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


DroAna_CAF1_left   ACA--ATCTGGG-TGTCTGAATTTTCTTTTTATTTTTCTATTTT--TG-A-TTTTGTTTCACAACCAATTCACTTTTTGT-TATTTTTTTTTTTTT-G-----TT-TTTGAAATATAAGA
DroEre_CAF1_left   TAT--ATTAAAA-ATCGC-TGTGAATAATTATGTTACAG-TCAG-GAA-A-TTTTACTTCGATTTTAG-AACTCCTCCTT-CACAGCCAATTCACT-T-----TC-TGTTTTTAATTCCA
DroGri_CAF1_left   ACT--AAATTAG-AATAC-AATTAATGCACATTTTAGAT-GACACCAA-T-TCACTGAACCG-TTGATTTTGATATATATATATATATTTTTTTAT-T-----AT-TTTGTAATCAAATT
DroMel_CAF1_left   AAA--AGTATAA-ACTAT-AA-TAGATCGCTTTGAATAGTAGTT--AT-G-TTACAATCAGCAAATTTTACTCCTTTCTT-CACATCCAATTCACT-T-----TC-GGTTTAAAATTTCA
DroMoj_CAF1_left   AAT--GCAATCT-GAACGGCTTATTAACTTATATCAAATATATATTTA-A-AGACACAATTTCACTCGAAT--TTGTTAA-ATTTCCTTGTTCATT-T---T-TT-TTTTTCAATTGTTT
DroPer_CAF1_left   GAA--TCGTCAAATGGTT-TC--AACAATTTCTCCATAT-CCTTCCAT-A-TCACTCGATGATGAGAACACGACCAATTT-CACTTG-TTTTTTCT-T-----TC-AATTTCAAATTCAA
DroPse_CAF1_left   GAA--TCGTCAAATGGTT-TC--AACAATTTCTCCATAT-CCTTCCAT-A-TCACTTGATGATGAGAACACGACCAATTT-CACTTG-TTTTTACT-T-----TC-AATTTCAAATTCAA
DroSec_CAF1_left   TTT--ATAAAAG-TATAA-AC-TATAATAGATCGCTGTGAATAG--TT-G-TTACAATCAGCAAATTTTAATCCTTTCTT-CACTTCCAATTCACT-T-----TC-GGTTTACAATTTCA
DroSim_CAF1_left   TAT--AAAAGTA-TAAAC-TATAATAGATCGCTGTGAAT-AGTT--AT-G-TTACAATCAGCAAATTTTACTCCTTTCTT-CACTTCCAATTCACT-T-----TC-GGTTTGCAATTTCA
DroWil_CAF1_left   TTA--AATTTTCTGTTGC-AATAAATAATTTGCTTAATA-ATCTT-TTGT-TTTTTTCACTTTTTTTTTAAC-ACCAATT-CACTTTATTTTTATT-TGTTTTGC-TTTTT-TGTTAGGA
DroYak_CAF1_left   ATGTATTTAAAA-AAGTA-TA-TATTAAAAATCGCTGTGAATAA--AT-T-TTACATATATG-CATAGAACT-CCTCCTT-TACAACCAATTCACT-T-----TT-TGTTTAAAATTCAA
DroVir_CAF1_left   TTA--TCTAAGGATATAT-TTTAGGAAAATAATTGATACATATTC-AG-GGACAATTTATTCACATTTCAGACACGAATT-CACTGTAATTTTGTTAT-----ATTAAATCGATTTGTTT

