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


DroAna_CAF1_left   TT----GTATCGAA-ACAGAGAA-AAATGCTCTATGCTCTATATTGTTAT-ATTATGAGATC-GCTACA-GAACGGC--TAAA--T-AAAGTAAATTAACAAGTCAACA-AATAAAAAGT
DroGri_CAF1_left   CG----AGACCAGT-ACCCAACCGCATTCAACAACATTAAACGAAGTAAT-TTAACTAAAGT-TAATCA-AAATCTA--TTTTACT-CTATTGCTTAAATAAGAACAAA-AACAAAATTA
DroMoj_CAF1_left   GT----TTATTTTTGAGTCC---AAAACCAGCATCACTAAATAAAGTAAT-TTAATTAAAAC-TAATCA-AGCTCAATTGTTT-CTTTTATTGTCGAAATA-AATAAAA-AAAAATAAAT
DroVir_CAF1_left   TA----TATT--TTGAAACC---AGCACCAGCATCA--ATCCTAAATAAA-TTAATTTAATT-AAAT------GTAATCAAGA-TCAATTGTTTCTCCAC--ACAATTG-TGTGACAAAA
DroEre_CAF1_left   TA----TTATT-TGGCCAAA---CGAGTAATTT--CAT-AAGTTATATGCAAGAAAAAGATTGTTTCAAAGCTC-GAA-TAAAGTA-TCACGAGCTAAACACGGTTCGA----AAAAAAA
DroMel_CAF1_left   T-----GTGC--TGGTTAAA---CAAGTATTTT--CAC-AAGATA-TATGCGATGAAAGATT-CTTAAAAGGTC-TGA-AAAAATA-TCTCGGGTTAAAATTGGTTCGACAAAAAAAAAA
DroPer_CAF1_left   AA----CAGA--AAGTTATA---TTATCTATATT-ATCTTTTGAGATCGC-CGCAGAACGGC-TTAATA-AAGT-AAA-TTAACAG-AT--AAATTATGCAACTATCAA----AAAAAG-
DroPse_CAF1_left   AA----CAGA--AAGTTATA---TTATCTATATT-ATCTTTTGAGATCGC-CGCAGAACGGC-TTAATA-AAGT-AAA-TTAACAG-AT--AAATTATGCAACTATCAA----AAAAAG-
DroSec_CAF1_left   TATACGAAC---ACATTAAA---TGAGAGTTTC--AAT-AAAGTATTTGCACAAAATATATT-CTTAAAAGGTC-TGA-AAAAATA-TCTCTGGTTAAACTTGGTTCGA----AAA-AAA
DroSim_CAF1_left   AT-ACGAACA--CATTAAAT---GAGTGTTTCA--GTC-AA-GTATTTGCAGAAAATATATT-CTTAAAAGGTC-CGA-AAAAATA-TCTCTAGTTAAACTTGGTTCGA----AAAAAAA
DroYak_CAF1_left   GT----ATAGC-AAGCTAGC---TAAACAAGTAATTTCAAACTTGTATGC-GAAAAAAGATT-GCTAAAAGCAT-AAA-TAAATCA-TCCTAAGCTAAACATGGTTAA-----AAAAAAA

