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


DroAna_CAF1_left   GGC-AGAGACTTCC-TGCAGAAAAG-ACTCCCCAAGTGCAACATT-G-A---TGGGG-AGTTGGGCGGCTGAAAGTGGTTCTTGTCCGCGCTG-----AGCTTTCGCGCGAAAAGCTCAT
DroEre_CAF1_left   AAAGTG---CAGCT--AATGAAGCAAACTCTTG-CGAAAACTTTGTCTGCAGCTTGG-TGAAAAGCGGGAAA-AACGGTTTGTGTCTCTGCTG-----AGCTTTG-CGCGAAAAGCGAAT
DroGri_CAF1_left   AAT-AT---AAAAAGAGACGAA-AATTAGCCAA-GTGAAAAGT-GCAATAAGAAACA-TG--CAGCAGCAGA-TATGGTTTGTGTCCCCACTA-----AGCTTTC-GTTGAAAAAAAGCT
DroMel_CAF1_left   AAAGTG---CAGCT-AAATGAAACTGTCGCTTG-CGGAAACTTTGTCTACAGCTTGG-TGAAAAGCG-GAAA-AACGGTTTGTGTCTCTGCTG-----AGCTTTT-TGCGAAAAGCGAAT
DroMoj_CAF1_left   TAACAG---CTACA-TCTA-A---AACTATAAC-AACAAAGCACGACTGCAACTGAATTGAACAATGGCAGC-TGGTTTGTGTCTTCGCTAAG-----CTTTTTC-ATCTGAGTAAGCTT
DroPer_CAF1_left   GCC-CG---AAACA-GCTTGGA-CTGCAGCCACATACATCGAGAGGGAGGAGCGAGC-GAGCGGGCGAGCGA-AATAGTTTGTGTCCGCGCTG-----AGCTTTC-AGCTGAAAGCTCTT
DroPse_CAF1_left   GCC-CG---AAACA-GCTTGGA-CTGCAGCCACATACATCGAGAGGGAGGAGCGAGC-GAGCGGGCGAGCGA-AATAGTTTGTGTCCGCGCTG-----AGCTTTC-AGCTGAAAGCTCTT
DroSec_CAF1_left   AAG-TG---CAGCT-AAATGAAACTGTCGCTTG-TGGAAACTTTGTCTGCAGCTTGG-TGAAAAGCGGGAAA-AACGGTTTGTGTCTCTGCTG-----AGCTTTT-CGCGAAAAGCGAAT
DroSim_CAF1_left   AAG-TG---CAGCT-AAATGAAACTGTCGCTTG-TGGAAACTTTGTCTGCAGCTTGG-TGAAAAGCGGGAAA-AACGGTTTGTGTCTCTGCTG-----AGCTTTT-CGCGAAAAGCGAAT
DroVir_CAF1_left   AAA-AA---AAAAA-CAACGGCAAATGCAGCAG-CAGAAGCGAGCAAGAGTAGCTGC-AGTAGAGCTGCGTG-CTGGGTTTGTGTCCATGCTA-----AGCTTTC-GCTAAAAAGCTTT-
DroYak_CAF1_left   AAG-TG---CAGCT-AAATGAATCTAACTCTTG-CAAAAACTTTGCCTGCAGCTTGG-TGAAAAGCGGGAAA-AACGGTTTGTGTCTCTGCTG-----AGCTTTT-CGCGAAAAGCGAAT
DroWil_CAF1_left   AAC-AA---TGCGAGCAATCAA-CC-ACAATAAGGAG-AAGCCAGCCAGCTAAAAGA-AAAA--AACAAAAA-AAAACATTGGTTCATTTCAATGCTAAAAGCTC-CAAAAAGCTTTCTA

