AAGC
DroMel_CAF1_left   ------CAGT------CAAT
DroSec_CAF1_left   ------CAGTA-----AATA
DroSim_CAF1_left   CAATAATTGTTTTGGGGTTT
DroYak_CAF1_left   ------CAGTCAAT-AATTG
DroPer_CAF1_left   ----------------CTTA
DroPse_CAF1_left   ------CAGAA-----AACA