DroAna_CAF1_left   TGTGCAAAAAAATCCCT-TTCGCTGCGGACAGGATTCGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCGCTCGGACACCGCAGCTTGAGAGAATTGTGTGT-
DroGri_CAF1_left   ATACAAAAAAAAAACTA-TTCGCTGCGGACAGGATTCGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCAACGAGACGATTGGTGG-
DroMoj_CAF1_left   AAAATAAAAAATAAATA-TTCGCTGCGGACAGGATTCGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCTCCGATTCAAGCGC-CGC
DroVir_CAF1_left   AAAA-ATTTCGTATAGC-CCCGCTGCGGACAGGATTCGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCTTCGAATCGAGCGGCGC-
DroEre_CAF1_left   AGTG-TTACAACCACAC-ATCGCTGCGGACAGGACTTGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCCTTATCGAAGGCAGCTC-
DroMel_CAF1_left   CGTG-TTACAACTACACTATCGCTGCGGACAGGACTTGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCCTTATTGAAGTCCGCTC-
DroPer_CAF1_left   A-AA-GAATTCTTATAT-CCCGCTGCGGACAGGATTCGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCACATTTCATTTGCGTGT-
DroPse_CAF1_left   A-AA-GAATTCTTATAT-CCCGCTGCGGACAGGATTCGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCACATTTCATTTTCGTGT-
DroSec_CAF1_left   AGCG-GTACAA-GACAC-ATCGCTGCGGACAGGACTTGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCCTTATCGAATTTCGCTC-
DroSim_CAF1_left   AGTG-TTACAACCACAC-ATCGCTGCGGACAGGACTTGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCCTTATCGAAGTCCGCTC-
DroYak_CAF1_left   AGTG-CTACAT-CGCAC-ATCGCTGCGGACAGGACTTGAACCTGTGCGGGTAGAACCCAATGGATTTCAAGTCCATCTCCTTAACCACTCGGACACCGCAGCCTTATCGAAGGCTGCTC-

DroAna_CAF1_left   CAA-ATGATTATGTAA-TT-CTAAGGGAGAGAACATTACAGT-GGATGTGGCAAACTAAGAAAAGAATCATTTG-CTTAATTAATTTTTAAATAT-ATA
DroGri_CAF1_left   CAA-ACTGCCAACAAT-TTATCACAGCGCTCGGAGATGCTGC--TACTTGGATAACAGATGGCGCTAACTTGCT-TACATATTAATATCATAGATGGCG
DroMoj_CAF1_left   CAA-ATTGCAAACAAT-TCTGTTCAGTATATTGTGTCTCAAAAGTATACG--TGCAATAGATG-GCGCTAAGTAATATTTCGAATTAGCATTCATAGAT
DroVir_CAF1_left   CAAACTGCT-AACAAC-TTATCTTAGTAGTCTCATCTGGACTTATTTTCTTACAGCAGATGGCGCT-TCAGGGC--ATTTCACATTTATTTTCATAGAT
DroEre_CAF1_left   CAT-TTGTGTGTAATATTTCGCGCTGCATAATTCTATGCAGA--TAAACATCTGAATTTCTGCA-ATGGGAATA-GTAGTAG-ATATTCCAAAACATAA
DroMel_CAF1_left   CAT-TTGTCACTGATATCTCTCCCTGCATAATTCTATGCTGA--TAAGCATCTGAATTTCTGCA-AAGCGATGA-CAGTAAA-TCACTAGATATTTGAA
DroPer_CAF1_left   CAA-ATTTGCCACTTGATAGGCGCCGTAAAGCGCC-TCCTGT--G-AGGAACGTTA-GGCA--A-AAACATTAA-CTAAGAA-GCGGCGGAGATAAACC
DroPse_CAF1_left   CAA-ATGTGCCACTTGATAGGCGCCGTAAAGCGCC-TCCTGT--G-AGGAACGTTA-GGCA--A-AAACATTAA-CTAAGAA-GGGGCGGAGATAAACC
DroSec_CAF1_left   CAT-TTGCTCCTGATATCTCTCCCTGCATAATTCTATGCTGA--TAAGCATCTGCATTTCTGCA-AAGGGATGA-AAGTAAA-TCGCTTGATATTTGAA
DroSim_CAF1_left   CAT-TTGTTCCTCATATCTCTCCCTGCATAATTCTATGCTGA--TAAGCATCTGCATTTCTGCA-AAGGGATGA-CAGTAAA-TCGCTAGATATTTGAA
DroYak_CAF1_left   CAT-TTGTATGTCATATTTCGCGCTGCATAATTCTATGCAGA--TAAAAATCGGTAGTTCTGCA-AATTTCTGC-AATGGGA-ATGAATAGTGGTAGAT