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


DroAna_CAF1_left   GGCTGTGTCAGCT---CCGGCAAGAAGTACCCGCCGCACATCGAAGAGGAACGCCCAGGTCA-GTA----------------CCAGCA-TATCT---AAGCATCTT-GTGGTTGATCT-G
DroEre_CAF1_left   GC----TGCAACGCTACCAACGAGAAGCACCCGTCGCACATCCAAGCGGAACGTACAGGTCA-GTT----------------C-ATCC-CACGTATGTAGTTGCCG-CCTTATCCA-G-A
DroMel_CAF1_left   CCCGGCTGCATCGCTGCCAACCAGAAGCACCCGGCGCACATCCAAGCGGAACGTACAGGTCA-GTT----------------C-ATCC-CACG----TAGTTACCG-CCTCTTCCA-G-A
DroPer_CAF1_left   AGTGTCCACAAGGACCTCCAAGCGCACATCCAGGCG-ACACGCGCAGGTCAGTACACCCACA-GAG----------------C-AGAC-ACAC----AGCCCACAG-TCACCTCCT-CCT
DroPse_CAF1_left   AGTGTCCACAAGGACCTCCAAGCGCACATCTAGGCG-ACACGCGCAGGTCAGTACACCCACA-CAG----------------C-AGAC-ACAC----AGCCCACAG-TCACCTCCT-CCT
DroSec_CAF1_left   CCCGGCTGCATCGCTGCCAACGAAAAGCACCCGACGCACATCCAAGCGGAACGTACAGGTCA-GTT----------------C-ATCC-CACG----TAGCTACAG-CCTCATCCA-G-A
DroSim_CAF1_left   CCCGGCTGCATCGCTGCCAACGAGAAGCACCCGACGCACATCCAAGCGGAACGTACAGGTCA-GTT----------------C-ATCC-CACG----TAGCTACAG-CCTCATCCA-G-A
DroVir_CAF1_left   ACGCGTCGCACATCTA--AGCGGCAAGCGCAGGTC-AGTATCTCACACACACACACACACAC-ACA----------------C-ATTCATATG----CTTGCCCAAACAATTTTCT-G-T
DroWil_CAF1_left   TCCA-CGGTAGTA---GCGACCAGGACAACGAGGCGTACATCGAAACGGCAAGCGCAGGTCAGTAT----------------C-ATAT-GTTTAT--AGTATGCAG-CCTCTTTAA-G-A
DroYak_CAF1_left   CCCGGCTGCATCGCTACCAACGAGGAGCACCCGGCGCACATCCAAGCGGAACGTACAGGTCA-GTT----------------C-ATCC-CACG----AAGTTGCCG-CCTTATACA-G-A
DroGri_CAF1_left   CCAA-------CGC---------GAACCACACGTCGCACATCCAAGCGCCAAGCACAGGTCA-GTAACACACACACACTCACA-AACA-CACC----ATGCGTGTG-CT-TCTGCT-TTT

