CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GGGA-GA-ATAATAT-ATCAG-C--AGCAACAGT-TCCC-TGGGGCTA-ACACCGGAATAAT-ATTTGTCGTCGGATAACGAAAAATCACAGAACA-TTCTCGGGTTTGGCTGTTTGGC- DroMoj_CAF1_left CAGC-AGTTCCCTGCGGTTAA-A--CGCAATCTC-TCTG-GATATATG-TCTGCGAATACTG-TGCTCATGTTTCACTTTAT--A-TTTGGCAATTGGCGAAAAATAATGCTGTCTGGC- DroPer_CAF1_left TGGG-TGGATAATAT-ATCAG-C--AGCAGCGGT-TCCC-TGCGGTTG-GGGACACGGCACG-GGGATTTGTGAGTAACTGG--AAGCACTGCACAACGCGATTCCTTGGCTGTTTGGC- DroPse_CAF1_left TGGG-TGGATAATAT-ATCAG-C--AGCAGCGGT-TCCC-TGCGGTTG-GGGACACGGCACG-GGGATTTGTCAGTAACTGG--AAGCACTGCACAACGCGATTCCTTGGCTGTTTGGC- DroWil_CAF1_left ATAT-CAGCAGCGAC-AGTTCCC--TGCGGTTAA-ACAAAAACTTTAA-AAAACACTTCACT---AAATAATATTTTTGTTA--ATATTTTGAATGTGTTGTTGTTGTTGTTGTGGGGC- DroEre_CAF1_left GTGA-TATAGGAGTT-TTCAA-TAATATATCAGCAGCAG-AGGTTCCC-TGGGGTTAAAAAC-GGTATGGGTTTTCGTGCAC--CAAA---ATAAGGCAACAAAATGATGATGTTAGGC- DroGri_CAF1_left TCGT-GTATAA--AT-ATGGT-TGTATATCAGCA-GCAGCAGTTC-CCTGT-GGTTAAACATAGCATTGGTGAA-TTTATGC--AGCGGTTGATAACATTACTCATTTTGTTGTACGGC- DroMel_CAF1_left ATA--TAGTAG-TTT-TTCAA-TAATATATCAGCAGCAG-AAGTTCCC-TTGGGTTAAAAAC-GGCATGGTTATTCGTGTGC--CAAAAA-AAAAAAAAATTAAATAATGATGTTAGGC- DroSec_CAF1_left TGATATAGGAG-TTT-TTCAA-TAATATATCAGCAGCAG-AAGTTCCC-TGGGGTTAAAAAC-GGCATGGTTATTCGTGTGC--AAAA---AAAAGTAAATTAAATAATGATGTAAAATG DroSim_CAF1_left TA---TAGGAG-TTT-TTCAA-TAATATATCAGCAGCAG-AAGTTCCC-TGGGGTTAAAAAC-GGCATGGTTATTCGTGTGC--GAAAAAAAAAAGTAAATTAAATAATGATGTAAAATG DroVir_CAF1_left ACAG-TATATC--AG-CAGCA-GCAGTTCCCTGCGGTTA-AACATAGC-ACATAAGAAATTT-GTCAGCAAATA-TTTATTC--AATTTTCACAATTTAAGAAATCAACGTTGTACGGC- DroYak_CAF1_left GATA-TAGAAG-TTT-CTCAA-TAATATATCAGCAGCAG-AGGTTCCC-TGCGGTTAAAAAC-GGTATGGTTACTTGTGAGC--AAAAAA-AGCAACAAATTA-TTAATGATGTTAGGC- DroAna_CAF1_left ACTTTAGGTGCAAAAAGAACAGCCACTGTGATATAGATTT-----TGAAACTTACAGCACAGCCACTATTCTCTCTACTTTAAAGGCGGGTAT-C-CTGCGA-GTCCTGT-CACCTAAC- DroMoj_CAF1_left CATTTAGGTACAAAAAGAACAGCCACTGTGATATAAATGC----AACAGATATAC-TCACAGCATCTATTCTCTCTACTTTAAAGGCGAAAAAAC-ACTAGA-GAAAT---AAATAT-AT DroPer_CAF1_left ACTTTAGGTACAAAAAGAACAGCCACTGTGATATATAGAG-TC-GAAGGACATATAGCACAGCAACTATTCTCTCTACTTCAAAGGCTGGTGTGG-TCTCCA-TCGCT---GAGTGT-TT DroPse_CAF1_left ACTTTAGGTACAAAAAGAACAGCCACTGTGATATATAGAG-TC-GAAGGACATATAGCACAGCAACTATTCTCTCTACTTCAAAGGCTGGTGTGG-TCTCCA-CCGCT---GAGCGT-TT DroWil_CAF1_left ACTTTAGGCACAAAAAGAACAGCCACTGTGATATGAAATT-GA-AAAGGGCATAAAACACAGCAACTATTCTCTCTACTTTAAAGGCTGGTTG-A-AAACCA-CTTGA-AAACTTTG-C- DroEre_CAF1_left