DroAna_CAF1_left   --------------T-TGTGTGCATCGGCTGCTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTT--GCATCC-TTT
DroEre_CAF1_left   T----------TT-C-CATATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTG--GCGTCC-TTG
DroGri_CAF1_left   T----------TT-C-GCTGTGCAATTGCCACTGGGATATTGCCCTGTGCTCGCTTTGAATATTGTGTAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTG--GCGCAC-ATG
DroMel_CAF1_left   T----------TT-C-CATATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTG--GCATCC-TTG
DroMoj_CAF1_left   T----------CT-C-TCTGTGCAATTGCCGCTGGGATAC-ACCCTGTGCTCGCTTTGA-GTTTA-TGTTGCAAGTGAACACAGCTGGTGGTATCCAGAGGCCGTTGA--CAGCCA-ATG
DroPer_CAF1_left   CCGTGTCTCGTGT-C-TCTGTGCAACTGCCGTTGGGATAC-ACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTTCT--GCAACA-ATG
DroPse_CAF1_left   CCGTGTCTCGTGT-C-TCTGTGCAACTGCCGTTGGGATAC-ACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTTCT--GCAACA-ATG
DroSec_CAF1_left   T----------TT-C-CATATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTG--GCATCC-TTG
DroSim_CAF1_left   T----------TT-C-CATATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTG--GCATCCTTTG
DroVir_CAF1_left   --------------T-TCAGTGCAATTGCCGCTGGGATAC-ACCCTGTGCTCGCTTTGAA--TTGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTGG--CAGCCA-ATG
DroYak_CAF1_left   T----------TT-C-CATATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTG--GCGTCC-TTG
DroWil_CAF1_left   G----------ATTCTTCTGTGCAACTGCCACTGGGATAC-ACCCTGTGCTCGCTTTGAATATTGTGCAAACAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTTTTGCATCC-ATG

DroAna_CAF1_left   CAACTTCAAGG-ATAACAACAGCAACAACAACAACAGCA-ACAACATCAAGGA-CCTG---GCTTTGGGTG-AGTCTGGCCAACA-----GCTTTTCAAGTTTG
DroEre_CAF1_left   CTGCTCCAGAA-ACTCCAAGGACAACGAGAATGCCCCA--CTGAGAACGTCATTAGAG---GGTAAGTGCG-TGTTCAGATCTAC-----CAGTTTCCTGCTCA
DroGri_CAF1_left   CAACAACAACA-ACAAGAGCAACAACTACAGCAACAACT-ACAACAACAGCAGCTGCA---ACAACAACCA-GGGCGATTGCAAG-----TGCCAGC-ACAGGG
DroMel_CAF1_left   CTGCACCACAAAACTCCAAGGATAACGAGAATGCCCCA--CAGAGAAGTTCATTACAG---GGTAAGTGCG-TATTCAGATCTAC-----CAGTTTCCTG-CTC
DroMoj_CAF1_left   CAACAACAGCA-ACAACCACTACAACAACGACGACGACA-GCAACATCAACAA--CAG---GCACAGGGTGAGTAGCGCTTCAAG-----TTGATCGAAGGTGT
DroPer_CAF1_left   CAACATCAGCA-ACAACAACAGCAACGAGAACAACAACA-ATTACAGG-G-----TGA---GTCATGCCAC-TGTTGAACATTCCGTTTATTCTTTCTTTTATT
DroPse_CAF1_left   CAACATCAGCA-ACAACAACAGCAACAGCAACGAGAACA-ACAACAATTACAGGGTGA---GTCATGCCAC-AGTTGAACATTTCGTTTAATCTTT------TG
DroSec_CAF1_left   CTGCTCCACAA-ACTCCAAGAATAACGAGAATGCCCCA--CCGGGAAGTTCATTACAG---GGTAAGTGCA-TCTTCAGATCTAC-----CAGTTTCCTGCTCA
DroSim_CAF1_left   CTGCTCCACAA-ACTCCAAGGATAACGGGAAAGCCCCA--TCGAGAAGTTCATTACAG---GGTAAGTGCA-TCTTCAGATCTAT-----CAGTTTCCTG-CTC
DroVir_CAF1_left   CAACAATTGCA-ACAACTGCAACAACAACAACTGCAACA-ACAACAACTGCAACAGCA---ACAACAACAA-CGAATACTGCAAC-----AA-CTTGAGGCAGC
DroYak_CAF1_left   CTGCTCCAGAA-ACTCCAAGGATAACGAGAACGCCCCC--GAGAATGTGCCACGAACTTCATTGG---AGG-GTAAGTGCGTCTT-----CAGATTCTACGTCT
DroWil_CAF1_left   CAACACCAAAA-GATAAATATTCTTCGCCAGGAAAGGCACTCCACATAGGTAAGTCCG---AGAATTTGCA-TTAGTT-TTATGC-----CTTCT-TATGTTAA