CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left AATTAGTGCGAA----TTGA--T-TTATGCCA----CTGCCGCGGCA--TTGA--TATCGCAAAACG-TGTTAATGA--A-ACGCAAACAGCTCATGAAACTCGGCCCAATCTG-GCCAT DroMel_CAF1_left GATTTATGCCATTGCTATCA-C--CGA-TCTG-TATGTGTGGCACAACG--TGCTTAATGAAATGCA-AA--CAGCG--C-CCTAATGAAACTCGGCTCGATTTCACCGCATTCGAGAAT DroPer_CAF1_left CAGGGCAGCCGGCAACAAAA-CG-TGCTTAAT----GAAATGCAAAC--AATA--TTCAATTTAATTCAATTCTGTA--T-CTGTGTATTTGTATGTGTATTTGTATGTGACGCGTGTGT DroPse_CAF1_left CGATGCTCTCCG----GCAG--G-GCAGGGCAGC--CGGCAACAAAACGTGCT--TAATGAAATGCA-AACAATATTCAA-TTTAATTCAATTCTGTGTATTTGTATGTGACGCGTGTGT DroSec_CAF1_left GATTTATGCCATTGATATCA-C--CGA-TCTG-AATGTGTGGCACAACG--TGCTTAATGAAATGCA-AA--CAGCG--C-CCTAATGAAACTCGGCTCGCTTTCGCCACATTCGAGA-T DroSim_CAF1_left GATTTATGCCATTGATATCA-C--CGA-TCCG-AATGTGTGGCACAACG--TGCCTAATGAAATGCA-AA--CAGCG--T-CCTAATGAAACTCGGCTCGATTTCGCCGCATTCAAAAAT DroYak_CAF1_left TTAGTGCGAATTGATTTATG-CCACTG-CCAG-CGCATTGATATCACCG--AAATGGATGTATAGCC-AA--AC--G--T-GTTACTGAAACTCGGCTTAATTTCGCCATATTCCAGAAT DroAna_CAF1_left CCCAATCGTTATACCCACGGGC--TCA-GCAA-TAAAACGTGCTTAATG--AAATGCAAACA-GTGA-CA--GAG-A--AGCTGAACAAAAAAGTGTATTTGATTTAATTTTTCGTGAAT DroEre_CAF1_left TTCCT-CTGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTT-TTCCTAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGCCAACTAAATTCGAGTGAACT DroMel_CAF1_left TTCCACCTGCAAC-ACTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTTT-TCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGACAACGAAAGCCTAGTGAACT DroPer_CAF1_left GCTTATGTACAACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTTTATCAAGTATTTGGTCCCCTTCAACCAGCTGT-ATCAGTGGTTGATTCCAACAAAAAACAAAAGGCGC DroPse_CAF1_left GCTTATGTACAACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTTTATCAAGTATTTGGTCCCCTTCAACCAGCTGT-ATCAGTGGTTGATTCCAACAAAAAACAAAAGGTGC DroSec_CAF1_left TTGCACCTGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTTT-TTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGCTGACATCGAAAGCCTAGCGAACT DroSim_CAF1_left CTGCACCTGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTTT-TTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGCTGACATCGAAAGCCGAGGGAACT DroYak_CAF1_left TTCCTCCTGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTTTTCCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGACAACGAAGTACGAGTAAACT DroAna_CAF1_left GATTATCTGCAAC-GCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATCTTTTCAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATGACAACAAAGTACAAGTGAAAA DroEre_CAF1_left G--TGCACTGTGACCT-GTGAACTGTGACCTGTGA--------------------ACTGC--AACAAAAGTGTGAGCTTTACTTAGCGAAAAATATGGACAGCAGCTGGGA----TAAGT DroMel_CAF1_left GCGATGGATTACCATTTTCC--AT---------------GGACTAAAAGGT----GAGCTGTAT-TAATCCGTAAAATATGGA----------------CAAC--AGCTCAGA--TCAAC DroPer_CAF1_left C--AACAAATAATAAA-GTGAACAAAAA-AATATA--------------------AAATA--AATTAATTAGTGAGCTGAA---------------TGCAA-AA-TATTTT----GCACT DroPse_CAF1_left C--AACAAATAATAAA-GTGAAAAA----AATATA--------------------AAATA--AATTAATTAGTGAGCTGAA---------------TGCAA-AA-TACTTTGCACTGC-- DroSec_CAF1_left GCGATGGATTATTATTTTCC--A-------------------------GGT----GAGCTGTAT-TAATCCGTGAAATATGGA-------------------C--AGCTCAGA--TAAAC DroSim_CAF1_left GCGATGGATTATTATTTTCC--A-------------------------GGT----GAGCTGTAT-TAATCCGTGAAATATGGA----------------CAAC--AGCTCAGA--TAAAC DroYak_CAF1_left GTGATAGACAGACTGAAAGC-GTAAATTACTATTTTTTCAAACAAAAATGTGGGATGTATTTAT-TTATCCGTTA-AAATGGA----------------CAAA--ACCTAAGA--TAAGT DroAna_CAF1_left GTGATTTATT-CAAAA-GTATACAATAA-ATAAAA--------------------TCGATT-CC-TTAGCTTACTTAGATAGC----------------CAAA--AGCGATGG--CCAAA DroEre_CAF1_left ACTCTTATTAAT-CGAAATATTAAGTAATATTAAGAAAGCCTTT-------------T---T DroMel_CAF1_left ACTCTT-ATTAATTCAAATATGTA-AAAAATAAAGCCTGCGAGT-------------G---T DroPer_CAF1_left GCATTTAATCTTGGAAAATATTC--ATGGATCGAACAA---CAA-------------C---A DroPse_CAF1_left --ATTTAATCTTGGAAAATATTC--ATGGATCGAACAACAAAAA-------------A---A DroSec_CAF1_left ACTCTT-ATTAATCCAAATATGCA-AATAA---GGCCTGCGAGTGTATGCAAAATATGGTAT DroSim_CAF1_left ACTCTT-ATTAATCCAAATATGCA-AATAA---AGCCTGCGAGTGTATGCAAAATATG---G DroYak_CAF1_left ACGCTT-ATTAACCCATATATGTT----AGTAAAGCCTGCAAAC-------------G---T DroAna_CAF1_left ACATC--TTTTAGGTAAAGT-GTG-G------ACAACTAACTAG-------------T---T