CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TACCAAAGCTTACCATTTGCTGA-CC--ACAACTTGCTTTTGGCCA---AATGTTAATTTAGCTTGTCTTGCACTTTGGCC--AACACCTTTTTCGGCCACTTG--GGCCGCCTTGCATT DroEre_CAF1_left AACGA--GCAGAAGCTGACCACA-GC--TGGCCTTTCTCTTGGCCA---ACTGTTAATTTGGCTTGGCTTGCACTTCTGTAA-AACACCTTTTTCGGACACTTT-CGGCCGCCCACAATG DroMel_CAF1_left AACGA--GCTGAAGTTGACCACA-AC--TTGCCTTTCTCTTGGCCA---AATGTTAATTTGGCTTGGCTTGCACTTTAGTAA-AACACCTTTTTCGGACACTTT-CGGCCGCCCACAATG DroPer_CAF1_left TAACT--G--AAATTTGACCAAA-AACCTTGCCTTTCACTTGGCCA---TTTGGCCATTTAGCTTGTCTTGCACTTTAGTTTGGACACCTTTTTTGGACACTTG-GT-GCGCTGTCGATG DroPse_CAF1_left TAACT--G--AAATTTGACCAAA-AACCTTGCCTTTCACTTGGCCA---TTTGGGCATTTAGCTTGTCTTGCACTTTAGTTTGGACACCTTTTTTGGACACTTG-GT-GCGCTGTCGATG DroSec_CAF1_left AACGA--GCTGAAGTTGACCACA-AC--TTGCCTTTCTCTTGGCCA---AATGTTAATTTGGCTTCGCTTGCACTTCAGTAA-AACACCTTTTTCGGACACTTT-CGGACGCCCACAATG DroSim_CAF1_left AACGA--GCTGAAGTTGACCACA-AC--TTGCCTTTCTCTTGGCCA---AATGTTAATTTGGCTTGGCTTGCACTTTAGTAA-AACACCTTTTTCGGACACTTT-CGGCCGCCCACAATG DroVir_CAF1_left CCAAG--TATTGGCCGGGCCAAAAGC--TTTCCCTTCACTTTTGCT---TTTCGCTGGCATTGCACTTTGTCAACACTTTTG-GCCACTTGA--GCATGAGAATTGTTTGGCCAGCAACA DroYak_CAF1_left AACAA--GCAGAAGTTGACCACA-AC--TGGCCTTTCTCTTGGCCA---AATGTTAATTTGGCTTGGCTTGCACTTTAGTGA-AACACCTTTTTCGGACACTTT-CGGCAATCCACAATG DroWil_CAF1_left ATTCT--GTGGT----TACCTT---T--GGGCCTTCAATTTGGCTTTCACTCTTTGTTTCAATTGGCCAATAATGTCAACAA-TTGTCTTTTAACATAAACTGA-AGTGGTCAAATAATG DroAna_CAF1_left CGGAA-GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATACCCCGCATCTCCAATTGGATTG--G-GATTATTTCCCTTT-----TTTTTTTGT DroEre_CAF1_left CAT-G-GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAATTGGATTA--T-TTCCCTTTTTTGCCAA--GTACAACACG DroMel_CAF1_left CAT-G-GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATACCCCGCATCTCCAATTGGATTA--T-TTCCCTTTTTTGCCAA--GTAAAACACG DroPer_CAF1_left CAT-GAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAATAGGATTT--C-CTTATTTTCCTCGCCT--TTTTTTGTTG DroPse_CAF1_left CAT-GAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAATAGGATTT--C-CTTATTTTCCTCGCCT--TTTTTTGTTG DroSec_CAF1_left CAT-G-GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAATTGGATTA--T-TTCCCTTTTTTGCCAA--GTAAAACACG DroSim_CAF1_left CAT-G-GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAATTGGATTA--T-TTCCCTTTTTTGCCAA--GTAAAACACG DroVir_CAF1_left CA--T-GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAAGTTGTACA--ATATCCAGGAAAATGGAA--TTTTTTGCTA DroYak_CAF1_left CAT---GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAATTGGATTA--T-TTCCCTT-TTTGCCAA--GTGAAACACG DroWil_CAF1_left CATAT-GGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAGAAAATCGGAAT-ATATTCGGTTGAATATTTTTTCTTTTGG DroAna_CAF1_left -T---GTTTTGCTCAGAGAAGAATATGCAGACGTCGGCAGTTTTGTC----TTTTATATTCTGGGGCTTATG-TTAAGGA--AG DroEre_CAF1_left CA---GACGTCGGCAGTTTTG-----TCTTTTGCATTCCGGTACTTA----TGTATATGTTGG-GG-GTAAGAAGTTGCCACTA DroMel_CAF1_left CA---GACGTCGGCAGTTTTG-----TCTTTTGCATTCCGGGACTTATGTATGTATGTGTTGGGGG-GTAAGAAGTT-----GC DroPer_CAF1_left CG---GGAGACGAATACGCAA-----ACGTCGGCAGTTT-TGTCTTT----TGCATTCCGGGGCGGCTTATGTCGAG-GAAGAA DroPse_CAF1_left CG---GGAGACGAATACGCAA-----ACGTCGGCAGATT-TGTCTTT----TGCATTCCGGGGCGGCTTATGTCGAG-GAAGAA DroSec_CAF1_left CA---GACGTCGGCAGTTTTG-----TCTTTTGCATTCCGGGACTTA----TGTATGTGTTGGGGGGATAAGAAGTTGCC--AC DroSim_CAF1_left CA---GACGTCGGCAGTTTTG-----TCTTTTGCATTCCGGGACTTA----TGTATGTGTTGGGGG-GTAAGAAGTTGCCA-CT DroVir_CAF1_left CC---GCCGATAG-ACGAAAC-----AAATACGCAGACGTCTGCATT----TTTGATAGTCAAGAA-GCAGGCGCATTAATGAA DroYak_CAF1_left CA---GACGTCGGCAGTTTTG-----TCTTTTGCATTCCGGGACTTA----TGTATATGTTGGGGG-GTAAAAATTTGCCACTA DroWil_CAF1_left TTTTCGAACAAA--TATGCAG-----ACGTCTGCAATTT-TTTGTTC----T--TTGCCTTTGCTTTTAATGCCGTCGAAGATG