DroAna_CAF1_left   TTTATGTTGTTTCCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAAGCAACATCGTGCCG-ATG-AAGAT
DroEre_CAF1_left   TTTACGTTGTCTCCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAATCAACATCGTA-CG-GTT-GAAGA
DroGri_CAF1_left   TTCATGTTGTTCTCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTCGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAAGCAACATCAAA-AG-TATATATTT
DroMel_CAF1_left   TTTACGTTGTCTCCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAATCAACATCGTA-CA-GGT-AAGGA
DroMoj_CAF1_left   CTCTTGTTGTTTTCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTCGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAAGCAACATCAAA-TT-TCTTTTGAT
DroPer_CAF1_left   TTTACGTTGTTTCCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAAGCAACATCATA-AT-AGATGTGGC
DroPse_CAF1_left   TTTACGTTGTTTTCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAAGCAACATCATA-AT-AGATGTGGC
DroSec_CAF1_left   TTTACGTTGTCTCCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAATCAACATCGTA-CG-GGT-GAGGA
DroSim_CAF1_left   TTTACGTTGTCTCCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAATCAACATCGTA-CG-GGT-GAGGA
DroWil_CAF1_left   TTTGTGTTGTTTTCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAAGCAACATCAAT-ATTTCC-TT-TT
DroYak_CAF1_left   TTTACGTTGTCTCCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTTGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAATCAACATCGTA-CG-GAT-GAAGA
DroVir_CAF1_left   TTCGTGTTGTTTTCCGTTGATTATCCTAGCTCATCAAAGCTGGCTGTGATATGCGTCGGGTATCCATATCACAACCACTTGATGAGGCTTAGATAAGCAACATCAAA-AT-TCATTTGAT

DroAna_CAF1_left   ATAATTTA-TTCTCAATATTGCA--CCAGATTTTTGTTTTT-TTTTTCAG-CCA--G-CAGCTCCTTCACTT-CCCCATAGGCCAT-TTT-AGCTAAA
DroEre_CAF1_left   ACA-GTAT-CTTCAACTTCATGA--ATGTGTTAGTAAC--A-ATATTGCA-CCGGAT-GTGTGTAGTCAGTT-CGACAGCGTTCTAAGTCAGAGATGT
DroGri_CAF1_left   -GA-TGTC-AATCAGTTGTTTTT--CATACTTATATATATA--TATAAAT-ATATAG-TTTTTTTTTGATTA-TGATTTGTGTTTCCAAT-TCCAATT
DroMel_CAF1_left   ACA-GTTT-CCTTAACTTTATGA--ATTAGTAACATGGTTA-GTAACAAT-ATT-GCACCGCATGTGT-GTA-AGTCAGTTCGATAGGGC-CCCCTAA
DroMoj_CAF1_left   GCA-GAGTTCCGATT--GATTTT--TTAAACTGA-TGTTCCACATTATAA-TACAGG-CTGGCCGAATAAGA-G--CAATAGGAAAGGGAATTGCAAT
DroPer_CAF1_left   ATT-AT-T-TTTCAATGGTTCATGGTTCAATGGT-GGTTAAATCATACAA-AATCTG-CAGTATTATAAATT-AAAACG--TGTGTACT-AATTGT-T
DroPse_CAF1_left   ATT-AT-T-TTTCAATTGTTCAT--TTCAATGGT-GGTTAAATCATACAA-AATCTG-CAGTATTATAAATT-AAAACG--TGTGTACTAAATTGTTT
DroSec_CAF1_left   GCA-GTTT-CCTCAACTTCATGA--ATTAGTAATAGGGTTA-GTAACAAT-ATTGCA-CCGCATGTGTGTGT-AGTCAGTTCGATAGGGT--CCTAAG
DroSim_CAF1_left   GCA-GTTT-CCTCAACTTCATGA--ATTAGTAACAGGGTTA-GTAACAAT-ATTGCA-CCGCATGTGTGTGT-AGTCAGTTCGATAGGGC--CCTAAG
DroWil_CAF1_left   TGT-TTTA-ATTTTGGAAAATGA--TGTCATTTGATTGAAT-TTGTTTAT-TGATAA-AAATATTTTTTTCT-TTCTTT-T-TTTTGCTAATGAAGGA
DroYak_CAF1_left   ACA-GTTT-CTTCAACTTCATGA--ATGGGTTAGTAACTAT-ATTGCACCGTGTGTG-TTGTGTGTGAT----CAATGCGACAACCGCGCCCTAAGTC
DroVir_CAF1_left   GCA-GTC--G-GTTTTTTCTTGT--TTTGAAGCCCAAATAA-TGTTTCCG-ATTCCA-GCCCATTCCAAATTCCATTCC--TAACTGGGCTTGATGTA