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


DroAna_CAF1_left   C-CT--TCAGC-CCA-AATCTTC-T-T--AATTCTTCA---ACGTTAAATGTGATTACCTAAATTTAATAAAATTAGTTATT----AAAAAAAG---ATAAAAAAAAGAACTTTGCAAC-
DroMel_CAF1_left   CGCT--ACAGC-CCA-AGGCCTA-A-A--CATATACCATG-ATTTGTTATCAAAAT-TAG--AAAGTTGTTACCAATAAAAA--AAAAAGATAC---GCCAAAAATAATG--ACA--TGA
DroMoj_CAF1_left   T-TGTAGAGTA-GCA-TGTTACC-T-A--ATTATAAAAAA-TGTATATTAAAATTA-TAG---TTTAATAAAAGTAAAAAAC--TAGATGACAC---TTCAAGTTTTAAG--TCG--AAG
DroPer_CAF1_left   G------CAGC-CAA-AGGCCTG-A-A--TTAAAAGTT---ATACTCTGTAGATAC-TAGATAAAATTAAAAAAATATTTAA----AATCAAAC---TGCAACTAAAAAA--AAATTGT-
DroPse_CAF1_left   G------CAGC-CGA-AGGCCTG-A-A--TTAAAAGTT---ATACTCTGTAGATAC-TAGATAAAATTAAAAAAATATTTAA----AATCAAAC---TGCAACTAAAAAA--GAATTGT-
DroSec_CAF1_left   G-CT--GCAGC-CCA-AGGCCTA-GGA--GACATGCAATG-ATTTGTTATCAAAAT-TAG--GTAGTTGTTATCAATAAAAA--AAAAAGATAC---GCCAAAAAGAATT--ACA--TGA
DroSim_CAF1_left   CGCT--GCAGC-CCA-AGGCCTA-G-A--GACATGCAATG-ATTTGTTATCAAAAT-TAG--ATAGTTGTTATCAATAAAAA--AAAAAGATAC---GCCAAAAAGAAGT--ACA--TGA
DroVir_CAF1_left   T-TT--ACGGC-ATT-GTTACCT-A-AGTTATAGTGGA---TGTTAATTAAAATTG-TAAAGTAAAAAATAAA-ATTCAAAG----CAAAAAAGATTAGCAGCCTTTTCA---AATGAC-
DroYak_CAF1_left   G-CT--GCAGC-CCA-AGGCCTA-A-A--GACATACCATG-ATTTGTTATCAAAAT-TAG--AAAGTTGTTATCATTAAAAAAAAAAAAGATAC---GCCAAAAA-ATTT--ACT--CGA
DroGri_CAF1_left   C-AC--CTTGTTATTTCA-GTTGTA-A--TTAAATGTGGGATAGAAATTAGACTAAAAAT-----AAAAGAAA-AAATAAAA--AAATTGCATC--GAACTTCAATTTTA--TTGAAG--
DroWil_CAF1_left   C-AA--AGTTT-AAAGTTTTCCA-T-G--CACGTTGTTATTATCAAAATTCTAGATCATG-----ATAAAATA-AATTATTG--ACAATACAAA--AAAAAAAATCTCAC--TGTTTTCA

DroAna_CAF1_left   --TTTTTTGTTGTCATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGTGGACGCTTTGCCAATGACTCATACAAG
DroMel_CAF1_left   -ACTA-ATCATTTCATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGTGGACGGCTTTCCAATGACTCATACGAG
DroMoj_CAF1_left   -TTCC-ATTTTTACATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGTGGACGCTTTGCCAATAACTTATACAAG
DroPer_CAF1_left   --CAC-TGACGGACATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAAGTGGTGGACGCTGTGCCAATGACTCACTCGAA
DroPse_CAF1_left   --CAC-TGACGGACATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAAGTGGTGGACGCTGTGCCAATGACTCACTCGAA
DroSec_CAF1_left   -ACAT-ATAGTTTCATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGTGGACGGCATTCCAATGACTCATACGAA
DroSim_CAF1_left   -ACAT-ATAGTTTCATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGTGGACGGCATTCCAATGACTCATACGAA
DroVir_CAF1_left   --CACATTTTTATCATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGTGGACGCTTTGCCAATAACTTATACAAG
DroYak_CAF1_left   -ACTA-ATCGTTTCATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGAGGACGGCTTTCCAATGACTCATAGAAG
DroGri_CAF1_left   -TTCA-AACTTGACATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGTGGACGCTTTGCCAATAACTTATACAAG
DroWil_CAF1_left   CATTA-GTGACAACATCCCTTGCGGGGATCGAACCCGCGACCTTTGGATTAGAAGTCCAACGCGCTATCCTCTGCGCCAAAGGGACAGGTGGAGGACGCTTTGCCAATGACTTATACAAG

DroAna_CAF1_left   CCAAGGGGACTTTTTTCCTCTGGAAACACAATAAAAAGCTTTC-AAATATCTTTAATTTGCTTAAAAAACA-TTAAAA-AATCAATT
DroMel_CAF1_left   CTAAGGGGAGTTCTAGCAGTTGCAAAACGGATAAAACAGCTTT-CACTCATTTTTTATTATTTAACAAGTA-CATCAT-ATGATCCA
DroMoj_CAF1_left   CCAAGTCGAGTTTTTTCAAACTATTCTAAAGCAAAAGCTCACTGCGCCTGCCGGCTGC-CTACAAAAAATT-TATAAC-ACATCTAA
DroPer_CAF1_left   CCCAGTGGAGTTTTGACAGCTGGAATCCCGATAAAATACCTCA-AACCATCTTTAATTGCTTGATTATATA-TCCAAT-AATTAATT
DroPse_CAF1_left   CCCAGTGGAGTTTTGACAGCTGGAATCCCGATAAAATACCTCA-AACCATCTTTAATTGCTTGTTAATATA-TCCAAT-AATTAATT
DroSec_CAF1_left   CTAAGGGGAGTTCTAGCAGTTGCAAAACGGATAAAACAGTTTT-CATTCATTTTTTATTATTTCAAAAGTA-CATTAA-ATAATCCA
DroSim_CAF1_left   CTAAGGGGAGTTCTAGCAGTTGCAAAACGGATAAAACAGTTCT-GAATCATTTTTTATTATTTAACAAGTA-CATTAA-ATATTCCA
DroVir_CAF1_left   CCAAGTGGAGTTTTTTCAACCAATTCTCAGGCAAAGCTCGTTC-TGCGCCTGCTGGCTTCCTACAAAATAA-TTCAAA-ACTGTTCT
DroYak_CAF1_left   CTAAGGGGAGTTTC-GCAATTGCAAAACGGATAAAACAGCTTT-CACTCATCTTTTATTATTCAGAAAGTA-CATAAAGTAATCCAT
DroGri_CAF1_left   TCAAGTGGAGTTTTTACCGTAAAATTCTCGAACAAAAGCTCAT-ATTGCGCCTGCAGGTGGCCTATGAAAT-AATTGC-AAGAGCAT
DroWil_CAF1_left   CCAAGTGATACTTTTTGACTGAAATATACTTAAAAAAGCTTGC-CCATAGCTT-TATTTATTAATAATTTTATCCAAA-ACACCAAG