CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ATTCTTTG--TTAA-GAA--CCTTTGCCAAT-TA-T--TCGCAAATGAG--CA--AGTGGGGCAGTAAGCGAGCTTGTGGCTGCCAAGGTC-GCATATGACGAGGTGGCCGAGAGGTTAA DroEre_CAF1_left GCCTTTCA--CCGA-TAA--GAACTAACACT-GC-T--TGCCTGCAAAG--CA--AGCGGTGCACGAAATGAGCATTTGGCTATCAAGGTC-ACATAAGACGAGGTGGCCGAGAGGTTAA DroGri_CAF1_left AAACAAAC--A-GACTGT--TGTGTCAAAAG-ATTG--TTATAG-AGCC--CG--AAAAGAGTTCAGAACCATCATTGGGCCGGCGCCTGG-CAAGAAGACGAGGTGGCCGAGTGGTTAA DroMel_CAF1_left GCATTTAA--CCGA-TAA--GAACGAGCACT-GC-T--TGCCGGTAAAG--CA--AGCGGTCCACGAAATGAGCATTTGGCTGTCAAGGTT-GCATAAGACGAGGTGGCCGAGAGGTTAA DroPer_CAF1_left ATAAGAAC--TATG-TTG--GAGGCGGAGTG-GT-T--GCTTTGGTGGC--AA--AGCGGTGCACCAAACCAGCATCTGTCTGCCAAGGCC-GCATATGACGAGGTGGCCGAGAGGTTAA DroPse_CAF1_left ATAAGAAC--TATG-TCG--AAGGGGGAGTG-AT-T--GCTTTGGTGGC--AA--AGCGGTGCAGCAAACCAGCATCTGTCTGCCAAGGCC-GCATATGACGAGGTGGCCGAGAGGTTAA DroSec_CAF1_left GCCTTAGA--ACGA-CAA--GAATGAACACT-GC-T--TGCCGGTAAAG--CA--AGCGGTCCAGGAAATGAGCATTTGGCTGCCACGATT-GCATAAGACGAGGTGGCCGAGAGGTTAA DroVir_CAF1_left ACACTACTGAACTG-CTT--TTTATAGGTTA-AG-ACTGCA--T-ATAT--GCCGACTACATC----AACTAGAACCTTAGGACTACCCCCGACACGTGACGAGGTGGCCGAGTGGTTAA DroWil_CAF1_left AAAACTGC--TTTA-ACTGCTTGCTGTCGTT-AA-C--AATGTGCATAG--GC--ACTAACAACGAGAATGAACATTGAGCTGGCGTTG---CCCAACGACGAGGTGGCCGAGAGGTTAA DroYak_CAF1_left GCCTTTCA--AAGT-ATA--GAACCAACACT-GC-T--TGCCTGTAAAG--CA--AGCGGTGCAGGAAATGAGCATTTGGCTGCCAAGGTC-ACATAAGACGAGGTGGCCGAGAGGTTAA DroMoj_CAF1_left ACACACAA--TTGC-ACT--GCTTCAGAATAAAT-C--ATTTTGCACTCGGCA--ATAATAACTAGTAG-AGTCTTAGAACTACCCTT--G-ACACGTGACGAGGTGGCCGAGTGGTTAA DroAna_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGGTTT----GCTTTTTGCCGCCCCCATTATTT-TTGGTTT---TTGTTTATT--TATCCCC DroEre_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGTGAT----TCTTTTTACA-ATT-T--------TTTACCT---TCATCGTAA--GTTGAAT DroGri_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGGAAT----TCCTTTTTTA-ATTCT-----TGTTAGTTTT---ATTTTTTTA--AAATTTA DroMel_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGTGTT----TTCTTTTTGA-CTTTT--------TTTAACA---TGAAC-AAA--GTTGAAT DroPer_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGGGAA----ACTTTTTGATGCCATCTTTTTCTTTCCTTTT---TATTTTCTA--AAACTAT DroPse_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGGGAA----ACTTTTTGATGCCGTCTTTTTTTTTAGTTTT---TATTTTGTA--AAACTAT DroSec_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGCGTTATTTTTGTTTTACA-TTTTT--------TTTAACA---TCAAC-AAA--GTTGAAA