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


DroAna_CAF1_left   TTTTAGT-------AAAGGGCTAAG------AA-ATATATTAAGACAAG---TT-A-TAAGTACATC-TTTATATC-TGCCAAGACTCT-GAACGAGTCA----GA----CACCACTTT-
DroEre_CAF1_left   TTATATCACACCCTTTGTT--GTCATATTATACATATGTATATACA--A---TAAC-CATGACAATCTGGTT-TGTTTGT-T------G-TCACTTTGGC---------GAGC-TTCGCT
DroGri_CAF1_left   NNNNNNNNNNNNNNNNNNNNNNNNN-------NNNNNNNNNNNNNNNNNNNNNN-N-NNNNNNNNNNNNNNTTATA---ATA------T-GAATTGGTT--------TTGGAACA--TGA
DroMel_CAF1_left   CTTTCGTAATATCGTATCCGAAGCA-------CTTGTTAATCATATAAAAGTTT-A-GCTTACCATACAATCTGTT---TTA------C-TTTTTGTGA--------CAACTTTG--CAA
DroMoj_CAF1_left   GTTTTTTGGAATTAATATATTAAAA-------AAAAATTACTTGTTATC---AG-C-AAAGCTTTGCTGTTTGATT-TAATA------A-T-AC-ATGAAAAATGTGCTGTATTAGTAAA
DroPer_CAF1_left   AAAGTTTTGGTTGTTGGCGGCGAAG------AA-CACATAAAATTTTAT---AA-T-TTTCTTTGGCGGAGAATTA-AAAATAAA------------AAA----ATTCCTAGTCATTTCT
DroPse_CAF1_left   TATGGCCGTTGAGTAGAAAATAAAC------AAAAACTTAATATTTTAT---AA-T-TTGCTTTGGCGGAGAATTA-AAAATAA-------------AAA----ATTCCTAGTCATTTCT
DroWil_CAF1_left   TGTTGAAAATCTATTTTTATAACAT-------TTAATACAAAAGAATAAC-TTT-A-TACTTCTTTTCAATGATGA---TTG------G-CTTAATTTG--------GAATGTTG--AAT
DroYak_CAF1_left   CAACGCTTGCAGTCCAGAAGAAAAA-----TGTATATACATATGTATTC---AC-C-CTAT-AAATCTGATGGGTA-TTATT------G-CCACTTTTGCGAGCTCGC----------CG
DroSim_CAF1_left   GCGCGCCGCATAAGCACGGTCTACGC-----GTATGTAGTCTACGCTCATTCTT-ATCAGTAGCTCCCG----CTC-CTCAGAGG--TGGCTGAAGAGA--------CTA-ATTGGGCAA