DroAna_CAF1_left   TAAAT-ATCCAGTGATGTAGACTATTGCAA-----TGTGCGTATGTGGCGTTGTTCCATACGCACATGACTC--CCCCATT-GG--GGGGCAAATGATTACCT----GCAAGG------G
DroEre_CAF1_left   TCATT-AGCCCATGATGTAAACGATTGCAATTTCCAGTGCGGATGTGGCGTTGTTCCATTCGCACATGATTCTTCTCCCCG-GA--GGAGTTAGTGATTACCT----GCAAGG------G
DroMel_CAF1_left   TCATC-AGCCAATGATGTAAACGATTGCAATTTCCAGTGTGGGTGTGGCGTTGTTCCATCCGCACATGATTCTTCTCCCTG-GA--GGAGCGAGTGATTACCT----GCAAGG------G
DroPer_CAF1_left   CCTGC-TACAATTGATGAGAAAAAATGCATGTCTTCATGCGGATGTGGCGTTGTTCCGTTCGCATATGATGCCCCACAGCA-CA--TGATTTTCTGCA-AGGG----CCAACTGATGT-A
DroPse_CAF1_left   CCTGC-TACAATTGATGAGAAAAAATGCATGTCTTCATGCGGATGTGGCGTTGTTCCGTTCGCATATGATGCCCCACAGCA-CA--TGATTTTCTGCA-AGGG----CCAACTGATGT-A
DroSec_CAF1_left   TCATC-AGCCAATGATGTAAACGATTGCAATTTCCAGTGTGGGTGTGGCGTTGTTCCATCCGCACATGATTCTTCTCCCTG-GA--GGAGCGAGTGATTACCT----GCAAGG------G
DroSim_CAF1_left   TCATC-AGCCAATGATGTAAACGATTGCAATTTCCAGTGTGGGTGTGGCGTTGTTCCATCCGCACATGATTCTTCTCCCGGAGA--CGAGTGATA--CTGCAG----GCAACTGAAGGCG
DroVir_CAF1_left   ACGGT-TTGTATTTGATGAAAAACATG-CATCTTCA-TGCGGATGTGGCGTTGTTCCATTCGCAAATGATGGTTTCCACGTGATTCTCTGCAAGGGCCAACTG----ATAAAT-------
DroWil_CAF1_left   TTAGTTTGCAGTTGATGAAAAAAAACG-CATCTTCCATGCGGATGTGGCGTTGTTCCATTCGTATATGATGTTCCAAATGA-TT-TTCTGCAAGGGCCAACTGATGACGCAAA------C
DroYak_CAF1_left   TCATT-AGCCCATGATGTAAACGATTGCAATTTCCAGTGCGGATGTGGCGTTGTTCCATCCGCACATGATACTTCTCCTCG-GA--GGAGCGAGTGATTACCT----GCAAGG------G
DroGri_CAF1_left   TGGTT-TGCAATTTGATGAAAAAATACGCA-TCTTCATGCGGATGTGGCGTTGTTCCATTCGCAAATGATGGCCTCCACAT--------------GATTCTCT----GCAAGG------G

DroAna_CAF1_left   C-------CAACTGAGTTCACAG--------ACC-C-------------------------------------------------A-------AC--C---AA--GTGAG
DroEre_CAF1_left   C-------CAAC-----------------------------------------------------------------------------------------------TGA
DroMel_CAF1_left   C-------CAACTGAAGGCACAG--C-----ATC-CA---C---AA--ATG--CTCTGA-G--AAA--TG----CCGGGAACCTTCATTAACGAC--TTTTAATCCTTTC
DroPer_CAF1_left   G-------CAATCGAAG---CCA--T-----CGC-CA---C---AG--CAT--TGCATT-T--GAT--GT----CCTAAAATATTTTCTAATCACATTCAATACGCCTTG
DroPse_CAF1_left   G-------CAATCGAAG---CCA--T-----CGC-CA---C---AG--CAT--TGCATT-T--GAT--GT----CCTCAAATATTTTCTAATCACATTCAATACGCCTTG
DroSec_CAF1_left   C-------CAACTGAAGGCACAG--C-----ATC-CA---C---TA--ATG--CACTGA-G--AAA--AG----GCTGGAACCGTTATTAACGAC--TTTTAAT-CCTTT
DroSim_CAF1_left   CATCCTTATGACTGAGATGGCGGACG-----TATACA---T---TT--TATCTTCCCTATGACAAAAAAA----GCAAAANNNNNN-NNNNNNNN--NNNNNNNNNNNNN
DroVir_CAF1_left   CAAAC---CAAGAAAAG--AGTT--CGAGAGGC--AG---C---TAATGC----AAGCT-C--ATT--GG----ACGACAGTTTTATCTAAAAAG-AGTTCTTCTCTTTC
DroWil_CAF1_left   G-------CAACCAAAAAAATAG--A-----TAC-TTTGAAAAATA--TAT--TTGTGC-C--AAA--TGATGAACTCAAAGCGCATGTTGCTAT--TACATTCTTGTTT
DroYak_CAF1_left   C-------CAACTGAAGGCACAG--C-----ATC-CA---A---TA--ATG--CATTGA-G--AAA--TG----CCGGTAGCAGTCATTAATAAC--CCTTAATCCTTTT
DroGri_CAF1_left   C-------CAACTGAT-------------------------------------------------------------AAA-------------------GCAAGCCAGAG