DroVir_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAAAT----ACTTTTTTGTATTTTTTAT-----GTGTTAA---TTAAA-TGC--TGTTATT DroWil_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAGATGATTTTTTTTTTGC-CGCTT--------AAATTGTATATTTTTTTAT--TCTTAAT DroYak_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGTGTT----TATTTTACTA-TTTTT--------TTTAACA---TCATATGAA--GTTAAAT DroMoj_CAF1_left GGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAAAC----ACCTTTTTGC-AAATT-----CTTATTTTTA---ACTCAAAGTTATTTTTAA DroAna_CAF1_left ACCGTTTAGT-TAGTTGTTTTGCTACCGTAGTCCAAAAATAA-ACTTTAA--AACACGGAGGACCATTAAAGCCG-------------ACACAATGCTCTGAAAAGCGA----------- DroEre_CAF1_left AACG-T--------TTTTTATGTTACCCAAAACTAAAAATAA-ACTTTGTTTACCGAG--TCA-TTAAAACACTG-------------ACAATAATG-TCCAG-ATGCA----------- DroGri_CAF1_left AATG-C--------TTTTAATTAAAATGTTTTGTAGTTTAGT-ACAA-----GCTGCT-GGTAACTTTCTATCTG-------------ATAAAAAT--TTGAG-CTAAA----------- DroMel_CAF1_left AACG-A--------TTT-------ACCGAAAACTAAAAATAA-ACGT-----TTCGAG--TCA-TTAAAACACAG-------------ACAATAAT--CCCAG-ATGCTTATCGGGTTTC DroPer_CAF1_left AATTAAATAACAGTGAGATATGCTACTGGTGAGTAAAAATAA-AACATG---TTCCGGCAGAAGCAATGTGAACC-------------ATT-AAAACAGCGAC-ACTGC----------- DroPse_CAF1_left AATTAAATAACAGTGAGATATGCTACCGGTGAGTAAAAATAA-AACATG---TTCCGGCTGAAGCAATGTGAACC-------------ATT-AAAACAGCGAC-ACTGC----------- DroSec_CAF1_left AGCG-A--------TTTTTATGTTACCGAAAACTAAAAATAA-ACGATGTGTTACGAG--TGA-TTAAAACACAG-------------ACAATAAC--CCCAG-ATGCT----------- DroVir_CAF1_left TTAA-A--------ACCGAATTAAATGCCTTACTAAACAAAG-AATT-AACTTATTTT-ATAGCCATTAAAAAAG-------------ATC-TAAGC-TTAAA-TTTCA----------- DroWil_CAF1_left AATT-T--------AATGATGGCACAATTTACCTTAGCATTT-AT--ATAGTTTAGCC--TTA-TAAAAAAGAGAGTAACGCTAGAATGCTACACAG-ATCGC-ATTCG----------- DroYak_CAF1_left AACG-T--------TTTTAATGCTACTGAAAACTAAAAATAA-ACTTTGTTTACCCAA--CCA-TTAAAACACAG-------------ACAATAGTG-TCCAG-ATGCT----------- DroMoj_CAF1_left AGTG-A--------GCTACCAACTATATTTAGTGGCAGCTACTTCGA-TTATCTTATG--AAA-GCCAATAAGAA-------------GCTCTTAAA-TTAAA-TTTCA----------- DroAna_CAF1_left G-A--T-GCT DroEre_CAF1_left A-A--T-CGT DroGri_CAF1_left G-T--T-TAA DroMel_CAF1_left AATTGA-ATT DroPer_CAF1_left G-A--C-GTG DroPse_CAF1_left A-A--C-GTG DroSec_CAF1_left T-AT-CGTGT DroVir_CAF1_left A-TC-T-ATA DroWil_CAF1_left C-T--T-TCG DroYak_CAF1_left A-A--T-CGT DroMoj_CAF1_left A-T--A-CCT