DroAna_CAF1_left   AA-GTA-CTGTAGTTGC-CT-GCGCAAAC-AT-CACATCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAAGCGT--TTGA
DroEre_CAF1_left   AAC--A-ATGCATTTTGGGA-ACTCAAAG-TC-AACCTCCCATATTGTCTAGTGGTTAGGATACCCGGCTCTCACCCGGGAGGCCCGGGTTCAATTCCCGGTATGGGAAGCTTGGTTCAA
DroGri_CAF1_left   ATAAAA-CCGGAATTTGGCT-GCGGACCA-AA-CATCTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAATTGTAAC-TC
DroMel_CAF1_left   CGTAAT-ATATATATTGGCT-ATAATCTA-ATACAGCTCCCATATTGTCTAGTGGTTAGGATACCCGGCTCTCACCCGGGAGGCCCGGGTTCAATTCCCGGTATGGGAAACTAATTT-CT
DroMoj_CAF1_left   TATATA-TTGAGAATTTGGATGTCGTGAA-GA-CACATCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCAATTCCCGGTATGGGAAGTTTGCTT-GA
DroPer_CAF1_left   AACAAA-ATGCAGTTTTGGA-CCAATGATGAC-TATATCCCATATGGTCTAGTGGCTAGGATATCTGGCTTTCACCCAGAAGGCCCGGGTTCAATTCCCGGTATGGGAAAGTACTCCTTT
DroPse_CAF1_left   AATAAA-ATGCAGTTTTGGA-CCAAAGACGAC-TATATCCCATATGGTCTAGTGGCTAGGATATCTGGCTTTCACCCAGAAGGCCCGGGTTCGATTCCCGGTATGGGAAAGTACTCTTTT
DroWil_CAF1_left   CACGAAAGCGCATTTTGACC-ACGCAACA-GC-CAAGTCCCATATTGTCTAGTGGTTAGGATATCCGGCTCTCACCCGGAAGGCCCGGGTTCGATTCCCGGTATGGGAAACTTTTTT-TG
DroYak_CAF1_left   GGTTAA-ACTTGTTTTGGAA-ACACAGAA-AT-CACCTCCCATATTGTCTAGTGGTTAGGATACCCGGCTCTCACCCGGGAGGCCCGGGTTCAATTCCCGGTATGGGAAACTGGATT-TC
DroSim_CAF1_left   CCTAGA-GTGCCTAAAAGTA-TCCCATGG-AG-AGTCTCCCATATTGTCTAGTGGTTAGGATACCCGGCTCTCACCCGGGAGGCCCGGGTTCAATTCCCGGTATGGAGGATTATTGTAAC

DroAna_CAF1_left   TAAGCTTT-AATTTTTTTCTTGTTT-TATTT-TT-T-AGATTTAAA--ATTTAAGAAATAAGAATGCATTT-TTATT-ATTTTGCTTAAAAAAATTTT
DroEre_CAF1_left   -GATTTAT-TAAATTTTTGAGCATATCCTTT-TTTGGCAT-CACAA--TTTAACATG--TTGCTTGATATT-GACAA-T-TAAAGAAAATAGAAAGTA
DroGri_CAF1_left   -AAGAGTT-TTTTTTTGCTATATAT-ATAAAATTTA-TAT-ATATA--TATAAATATACATATTCTTTTCA-T-GTTTAATAT-AAGTTGGAAATGAT
DroMel_CAF1_left   -TTTTGTA-TGTGACAATTACAGAA-AAAAAATTTA-TTT-TTATC--TTTGATGACAAAATCAAAAAATC-T-GAATCTGAA-GTCAGTTGTTGGAC
DroMoj_CAF1_left   -AAGCGCA-GAGACATTATTTTTTATTATTT-TTTT-TTT-TGATT--TTTTGATTTTTTTTTTTTTCACA-CTTTATTATAA--TAATTTATTGTAT
DroPer_CAF1_left   -TTATACT-TTTAGTGTTCTTCTGAACTCGT-CTCA-CAG-CGCCA--TCTGTTCGGACATTCTAGAAAGA-A-GTCTTGCCA--TTATCAGTATTTA
DroPse_CAF1_left   -TTATACT-TTTAGTGTTCTTCTGAACTCGT-CTCA-CAG-CGCCA--TCTGTTCGGACATTCTAGAAAGA-A-GTCTTGCCA--TTATCAGTATTTA
DroWil_CAF1_left   -CAATTCACATTTTATTTCATGTTG-ATTTCATTTG-ATA-ATAAA--CTTAAAGCTTAATGCTTACAATCAC-AA-TCATTT--CTTTATTCATTCC
DroYak_CAF1_left   -CAGTGAA-AAGTTTTTTTTTGCATCATCATAATTT-ATA-ATGTC--GCTTGATATAGGTATTTAACAAT-GACAGACACAG--AAAGTTTC-AACT
DroSim_CAF1_left   -GAGTAAG-CTTTCAAAGCTGGCTT-CTATT--TTT-TTT-TTTTTTTTTTTACAGAAAAAACTTAATTTT-CATCTTTGATG--ACAAAATC-AAGA