CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AA-TAAAAAATA-TAA-AAGCTTCAAAATTAGTAATATAAAAATATAAAAAATTGTTGAAACTCTA--CTGCA-TATTTTTA-GGAAAAGAAA---AGTTACAAAATTAAATGACACT-C DroEre_CAF1_left AT-A--GCAATGTTAT-CAGCAAGTGAAGCAAAAATGTCTTTAAGCGGGAATAGAGTTTTAGATTC--TATGA-ATTTATAAAATATATATAA---AATTTCATGAATAAATTGCATT-T DroMel_CAF1_left AT-ATTTTCAGGCTCAATAGCAAGCAAGC-AAGTT-ATAAAAAAATTATTTAAGCGTGAAATTAGATTTATAT-TATATTTT-TTGTAT--AA---AATATCATCCACTTAGAAT-GT-T DroSec_CAF1_left AA-ATAGCAATGTTATCCAGCAAGTCATA-AAAAATGTATTTAAGCGTCAAACTTGATTTAGATTT--CTTTT-T-TTTAAA-TTCCGTATAA---AATGTGAGAAATAAATGGAAGT-T DroSim_CAF1_left TAAATAGCAATGTTAT-AAGCAAGTCATA-AAAAATGTATTTAAGCGTGAAACTTGTTTGAGATTT--CTTTT-T-TTTAAA-TTCCGTATAA---AATGTCATAAATAAATGAAAGT-T DroYak_CAF1_left TG-GCATAATTTCAGGCTAAGTAGCAATG-TAATC-AAGCAAGTGATCCAAAAATGGTTATAAACA--TGAGT-CTTTTCTT-AGATTCTTTA---AATTTCATAAATAAATTGGATT-T DroPer_CAF1_left AA-AC---GTGGAAGCAAATTATTGAATT-CCAC-----TTTA-------AAT---------TTGA---ATAAGA-TCTATC-GTTCTTTAAA---TGCTTTGTTCGAATAA---ACC-C DroPse_CAF1_left T---------GGCAGCAAATTATTGATTT-CCAC-----TTTA-------AAT---------TTGA---ATGGGT-TCTATC-ATTCCTTTAAATATTTTTGATTCGAATAA---ACCCC DroAna_CAF1_left T-TCACTA-TTGATG-GCTTCGAGAAACCTCAACGCTCCTGAAAGCAAAGCTGTGATATGAATATGAAA-GCTACATGTCACCGCCACTTTAAGGAGGGTCGCAGTTCCCTAAAAAAATC DroEre_CAF1_left T-TCTTTAGTCGGCG-GGCGAGAAAAACCGCAACGCTCCTCAAAGCT-GGCTGTGATATGAATATTGCTGACAACATGTCACCGCCACTTTGAAGACAGTTGAAGTTTTCACT-ATT--G DroMel_CAF1_left T-CCTTAAGTCGCCG-GACGAGAAAAACCGCAACGCTCCTCAAAGCT-GGCTGTGATATGAATATTGTTGACAACATGTCACTGCCACTTTGAAGACAGTTGAAGTTTTTAGTTATT--T DroSec_CAF1_left T-TCTTAAGTCGGCG-GGCGAGAAAAACCACAACGCTCCTCAAAGCT-GGCTGTGATATGAATATTGTTGACAACATGTCACCGCCACTTTGAAGACAGTTGAAGTTTTCAGTTCTT--T DroSim_CAF1_left TTTTTTAAGTCGTCG-GGCGTGAAAAACCGCAACGCTCCTCAAAGCT-GGCTGTGATATGAATATTGTTGACAACATGTCACCGCCACTTTGAAGACAGTTGAAGTTTTCAGTTCTT--T DroYak_CAF1_left T-TCATTAGTCGGTT-GGCGAGAAAAACCGCAACGCTCCTCAAAGCT-GGCTGTGATATGAATATTGTTGACAACATGTCACCGCCACTTTGAAGACAGTTGAAGTTTTCACT-TTT--T DroPer_CAF1_left C-AATGAGGCGCATA-TTTCAGAAGGGCCGCAACGCTCT-CAAAGCT-GGCTGTGATATGAATATTATTACCAACACGTCACCGCCACTTTAAAGAGCGTCGCAGCATTCCTATAGTATC DroPse_CAF1_left C-AATGAGGCGCATATTTTCAGAAGGGCCGCAACGCTCCTCAAAGCT-GGCTGTGATATGAATATTATTACCAACACGTCACCGCCACTTTAAAGAGCGTCGCAGCTTTCCTATAGTATC DroAna_CAF1_left TGTATCCTTCAAAA--CCC-TTTCAAAAAACTATTC-AAAAAAGTGGATAAAGTACT-GGA------TAGTATTTTAGGTTTTTGTTTATTAGCAATATCACGTTGATGGATTTGGT--- DroEre_CAF1_left CGAATTGCACGAAT--CCC-CAACTATGCATAAAAC-A-------TCAGAGAGCAGC-AGCAGCAGGAGT-ATTTTCGGTT--CTTTTATTAGCAATATCACGTTGATGATTTTTGGTTT DroMel_CAF1_left TGATTTGCACGAAACTCCC-CAACTATGCATAAAAC-A-------TCAGAGAAGAGC-TGC------AGT-ATTTTCGGTT--CTTTTATTAGCAATATCACGTTGATGATTTTTGGTTT DroSec_CAF1_left TGATTTGCACGAAATGCCC-CAACTATGCATAAAAC-A-------G----------C-AGC------AGT-ATTTTCGGTA--CTTTTATTAGCAATATCACGTTGATGATTTTTGGTTT DroSim_CAF1_left TGATTTGCACGAAACGCCC-CAACTATGCATAAAAC-A-------G----------C-AGC------AGT-ATTTTCGGTT--CTTTTATTAGCAATATCACGTTGATGATTTTTGGTTT DroYak_CAF1_left CCATTTGCACGCAGTC-CC-CAACTATGCATAAAAC-A-------CCAGAGACCAGC-AGC------AGT-ATTTTCGGTT--CTTTTATTAGCAATATCACGTTGATGATTTTTGGTTT DroPer_CAF1_left CCATGGGATCTTCACTCCTTCCCCCAAAAAGTATATCT-TTAAA-GACCACAGGAACTACC------ATT-GATTTCGGTT--GTTTTATTAGCAATATCACGTTGATGATTTGGTG--- DroPse_CAF1_left CCATGGGATCTTAACTCCTTCCCCCAAAAAGTATATCT-TTAAA-GACCACAGGAACTACC------ATT-GATTTCGGTT--GTTTTATTAGCAATATCACGTTGATGATTTGGTG--- DroAna_CAF1_left -----------TTCGACT-TGTTTCGGGAATGG DroEre_CAF1_left ----------------TG-TT-TTTATTTTTCT DroMel_CAF1_left TGTTTTTATATTTCTGGG------------GTT DroSec_CAF1_left TGTTTTTATATTTCTGGG-AG-TGGGTTTCATG DroSim_CAF1_left TGTTTTTATATTTCTGGG-AG-TGGGTTTCATG DroYak_CAF1_left TGTTTTTATTTTTCTGGG------------AGT DroPer_CAF1_left ----------TTT-GTTTCTT-CGGGATCGGGG DroPse_CAF1_left ----------TTT-GTTTCTT-CGGGAACGGGG