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


DroEre_CAF1_left   TAAT-----AGTT-TCAAAGGCTTGATTGTAC-A-ATATGTACGTTATCCG-AATCT-TATTTAAAATAACTT--AAATT-----ATGCTTAAAACCGAAAAGTTGTGAATCAACCCCAT
DroGri_CAF1_left   ATAG-----GATT-AGTGTAATTTTTTTTTAA-A-ATTATTTTATATATAT-TATTA-TTCTATTTATTTATT--TAGAC-----AGTCTAAGAATTTTTCTTTGGAATTCTAAGAACTT
DroMel_CAF1_left   TTTA-----ATATTTGAACGATCTGATAGTTC-A-ATAAGACCGTTATCCA-AGTCT-TATTTAAAATTA-TT--TAATC-----ACCCTCAAAACCGAAAAGCTGTGAATCCACCCCAT
DroPer_CAF1_left   TGGG-----ACTA-TTTCTAATTTTACATAAC-TTTCCATGATTTCCACAG-AGCTT-TCTT--GGATTCCCTATGATTC-----GCCT-TGAAAATCGCAATTTTTGTGGCCACCCTCG
DroPse_CAF1_left   TGGT-----ATTA-TTTCTAATTTTACATAAC-TTTCAATGATTTCCACAG-AGCTT-TCTT--GGATTCCCTATGATTC-----GCTT-TGAAAATCGCAATTTTTGTGGCCACCCTCG
DroSec_CAF1_left   TTAA-----TATT-TGAGCGATCTGATAGTTC-A-ATGTGAACTTTATCCA-AATCT-TTTTTAAAATTACTT--TAATC-----ACCCTCAAAACCGAAAAGCTGTGAATCCACCCCAT
DroSim_CAF1_left   TTAA-----GGGC-ATGCTGATCTGATATTTC-A-ATGTGAACGTTATCCA-AATCT-TATTTAAAATTACTT--TAATC-----ACCCTCAAAGCCGAAAAGCTGTGAATCCACCCCAT
DroYak_CAF1_left   CTTG-----AAGT-TTATTTAAAGTTTTCAAG-G-CCTGGTTGTACACTAT-GCACG-TTATTCGAATTACTC--AAAAT-----ATCCTTAAAACTGAAAAGTTGTAAATCCACCCCAT
DroAna_CAF1_left   GCAA-----GAAA-AACATATAGTAGAGAGAA-A-AAACTTCATATACCTTAAATAAATTAGT-T-TAATTTATAATT-TTATTTGAAGAACGAAACTTTGAAAG------CAACCCTCT
DroMoj_CAF1_left   ATTGGTTTATTTT-TATTATTATTTTTTATTTAT-TTTATTTTATTTATTTTATTTTTTTTTC-A-ATTTAGTTTGAG-------ACACTTGAAATTTTATTTTGCCTAAACTAAATTTG
DroVir_CAF1_left   TTCA-----ATCC-CGGGTTTCGGCAGAACAC-T-TTTTTTTATAATTTAAGCAAGAAAAAGT-T-ATTTGTGAACA--------GCTTTCCAAATTGAAAATCTCTGTATTCA------

DroEre_CAF1_left   CACGTGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATTTTAA--CATTTTAATGCGTTTG--TAT--TAT-TTAATAT
DroGri_CAF1_left   AATGTGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATTCGGCCCAATCCTCATTTGGAGT--TTTTTTTTTGGTATTT
DroMel_CAF1_left   CACGTGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATTGGAA--A-TATTTATTTTAATG--CAT--TTC-CCA-AAT
DroPer_CAF1_left   AGGATGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATAGGAA--AATTTTTT-TTTGCTC--TAC---TT-CCACTGT
DroPse_CAF1_left   AGGATGTTTCCGTGGTGTAGCGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATGGGGA--AATCTTTTTTTTTCTC--TAC---TG-CCACTGT
DroSec_CAF1_left   CACGTGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATAGGAA--AATATTTATTTTAATG--CAT--TTC-CTAAAAT
DroSim_CAF1_left   CACGTGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATAGGGA--AATATTTATTTTAATG--CAT--TTC-CTAAAAT
DroYak_CAF1_left   CACGTGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATTGCAA--TT-ATTTATTTTCATG--CAT--CTT-CTGAAGA
DroAna_CAF1_left   CAAGAGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATTT--G--GGTTTCTT-TT-TTAATTAAA---C--GTTTTTT
DroMoj_CAF1_left   ACCAAGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAACGCCCCCGGTTCAATCCCGGGCGGAAACATATTGT--TATTTATTTTATAAAGA-TTT---CT-AAAAATA
DroVir_CAF1_left   -TTGTGTTTCCGTGGTGTAGTGGTTATCACATCCGCCTAACACGCGGAAGGCCCCCGGTTCAATCCCGGGCGGAAACATCATCT--AATCAAGACTATTTTTT-GTA---AT-CGAAAGT

DroEre_CAF1_left   -T--TA-AG-T-ACATATTTTT--------TGTTAAACA-TCTGA---GTTATGTGTCAA---TTTGT-CGA-TCCTC-TA-TA---CTGTT---TAAATTGT
DroGri_CAF1_left   -TATGA-GATT-AATTATCTCGTTATAAACAATATT--A-GAGCA---TACGTCAATTAA---GGTTAATGA-CCTTC-AT-GAGGCAAATG---CAACTTTG
DroMel_CAF1_left   -T--AT-TT-T-GCCTGTATAA--------CTTAAATAT-ATATA---TTTTGTAATGTG---ATTTA-TGT-GTCAC-TTTTGTCGGTCAC---CTGAAGTG
DroPer_CAF1_left   -G-AAT-TT-T-CAAATGAATT--------TACTTATTA-CTTTT---TATATTTAGAAAATGATTCA-CGC-TCCAA-AG-CTAATAAATC---AT--ATTT
DroPse_CAF1_left   -G-AAT-CT-T-CAAATAAATT--------TACTT-AC---TTTT---TATATTTAGAAAATGATTCA-CGC-TCCAA-AG-CTAATAAATC---ATATTTGG
DroSec_CAF1_left   -T--AT-TT-T-GCCTGTATAA--------TTTAAATAT-ATTTA---TTCTGTTATCTG---AGTTA-TGT-GTCAC-TT-TATCAGTCCC---CTGTAGTG
DroSim_CAF1_left   -T--AT-TT-T-GCCTTTTTAA--------TTTAAATAT-ATATA---AATTGTTATCTG---AGTTA-TGT-GTCAC-TT-TGTCGGTCCC---CCGTAGTA
DroYak_CAF1_left   -C--CG-TG-T--AATGTGTAT--------TATAAGATT-ATTGAGTAAGAATATATATT---TTTTG-TGA-AACAT-CT-GA--GTTATG---TGTCACTT
DroAna_CAF1_left   TT-ATA-GA-TAATACA-TTTT--------ACACAAAACCATTTA---AGTAAAAAAATA---TTCGA-GTTTAGTGT-CA-GTTTTTAGGC---CTTAAACT
DroMoj_CAF1_left   -T-TAT-TA-TATCACTCATTG--------CTGCTATTT-AAATG---ATTTGACATTGG---AGTTT-TTA-AAATA-TA-GCTTAAATGT---AATGGAGA
DroVir_CAF1_left   -C-TTCCAC-CAAAGTGTTTTA--------TCTTTATTC-GGCCC---ATGTGTACAAAT---CAATT-GTT-GTGAATAG-TTGGTAATTAAAACATGGGAT