ACTTTAGGTACAAAAAGAACAGCCACTGTGATATAGATATGATATATTAACTTACAGCACGGCAACTATTCCCTCTACTTTAAAGGCTGCGATTT-AGCTAA-GTAAG---CTGGCA-AC DroGri_CAF1_left ACTTTTGGTACAAAAAGAACAGCCACTGTGATATAGACAATAC-GTTCAACATACAGCACAGCATCTATTCTCTTTACATTAAAGGCTATAAACC-ACAAAT-CGGAA---ACGGAA-AT DroMel_CAF1_left ACTTTAGGTACAAAAAGAACAGCCACTGTGATATAGATATGGTATATTAACTTACAGCACAGCAACTATTCCCTCTACATTAAAGGCTGTGATTA-AGTTTAAGTAAG---CTGCCA-AC DroSec_CAF1_left CCTTTAGGTACAAAAAGAACAGCCACTGTGATATAGATATGGTATATTAACTTACAGCACAGCAACTATTCCCTCTACTTTAAAGGCTGTGATTA-AGTTTA-GTAAG---CTGCCA-AC DroSim_CAF1_left CCTTTAGGTACAAAAAGAACAGCCACTGTGATATAGATACGGTATATAAACTTACAGCACAGCAACTATTCCCTCTACTTTAAAGGCTGTGATTA-AGTTTA-GTAAG---CTGCCA-AC DroVir_CAF1_left GCTTCAGGTACAAAAAGAACAGCCACTGTGATATAGACCATAC-GCAAAACATACAGCACAGCGTCTATTCTCTCTACTTTAAAGGCTATAAACAGATAACT-GGGCG---ATATAG-TT DroYak_CAF1_left ACTTTAGGTACAAAAAGAACAGCCACTGTGATATAGATATTTGTTATTAACTTACAGCACAGCAACTATTCCCTCTACGTTAAAGGCTGTGATTA-AACTTA-GTGAG---ATGCCG-AC DroAna_CAF1_left -TCGTTATTT--TTGATGC-AT-T--TTGGACA-ACTGCATGCGT-----------TATAAAGG-AA---AATCACT--GTGATATGT-AACGAGGGATAAACG-CA- DroMoj_CAF1_left ATA--CACTT--ATAAATA-TTCA--CATTCAT-ATTGTAGTCTG-----------GGGGACTGCAC---GCGCTATAAAGGAAAATC-ACTGTGATATGTA---AC- DroPer_CAF1_left CGT--TTCCC--ATGTGTG-GC-T--GTGGGCG-CAGACATGCGC-----------TATAAAGG-AA---AATCACT--GTGATATGT-AACGGTGAATTAACGCAT- DroPse_CAF1_left CGT--TTCCC--ATGTGTG-GC-T--GTGGGCG-CAGACATGCGC-----------TATAAAGG-AA---AATCACT--GTGATATGT-AACGGTGAATTAACGCAT- DroWil_CAF1_left -TGGATATTG--TTGATATATT-G--GACAGAA-CATGCATGCGC-----------TATAAAGG-AA---AATCACT--GTGATATAT-AACGGTGAATCTA---AC- DroEre_CAF1_left TTT--GGCTTTCAT--TTC-CCATTGAT--GAG-TTTTG-GACTTTTTACATGCGTTATAAAGG-AA---AATCACT--GTGATATGT-T---AGGG----A---AC- DroGri_CAF1_left GCA--A-ACAGAAG--TCA-CA-ATTCT--CGCGATCAA-AATTTGAAACAGATCTCATC--GA-AAAC-AAATACC--GAATAAAGA-T---ATGT---AA---AA- DroMel_CAF1_left TTT--GACTTTCAT--TTT-CC-TTGAT--GAG-TTGTG-GACTTTAAACATGCGTTATAAAGG-AA---AATCACT--GTGATATGT-T---AGGA----A---AC- DroSec_CAF1_left T-T--GGCTTA-AT--TTT-CC-TTGAT--GAA-TTGTG-GACTTTAAACATGCGTTATAAAGG-AA---AATCACT--GTGATATGTTC---GGGAA--CA---AC- DroSim_CAF1_left T-T--GGCTTTCAT--TTT-CC-TTGAT--GAA-TTGTG-GACTTTTAACATGCGATATAAAGG-AA---AATCACT--GTGATATGT-T---GGGAA--CA---AC- DroVir_CAF1_left TTA--AGTCTATAT--AGA-CA-TGGAT--ATAGATCGT-ATGTGGTGTTGCTTTACGGG--CT-GCACGCGC-TAT--AAAGGAAAA-T---CACT--------GT- DroYak_CAF1_left TTT--GGCTTTCAT--TTC-CC-TTGAT--GAG-TTGTG-GACTTTGTACATGCGTTATAAAGG-AA---AATCACT--GTGATATGT-T---AGGG----A---ATA